BOL: All site blogs

Understating pacbio reads name !

BioJoker — Fri, 23 Nov 2018 07:36:46 -0600

m140415_143853_42175_c100635972550000001823121909121417_s1_p0/553/3100_11230 0.99 24
└1┘└─────2─────┘└──3─┘└────────────────4────────────────┘└5┘└6┘└7┘└────8────┘└─9─┘└10┘

"m" = movie
Time of Run Start (yymmdd_hhmmss)
Instrument Serial Number
SMRT Cell Barcode
Set Number (a.k.a. "Look Number". Deprecated field, used in earlier version of RS)
Part Number (usually "p0", "X0" when using expired reagents)
ZMW hole number
Subread Region (start_stop using polymerase read coordinates)
readScore
barcodeScore

How to set up SSH on Ubuntu 18.04

AnHo — Thu, 22 Nov 2018 10:12:00 -0600

SSH, also known as Secure Shell or Secure Socket Shell, is a network protocol that gives users, particularly system administrators, a secure way to access a computer over an unsecured network. SSH also refers to the suite of utilities that implement the SSH protocol.

Here are the commands used to connect by Secure SHell:

On the server side

sudo apt-get install ssh
sudo apt-get install openssh-server
sudo /etc/init.d/ssh start
sudo nano /etc/ssh/sshd_config
Uncomment port 22
Uncomment HostKey /etc/ssh/ssh_host_rsa_key
Uncomment AuthorizedKeysFile .ssh/authorized_keys .ssh/authorized_keys2
Set pubkey authentication to "yes"

sudo systemctl restart sshd.service # or sudo /etc/init.d/ssh reload

On the client side:
in ~/.ssh

ssh-keygen -t rsa # set passphrase or not
ssh-copy-id -i ~/.ssh/id_rsa user@100.100.10.100

--> write "yes" then password in

ssh user@100.100.10.100

--> write password --> you should be in

--> in /home/user/.ssh/config type:
Host WhateverName
HostName 100.100.10.100
User username
ForwardX11 yes
ForwardAgent yes
IdentityFile ~/.ssh/id_rsa

--> you should now be able to connect with :

ssh WhateverName

List of motif discovery tools !

Neel — Tue, 20 Nov 2018 03:54:26 -0600

In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three-dimensional arrangement of amino acids which may not be adjacent.

Following are the list of tools for motif discovery:

2Dsweep -- protein annotation by secondary structure elements

Perform secondary structure predictions on protein sequences.

3D-footprint -- database of DNA-binding protein structures

Find binding specificity information about DNA-protein complexes.

3D-footprint: DNA-binding protein database

Find information about the binding specificity of DNA-binding proteins.

3D-partner -- a web server to infer interacting partners and binding models

Predict interacting partners and binding models.

3MOTIF -- a protein structure visualization system for conserved sequence motifs

Use this web-based sequence motif visualization system to display sequence motif information in its appropriate three-dimensional (3D) context.

AFAWE -- Automatic functional annotation in a distributed Web Services Environment

Protein function prediction and annotation in an integrated environment powered by web service.

ANCHOR -- Prediction of Protein Binding Regions in Disordered Proteins

Find information about protein binding.

ANNIE -- ANNotation and Interpretation Environment for Protein Sequences

Use to predict function from de novo protein sequences.

Active Sequences Collection (ASC) database -- A new tool to assign functions to protein sequences

Search for short active protein sequences with demonstrated biological activities.

Blocks -- Ungapped segments in conserved protein sequences

Search for ungapped segments corresponding to the most highly conserved regions of proteins.

CASTp -- computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

Identify and measure surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.

CSA -- The Catalytic Site Atlas

To search for catalytic residue annotation for enzymes in the Protein Data Bank.

ConFunc -- Conserved residue Protein Function Prediction Server

Predict protein function using Gene Ontology.

ConSurf-DB -- evolutionary conservation profiles of protein structures database

Automatically calculate evolutionary conservation scores of key amino acid residues and map them on protein structures.

DBAli -- A Database of Structure Alignments

Mine the protein structure space.

DILIMOT -- discovery of linear motifs in proteins

Predict short linear motifs (3-8 residues) in a set of protein sequences.

Dasty2 -- an Ajax protein DAS client

A web client for visualizing protein sequence feature information using DAS.

DomainSweep -- protein annotation by domain analysis

Identify the domain architecture within a protein sequence.

E1DS -- catalytic site prediction based on 1D signatures of concurrent conservation

Predict enzyme catalytic site.

ELM -- Eukarotic Linear Motif Resource

Predict functional sites in eukaryotic proteins.

EXPASY Proteome Tools Collection

Use a collection of tools for protein analyses.

EXPASY-Findmod

Predict potential protein post-translational modifications and find potential single amino acid substitutions in peptides.

EzCatDB -- the Enzyme Catalytic-mechanism Database

Search for information related to the catalytic mechanisms of enzymes.

FFPred -- feature-based function prediction

An integrated feature-based function prediction server for vertebrate proteomes.

FingerPRINT Scan

Identify the closest matching PRINTS sequence motif fingerprints in a protein sequence.

FireDB -- a database of functionally important residues from proteins of known structure

Search for functional annotation of important sites in proteins with known structures.

Frog2 -- a FRee Online druG 3D conformation generator

Produce 3D conformations of small drug compounds.

HGPD -- Human Gene and Protein Database

A database presenting experiment-based results in human proteomics.

HHsenser -- exhaustive transitive profile search using HMMx96HMM comparison

Conduct exhaustive intermediate profile searches of a set of homologous protein sequences.

HotSpot Wizard -- Substrate Specificity Hot Spot Identification web server

Design protein mutations in site-directed mutagenesis.

INTREPID -- INformation-theoretic TREe traversal for Protein functional site IDentification

Use for protein functional site identification.

Integrating protein annotation resources through the Distributed Annotation System

Annotate protein using this integrated annotation resource.

InterProScan -- protein domains identifier

Identify protein family (and DNA) domains, patterns, motifs, protein families, and functional sites.

KFC -- Knowledge-based FADE and Contacts

Interactive forecasting of protein interaction hot spots.

MAGIIC-PRO -- detecting functional signatures by efficient discovery of long patterns in protein sequences

Discover long patterns in protein sequences.

MALISAM -- Manual ALIgnments for Structurally Analogous Motifs

Database containing pairs of structural analogs and their alignments.

MEME -- discovering and analyzing DNA and protein sequence motifs

Find sequence patterns in DNA and protein sequences.

MODPROPEP -- a program for knowledge-based modeling of protein-peptide complexes

A web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases.

MeMo -- a web tool for prediction of protein methylation modifications

Predict protein methylation sites.

MegaMotifBase -- a database of structural motifs in protein families and superfamilies

Find structural segments or motifs for protein structures.

Minimotif Miner -- a tool for investigating protein function

Find motifs in a protein sequence.

Motif3D -- Relating protein sequence motifs to 3D structure

Visualize protein sequence motifs on the 3D protein structures.

MotifScan

Find presence of any known protein motif (Prosite and Pfam) in a protein sequence.

MultiBind -- Multiple Alignment of Protein Binding Sites

Recognize spatial chemical binding patterns common to a set of protein structures.

NMT -- The MYR Predictor

Analyze proteins for the presence of N-terminal N-myristoylation site.

NetNGlyc -- N-Glycosylation sites prediction tool

Find the presence of N-Glycosylation sites in human proteins.

NetOGly 3.1 -- O-glycosylation sites prediction tool

Find the presence of O-GalNAc (mucin type) glycosylation sites in mammalian proteins.

NetPhos 2.0 -- Phosphorylation sites predictions

Analyze eukaryotic proteins for the presence of serine, threonine and tyrosine phosphorylation sites.

NetPhosK 1.0 Server -- kinase specific eukaryotic protein phosphorylation sites prediction tool

Find possible kinase specific phosphorylation sites in eukaryotic proteins.

NetworKIN -- a resource for exploring cellular phosphorylation networks

NeuroPred -- a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides

Predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences.

Non-Redundant Patent Sequences - Patented Sequence Database

Find information about patented nucleotide and protein sequences.

O-GLYCBASE

Search for information about glycoproteins with O-linked and C-linked glycosylation sites.

PANDORA -- Protein ANnotation Diagram ORiented Analysis

Find information about protein sequence annotations.

PAR-3D -- Protein Active site Residue - 3D structural motif

A server to predict protein active site residues.

PDBSite -- a database of the 3D structure of protein functional sites

Search for structural and functional information on the protein functional sites.

PDBSiteScan -- A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins

Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites.

PEDANT -- Protein Extraction, Description and ANalysis Tool

Conduct genome wide functional and structural analysis.

PHOSIDA -- Phosphorylation site database

Search for phosphorylation data of any protein of interest.

PHOSPHORYLATION SITE DATABASE

Search for information on prokaryotic proteins that undergo serine, threonine, or tyrosine phosphorylation.

PNU -- Protein Naming Utility

Determine correct names for proteins.

POODLE-S -- Predicition Of Order and Disorder by machine LEarning

Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.

PPISearch -- Protein-Protein Interaction Search

Find homologous protein-protein interactions across multiple species.

PPSearch

Search your query sequence against PROSITE pattern database for protein motifs.

PRIDB -- Protein-RNA Interface DataBase

Find information about protein-RNA complexes from the Protein Data Bank (PDB).

PRINTS and its automatic supplement, prePRINTS -- A compendium of protein fingerprints

Search for protein fingerprints.

PROSITE

Identify protein families and domains for a given protein sequence.

PRRDB -- Pattern Recognition Receptor Database

A comprehensive database of pattern-recognition receptors and their ligands.

PatMatch -- a program for finding patterns in peptide and nucleotide sequences

Search for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences.

PepCyber:P~PEP -- a database of human protein protein interactions mediated by phosphoprotein-binding domains

Database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions.

PeptideCutter -- protein cleavage sites prediction tool

Predicts potential protease cleavage sites and sites cleaved by chemicals in a given protein sequence.

Phobius -- A combined transmembrane topology and signal peptide predictor

Predict combined transmembrane topology and signal peptides.

Phospho.ELM -- a database of phosphorylation sites

Search for eukaryotic phosphorylation sites.

Phospho3D -- a database of three-dimensional structures of protein phosphorylation sites

Search for 3D structure and functional annotation of phosphorylation sites in proteins.

PhosphoSite -- A bioinformatics resource dedicated to physiological protein phosphorylation.

Search the database of in vivo phosphorylation sites of human and mouse proteins

PolyQ -- Polyglutamine Database

Find information about polyglutamine (polyQ) repeats.

Pratt Protein motif and pattern discovery

Find the presence of protein motifs and patterns in an amino acid sequence.

PrediSi -- Prediction of Signal Peptides and their Cleavage Positions

Predict signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences.

ProFunc -- a server for predicting protein function from 3D structure

Predict protein functions based on known structures.

ProMateus--an open research approach to protein-binding sites analysis

Predict the location of potential protein-protein binding sites for unbound proteins.

ProTeus -- identifying signatures in protein termini

Identify short linear signatures in protein termini.

ProtSweep -- protein annotation by homology

Analyze and identify newly obtained protein sequences.

Protemot -- prediction of protein binding sites with automatically extracted geometrical templates

Predict protein binding sites in a protein sequence based on geometrical analysis of protein tertiary substructures.

QuasiMotiFinder -- protein annotation by searching for evolutionarily conserved motif-like patterns

Search for evolutionarily conserved motif-like patterns in protein sequences.

RNABindR -- software for prediction of RNA binding residues in proteins

Web-based server for analyzing and predicting RNA binding sites in proteins.

SCANMOT -- searching for similar sequences using a simultaneous scan of multiple sequence motifs

Search for similarities between proteins by simultaneous matching of multiple motifs.

SDPpred -- A Tool for Prediction of Amino Acid Residues that Determine Differences in Functional Specificity of Homologous Proteins

Predict residues in protein sequences that determine the proteins' functional specificity.

SDR -- Specificity Determining Residues Database

Predict specificity-determining residues in protein families.

SLiMDisc -- Short, Linear Motif Discovery

Find shared motifs in proteins with a common attribute.

SUMOsp -- a web server for sumoylation site prediction

Conduct in silico sumoylation sites prediction.

SWAKK -- a web server for detecting positive selection in proteins using a sliding window substitution rate analysis

Detect protein sequence section under positive evolution selection.

ScanProsite

Search for motifs and patterns within protein sequences.

ScanProsite -- detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

Detect patterns, profiles and motifs in a protein sequence.

ScanSite 2.0 -- Proteome-wide prediction of cell signaling interactions using short sequence motifs

Search for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

SePreSA -- SErver for the PREdiction of populations susceptible to Serious Adverse drug reaction

Find information about populations carrying polymorphisms within protein binding pockets that make them susceptible to serious adverse drug reaction (SADR).

Sequence Motif Search

Search the presence of a motif in either amino acid sequence or nucleotide sequence.

Signal-3L -- A 3-layer approach for predicting signal peptides

Predict signal peptides.

SignalP -- Machine learning approaches to the prediction of signal peptides, their cleavage sites, and other protein sorting signals

Predict signal peptides and their cleavage sites.

Sulfinator -- tyrosine sulfation sites prediction tool

Predict the presence of tyrosine sulfation sites in protein sequences

SuperSite -- Ligand Binding Site Database

Look at protein structure from a ligand and binding site perspective.

Swiss EMBnet node web server

Use a collection of bioinformatics tools at this portal site.

T-REKS -- identification of Tandem REpeats in sequences with a K-meanS based algorithm

Find information about tandem repeats in proteins that carry fundamental biological functions and are related to a number of human diseases.

TMFunction -- The Functional Database of Membrane Proteins

Find information about functional residues in alpha-helical and beta-barrel membrane proteins.

TOPDOM -- Conservatively Located Domains and Motifs in Transmembrane Proteins

Database of domains and motifs with conservative location in transmembrane proteins.

The EMOTIF database

Search for highly conserved and specific protein sequence motifs.

TreeDet -- Predicting Functional Residues in Protein Sequence Alignments

Predict functional sites in protein sequence alignments use different methodologies.

W-ChIPMotifs -- ChIP-based protein Motif discovery web server

Find de novo protein motifs from chromatin immunoprecipitation data.

WebFEATURE -- an interactive web tool for identifying and visualizing functional sites on macromolecular structures

Scan query structures for functional sites in both proteins and nucleic acids.

WebProAnalyst -- an interactive tool for analysis of quantitative structurex96activity relationships in protein families

Analyze quantitative structure-activity relationship of related protein families.

eBLOCKs -- enumerating conserved protein blocks to achieve maximal sensitivity and specificity

Search for ungapped alignments of highly conserved regions among a protein family or superfamily.

eF-seek -- prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape

Predict the functional sites of proteins.

firestar -- prediction of functionally important residues using structural templates and alignment reliability

An expert system for predicting ligand-binding residues in protein structures.

iMOTdb -- a comprehensive collection of spatially interacting motifs in proteins

Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage.

Setting python version as default on Linux

Rahul Nayak — Tue, 04 Sep 2018 10:15:47 -0500

If you have a later version than 2.6 you'll need to set 2.6 as the default Python. Later versions would be 2.7 and 3.1; see what you have by typing

python -V

at the terminal. For purposes of this example we'll assume you have 3.1 installed. You'll next need to execute the following commands:

sudo apt-get install python2.6 idle-python2.6
sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.1 1
sudo update-alternatives --install /usr/bin/python python /usr/bin/python2.6 10
sudo update-alternatives --config python

This last command will allow you to choose which version of python to use by default. If you have done everything above correctly, python2.6 should already be set as the default. If it is not, choose it to be the default. From now on, running python should start version 2.6.

Undoing These Changes

In some cases (e.g., installing or updating certain packages), you'll get an error message if you've run the commands above. To update these packages, you'll have to temporarily undo these changes. Here's how to do that:

sudo update-alternatives --remove-all python
sudo ln -s python3.1 /usr/bin/python

Once you're done updating these packages, execute the commands at the top to set python2.6 as the default again.

Julia Programming Language, a Python and R rival

Radha Agarkar — Sat, 25 Aug 2018 04:46:39 -0500

Big data has grown to become one of the most lucrative fields. In fact, data scientists are some of the most sought people. They are usually hired to analyze, control and parse large chunks of data. Implementing these actions using traditional techniques is not a walk in the park. This is why most data scientists prefer using programming languages such as R and Python. However, there is one more programming language that can do the job. That is Julia programming language.

What Is Julia Language?

Julia is a programming language that came into the limelight in 2012. It is a general-purpose programming language that was designed for solving scientific computations. Julia was meant to be an alternative to Python, R and other programming languages that were mainly used for manipulating data. This is because it has numerous features that can minimize the complexities of numerical computations.

Julia optimizes on the best features of Python and R while at the same time overlooks their weaknesses. This explains why it is viewed as an alternative to these programming languages. For instance, it utilizes the readability and simplicity of Python then performs faster.

Julia is the most preferred programming language for data scientists and mathematicians. This is because its core features are similar to the ones that are used on most data software. Also, the language is ideal for these two subjects because its syntax is similar to the standard mathematical formulas.

Key Features Of Julia Language
Uses JIT Compilation
Parallelism
Dynamic Typing
Simple Syntax
Allows Metaprogramming
Accessible to Libraries
-1-Array Indexing

Julia Vs Python And R Programming Languages
1. Speed
Julia is faster than both Python and R. This is a very critical aspect that is given special attention in the big data programming. The high speed of Julia is because of JIT compilers. You will need to install external libraries on Python to achieve similar speed.

2. Syntax
Julia has a math-friendly syntax. The syntax of this programming language is similar to the mathematical formulas hence can be used to perform mathematical and scientific computations. This syntax makes it easier to learn than Python.

3. Parallelism
Although both Python and R use parallelism, Julia uses a top-level parallelism. Julia allows the processor to perform to the optimum level than what Python and R can achieve.

4. Versatility
Julia programming language is more versatile than Python and R. It allows a programmer to move from different codes and functions with ease.

The only area that Python and R are superior to Julia is in terms of community. Given that Julia is a new programming language, it has a small community as compared to others which have been around for years.

In overall Julia programming language is a better alternative that you can use to handle Big data projects. Despite having a small community, it is one of those programming languages that you can easily learn.

Converting a VCF into a FASTA given some reference !

Jit — Fri, 20 Jul 2018 10:03:53 -0500

Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528)

This script has been modified by others to convert InDels as well, e.g. this by David Eccles

./vcf2fq.pl -f <input.fasta> <all-site.vcf> > <output.fastq>

https://github.com/gringer/bioinfscripts/blob/master/vcf2fq.pl

https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl

Installing Salmon for Trinity !

Rahul Nayak — Tue, 03 Jul 2018 09:02:29 -0500

➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ conda install salmon
Solving environment: done

## Package Plan ##

environment location: /home/urbe/anaconda3

added / updated specs:
- salmon

The following packages will be downloaded:

package | build
---------------------------|-----------------
boost-1.64.0 | py36_4 331 KB conda-forge
jemalloc-5.1.0 | hfc679d8_0 8.2 MB conda-forge
boost-cpp-1.64.0 | 1 17.8 MB conda-forge
salmon-0.10.2 | 1 3.7 MB bioconda
conda-4.5.5 | py36_0 624 KB conda-forge
tbb-2018_20171205 | 0 1.2 MB conda-forge
------------------------------------------------------------
Total: 31.8 MB

The following NEW packages will be INSTALLED:

boost: 1.64.0-py36_4 conda-forge
boost-cpp: 1.64.0-1 conda-forge
jemalloc: 5.1.0-hfc679d8_0 conda-forge
salmon: 0.10.2-1 bioconda
tbb: 2018_20171205-0 conda-forge

The following packages will be UPDATED:

conda: 4.5.4-py36_0 conda-forge --> 4.5.5-py36_0 conda-forge

Proceed ([y]/n)? y

Downloading and Extracting Packages
boost-1.64.0 | 331 KB | ####################################################################################################################################### | 100%
jemalloc-5.1.0 | 8.2 MB | ####################################################################################################################################### | 100%
boost-cpp-1.64.0 | 17.8 MB | ####################################################################################################################################### | 100%
salmon-0.10.2 | 3.7 MB | ####################################################################################################################################### | 100%
conda-4.5.5 | 624 KB | ####################################################################################################################################### | 100%
tbb-2018_20171205 | 1.2 MB | ####################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Installing Trinity !

Rahul Nayak — Tue, 03 Jul 2018 04:31:15 -0500

Download this https://github.com/trinityrnaseq/trinityrnaseq/releases/tag/Trinity-v2.6.6

➜ cd trinityrnaseq-Trinity-v2.6.6

➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ make
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
&& sh ./configure --prefix=`pwd` && make install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[1]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm'
Making install in src
make[2]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm/src'
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT Fasta_entry.o -MD -MP -MF .deps/Fasta_entry.Tpo -c -o Fasta_entry.o Fasta_entry.cpp
mv -f .deps/Fasta_entry.Tpo .deps/Fasta_entry.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT IRKE_run.o -MD -MP -MF .deps/IRKE_run.Tpo -c -o IRKE_run.o IRKE_run.cpp
mv -f .deps/IRKE_run.Tpo .deps/IRKE_run.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT sequenceUtil.o -MD -MP -MF .deps/sequenceUtil.Tpo -c -o sequenceUtil.o sequenceUtil.cpp
mv -f .deps/sequenceUtil.Tpo .deps/sequenceUtil.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT IRKE.o -MD -MP -MF .deps/IRKE.Tpo -c -o IRKE.o IRKE.cpp
mv -f .deps/IRKE.Tpo .deps/IRKE.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT KmerCounter.o -MD -MP -MF .deps/KmerCounter.Tpo -c -o KmerCounter.o KmerCounter.cpp
mv -f .deps/KmerCounter.Tpo .deps/KmerCounter.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT string_util.o -MD -MP -MF .deps/string_util.Tpo -c -o string_util.o string_util.cpp
mv -f .deps/string_util.Tpo .deps/string_util.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT Fasta_reader.o -MD -MP -MF .deps/Fasta_reader.Tpo -c -o Fasta_reader.o Fasta_reader.cpp
mv -f .deps/Fasta_reader.Tpo .deps/Fasta_reader.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT stacktrace.o -MD -MP -MF .deps/stacktrace.Tpo -c -o stacktrace.o stacktrace.cpp
mv -f .deps/stacktrace.Tpo .deps/stacktrace.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT argProcessor.o -MD -MP -MF .deps/argProcessor.Tpo -c -o argProcessor.o argProcessor.cpp
mv -f .deps/argProcessor.Tpo .deps/argProcessor.Po
g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -o inchworm Fasta_entry.o IRKE_run.o sequenceUtil.o IRKE.o KmerCounter.o string_util.o Fasta_reader.o stacktrace.o argProcessor.o
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT cigar_tweaker.o -MD -MP -MF .deps/cigar_tweaker.Tpo -c -o cigar_tweaker.o cigar_tweaker.cpp
mv -f .deps/cigar_tweaker.Tpo .deps/cigar_tweaker.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT SAM_entry.o -MD -MP -MF .deps/SAM_entry.Tpo -c -o SAM_entry.o SAM_entry.cpp
mv -f .deps/SAM_entry.Tpo .deps/SAM_entry.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT SAM_reader.o -MD -MP -MF .deps/SAM_reader.Tpo -c -o SAM_reader.o SAM_reader.cpp
mv -f .deps/SAM_reader.Tpo .deps/SAM_reader.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT Cigar.o -MD -MP -MF .deps/Cigar.Tpo -c -o Cigar.o Cigar.cpp
mv -f .deps/Cigar.Tpo .deps/Cigar.Po
g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -o cigar_tweaker cigar_tweaker.o SAM_entry.o sequenceUtil.o SAM_reader.o Cigar.o string_util.o stacktrace.o Fasta_reader.o Fasta_entry.o
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT pull_reads_with_kmers.o -MD -MP -MF .deps/pull_reads_with_kmers.Tpo -c -o pull_reads_with_kmers.o pull_reads_with_kmers.cpp
mv -f .deps/pull_reads_with_kmers.Tpo .deps/pull_reads_with_kmers.Po
g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -o pull_reads_with_kmers pull_reads_with_kmers.o Fasta_reader.o Fasta_entry.o sequenceUtil.o KmerCounter.o string_util.o stacktrace.o argProcessor.o
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT FastaToDeBruijn.o -MD -MP -MF .deps/FastaToDeBruijn.Tpo -c -o FastaToDeBruijn.o FastaToDeBruijn.cpp
FastaToDeBruijn.cpp: In function ‘void createGraphPerRecord(std::vector >, int, bool, ArgProcessor)’:
FastaToDeBruijn.cpp:199:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (seq_region.size() < kmer_length) { continue; } // can be e
^
mv -f .deps/FastaToDeBruijn.Tpo .deps/FastaToDeBruijn.Po
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT DeBruijnGraph.o -MD -MP -MF .deps/DeBruijnGraph.Tpo -c -o DeBruijnGraph.o DeBruijnGraph.cpp
mv -f .deps/DeBruijnGraph.Tpo .deps/DeBruijnGraph.Po
g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -o FastaToDeBruijn FastaToDeBruijn.o argProcessor.o Fasta_reader.o Fasta_entry.o sequenceUtil.o string_util.o stacktrace.o DeBruijnGraph.o
g++ -DHAVE_CONFIG_H -I. -I.. -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT fastaToKmerCoverageStats.o -MD -MP -MF .deps/fastaToKmerCoverageStats.Tpo -c -o fastaToKmerCoverageStats.o fastaToKmerCoverageStats.cpp
fastaToKmerCoverageStats.cpp: In function ‘void populate_kmer_counter_from_reads(KmerCounter&, std::__cxx11::string&)’:
fastaToKmerCoverageStats.cpp:226:18: warning: unused variable ‘kmer_length’ [-Wunused-variable]
unsigned int kmer_length = kcounter.get_kmer_length();
^
mv -f .deps/fastaToKmerCoverageStats.Tpo .deps/fastaToKmerCoverageStats.Po
g++ -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -o fastaToKmerCoverageStats fastaToKmerCoverageStats.o argProcessor.o Fasta_reader.o Fasta_entry.o sequenceUtil.o string_util.o stacktrace.o KmerCounter.o
make[3]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm/src'
test -z "/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm/bin" || /bin/mkdir -p "/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm/bin"
/usr/bin/install -c inchworm cigar_tweaker pull_reads_with_kmers FastaToDeBruijn fastaToKmerCoverageStats '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm/bin'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm/src'
make[2]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm/src'
make[2]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm'
make[3]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm'
make[2]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm'
make[1]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Inchworm'
cd Chrysalis && make UNSUPPORTED=yes
make[1]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Chrysalis'
./MakeDepend.cc: In member function ‘bool makefile_builder::dependency::operator<(const makefile_builder::dependency&) const’:
./MakeDepend.cc:93:47: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
dependent_ == other.dependent_ &&
^
./MakeDepend.cc: In member function ‘bool makefile_builder::subdir_and_target::operator<(const makefile_builder::subdir_and_target&) const’:
./MakeDepend.cc:130:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
subdir_ == other.subdir_ &&
^
./MakeDepend.cc: In function ‘int main(int, char**)’:
./MakeDepend.cc:223:20: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
char * options = "Ad:g:u:fh";
^
./MakeDepend.cc: In member function ‘void makefile_builder::DumpDependencies(const string&)’:
./MakeDepend.cc:491:46: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
if ( ! this->FileIsSource( dependent ) && ! this->FileIsHeader( dependent
^
./MakeDepend.cc:493:44: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
this->FileIsHeader( dependent ) && this->FileIsSource( provider ) )
^
./MakeDepend.cc: In member function ‘bool makefile_builder::FileIsHeader(const string&) const’:
./MakeDepend.cc:1339:32: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
return ( filename.size() > 2 &&
^
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:04 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./aligns/KmerAlignCore.cc -o obj/aligns/KmerAlignCore.o
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:06 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/AACodons.cc -o obj/analysis/AACodons.o
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:09 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/BreakTransByPairs.cc -o obj/analysis/BreakTransByPairs.o
./analysis/BreakTransByPairs.cc: In function ‘int main(int, char**)’:
./analysis/BreakTransByPairs.cc:105:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; i > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)’:
./analysis/DeBruijnGraph.cc:473:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < left_extensions.size(); i++) {
^
./analysis/DeBruijnGraph.cc:476:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < right_extensions.size(); j++) {
^
./analysis/DeBruijnGraph.cc: In member function ‘void DeBruijnGraph::recursively_construct_kmer_extensions(kmer_int_type_t, std::vector&, std::vector >&, char, std::map&, int)’:
./analysis/DeBruijnGraph.cc:513:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < adjacent_kmers.size(); i++) {
^
./analysis/DeBruijnGraph.cc:527:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (kmer_extension_chars.size() == flank_extension_length) {
^
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:30 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/sequenceUtil.cc -o obj/analysis/sequenceUtil.o
./analysis/sequenceUtil.cc: In function ‘bool contains_non_gatc(std::__cxx11::string)’:
./analysis/sequenceUtil.cc:33:20: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if (_base_to_int[c] > 3)
^
./analysis/sequenceUtil.cc: In function ‘kmer_int_type_t kmer_to_intval(std::__cxx11::string)’:
./analysis/sequenceUtil.cc:264:26: warning: array subscript has type ‘char’ [-Wchar-subscripts]
int val = _base_to_int[c];
^
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:31 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/stacktrace.cc -o obj/analysis/stacktrace.o
/bin/rm -f lib_BubbleUpClustering_temp.a
ar -qc lib_BubbleUpClustering_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/BubbleUpClustering.o obj/analysis/DNAVector.o obj/analysis/DeBruijnGraph.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/analysis/sequenceUtil.o obj/analysis/stacktrace.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./BubbleUpClustering
g++ -ggdb3 -fopenmp -o ./BubbleUpClustering obj/analysis/BubbleUpClustering.o -L. -lm -pthread -l_BubbleUpClustering_temp
/bin/rm lib_BubbleUpClustering_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:32 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/Chrysalis.cc -o obj/analysis/Chrysalis.o
./analysis/Chrysalis.cc: In function ‘int main(int, char**)’:
./analysis/Chrysalis.cc:384:28: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:35 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/TranscriptomeGraph.cc -o obj/analysis/TranscriptomeGraph.o
./analysis/TranscriptomeGraph.cc: In function ‘int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)’:
./analysis/TranscriptomeGraph.cc:668:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; i<=d.isize()-k; i++) {
^
/bin/rm -f lib_Chrysalis_temp.a
ar -qc lib_Chrysalis_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/Chrysalis.o obj/analysis/DNAVector.o obj/analysis/TranscriptomeGraph.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./Chrysalis
g++ -ggdb3 -fopenmp -o ./Chrysalis obj/analysis/Chrysalis.o -L. -lm -pthread -l_Chrysalis_temp
/bin/rm lib_Chrysalis_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:39 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/CreateIwormFastaBundle.cc -o obj/analysis/CreateIwormFastaBundle.o
/bin/rm -f lib_CreateIwormFastaBundle_temp.a
ar -qc lib_CreateIwormFastaBundle_temp.a obj/analysis/AACodons.o obj/analysis/CreateIwormFastaBundle.o obj/analysis/DNAVector.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./CreateIwormFastaBundle
g++ -ggdb3 -fopenmp -o ./CreateIwormFastaBundle obj/analysis/CreateIwormFastaBundle.o -L. -lm -pthread -l_CreateIwormFastaBundle_temp
/bin/rm lib_CreateIwormFastaBundle_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:42 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/GraphFromFasta.cc -o obj/analysis/GraphFromFasta.o
./analysis/GraphFromFasta.cc: In function ‘bool SimpleHalves(const DNAVector&)’:
./analysis/GraphFromFasta.cc:255:15: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
&&
^
./analysis/GraphFromFasta.cc: In function ‘void report_iworm_graph(std::map&, std::map&)’:
./analysis/GraphFromFasta.cc:631:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < adjacent_nodes.size(); j++) {
^
./analysis/GraphFromFasta.cc: In function ‘int main(int, char**)’:
./analysis/GraphFromFasta.cc:1164:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; i bubble_up_cluster_growth(std::map&, std::map&)’:
./GraphFromFasta_MPI.cc:706:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < pool_vec.size(); i++) {
^
./GraphFromFasta_MPI.cc:727:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < pool_vec.size(); i++) {
^
./GraphFromFasta_MPI.cc:834:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < pool_vec.size(); i++) {
^
./GraphFromFasta_MPI.cc: In function ‘void add_unclustered_iworm_contigs(svec&, vecDNAVector&)’:
./GraphFromFasta_MPI.cc:1144:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < p.size(); i++) {
^
./GraphFromFasta_MPI.cc: In function ‘int main(int, char**)’:
./GraphFromFasta_MPI.cc:1453:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (iworm_counter % 1000 == 0 || iworm_counter == dna.size()-1) {
^
./GraphFromFasta_MPI.cc:1458:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j=0; j<=d.isize()-k; j++) {
^
./GraphFromFasta_MPI.cc:1479:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (c == i)
^
./GraphFromFasta_MPI.cc:1503:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (c == i)
^
./GraphFromFasta_MPI.cc:2235:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j=0; j<=d.isize()-k; j++) {
^
./GraphFromFasta_MPI.cc:2264:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (c == i) {
^
./GraphFromFasta_MPI.cc:2359:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (c == i) {
^
./GraphFromFasta_MPI.cc:2475:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; i ^
./GraphFromFasta_MPI.cc:2483:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < p.size(); j++) {
^
./GraphFromFasta_MPI.cc:2496:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < p.size(); j++) {
^
/bin/rm -f lib_GraphFromFasta_MPI_temp.a
ar -qc lib_GraphFromFasta_MPI_temp.a obj/GraphFromFasta_MPI.o obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/DeBruijnGraph.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/analysis/sequenceUtil.o obj/analysis/stacktrace.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./GraphFromFasta_MPI
g++ -ggdb3 -fopenmp -o ./GraphFromFasta_MPI obj/GraphFromFasta_MPI.o -L. -lm -pthread -l_GraphFromFasta_MPI_temp
/bin/rm lib_GraphFromFasta_MPI_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:53 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/IsoformAugment.cc -o obj/analysis/IsoformAugment.o
./analysis/IsoformAugment.cc: In function ‘int main(int, char**)’:
./analysis/IsoformAugment.cc:87:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j=0; j ^
./analysis/IsoformAugment.cc:122:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j=0; j ^
/bin/rm -f lib_IsoformAugment_temp.a
ar -qc lib_IsoformAugment_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/IsoformAugment.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./IsoformAugment
g++ -ggdb3 -fopenmp -o ./IsoformAugment obj/analysis/IsoformAugment.o -L. -lm -pthread -l_IsoformAugment_temp
/bin/rm lib_IsoformAugment_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:27:56 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/JoinTransByPairs.cc -o obj/analysis/JoinTransByPairs.o
./analysis/JoinTransByPairs.cc: In function ‘int main(int, char**)’:
./analysis/JoinTransByPairs.cc:293:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; i ^
./analysis/JoinTransByPairs.cc:341:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0; i ^
/bin/rm -f lib_JoinTransByPairs_temp.a
ar -qc lib_JoinTransByPairs_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/JoinTransByPairs.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./JoinTransByPairs
g++ -ggdb3 -fopenmp -o ./JoinTransByPairs obj/analysis/JoinTransByPairs.o -L. -lm -pthread -l_JoinTransByPairs_temp
/bin/rm lib_JoinTransByPairs_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:28:00 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/QuantifyGraph.cc -o obj/analysis/QuantifyGraph.o
/bin/rm -f lib_QuantifyGraph_temp.a
ar -qc lib_QuantifyGraph_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/analysis/QuantifyGraph.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./QuantifyGraph
g++ -ggdb3 -fopenmp -o ./QuantifyGraph obj/analysis/QuantifyGraph.o -L. -lm -pthread -l_QuantifyGraph_temp
/bin/rm lib_QuantifyGraph_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:28:03 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/ReadsToTranscripts.cc -o obj/analysis/ReadsToTranscripts.o
/bin/rm -f lib_ReadsToTranscripts_temp.a
ar -qc lib_ReadsToTranscripts_temp.a obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/NonRedKmerTable.o obj/analysis/ReadsToTranscripts.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./ReadsToTranscripts
g++ -ggdb3 -fopenmp -o ./ReadsToTranscripts obj/analysis/ReadsToTranscripts.o -L. -lm -pthread -l_ReadsToTranscripts_temp
/bin/rm lib_ReadsToTranscripts_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:28:09 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./ReadsToTranscripts_MPI.cc -o obj/ReadsToTranscripts_MPI.o
/bin/rm -f lib_ReadsToTranscripts_MPI_temp.a
ar -qc lib_ReadsToTranscripts_MPI_temp.a obj/ReadsToTranscripts_MPI.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/NonRedKmerTable.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./ReadsToTranscripts_MPI
g++ -ggdb3 -fopenmp -o ./ReadsToTranscripts_MPI obj/ReadsToTranscripts_MPI.o -L. -lm -pthread -l_ReadsToTranscripts_MPI_temp
/bin/rm lib_ReadsToTranscripts_MPI_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:28:14 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./ReadsToTranscripts_MPI_chang.cc -o obj/ReadsToTranscripts_MPI_chang.o
/bin/rm -f lib_ReadsToTranscripts_MPI_chang_temp.a
ar -qc lib_ReadsToTranscripts_MPI_chang_temp.a obj/ReadsToTranscripts_MPI_chang.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/NonRedKmerTable.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./ReadsToTranscripts_MPI_chang
g++ -ggdb3 -fopenmp -o ./ReadsToTranscripts_MPI_chang obj/ReadsToTranscripts_MPI_chang.o -L. -lm -pthread -l_ReadsToTranscripts_MPI_chang_temp
/bin/rm lib_ReadsToTranscripts_MPI_chang_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:28:18 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/RunButterfly.cc -o obj/analysis/RunButterfly.o
./analysis/RunButterfly.cc: In member function ‘void JobControl::ClearFiles()’:
./analysis/RunButterfly.cc:107:25: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
system(rm.c_str());
^
./analysis/RunButterfly.cc: In member function ‘void JobControl::Submit()’:
./analysis/RunButterfly.cc:77:27: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
system(theCmmd.c_str());
^
./analysis/RunButterfly.cc:85:27: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
system(theCmmd.c_str());
^
/bin/rm -f lib_RunButterfly_temp.a
ar -qc lib_RunButterfly_temp.a obj/analysis/RunButterfly.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./RunButterfly
g++ -ggdb3 -fopenmp -o ./RunButterfly obj/analysis/RunButterfly.o -L. -lm -pthread -l_RunButterfly_temp
/bin/rm lib_RunButterfly_temp.a
g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='"Die Jul 3 11:28:23 CEST 2018 "' -DMAKE_OS_RELEASE='"4.4.0-128-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp -iquote . -ISpines -fopenmp -c ./analysis/TranscriptomeFromVaryK.cc -o obj/analysis/TranscriptomeFromVaryK.o
./analysis/TranscriptomeFromVaryK.cc: In function ‘int main(int, char**)’:
./analysis/TranscriptomeFromVaryK.cc:216:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j=0; j<=d.lsize()-k; j++) {
^
./analysis/TranscriptomeFromVaryK.cc:218:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int x=j; x ^
/bin/rm -f lib_TranscriptomeFromVaryK_temp.a
ar -qc lib_TranscriptomeFromVaryK_temp.a obj/aligns/KmerAlignCore.o obj/analysis/AACodons.o obj/analysis/DNAVector.o obj/analysis/KmerTable.o obj/analysis/NonRedKmerTable.o obj/analysis/TranscriptomeFromVaryK.o obj/base/ErrorHandling.o obj/base/FileParser.o obj/base/StringUtil.o obj/util/mutil.o
./checkLock ./TranscriptomeFromVaryK
g++ -ggdb3 -fopenmp -o ./TranscriptomeFromVaryK obj/analysis/TranscriptomeFromVaryK.o -L. -lm -pthread -l_TranscriptomeFromVaryK_temp
/bin/rm lib_TranscriptomeFromVaryK_temp.a
make[1]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/Chrysalis'
cd trinity-plugins && make trinity_essentials
make[1]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins'
tar xvf seqtk-trinity.v0.0.2.tar.gz
seqtk-trinity-0.0.2/
seqtk-trinity-0.0.2/.gitignore
seqtk-trinity-0.0.2/LICENSE
seqtk-trinity-0.0.2/Makefile
seqtk-trinity-0.0.2/README.md
seqtk-trinity-0.0.2/khash.h
seqtk-trinity-0.0.2/kseq.h
seqtk-trinity-0.0.2/seqtk.c
seqtk-trinity-0.0.2/testing/
seqtk-trinity-0.0.2/testing/newformat_1.fq
seqtk-trinity-0.0.2/testing/newformat_2.fq
seqtk-trinity-0.0.2/testing/oldformat_1.fq
seqtk-trinity-0.0.2/testing/oldformat_2.fq
cd seqtk-trinity-0.0.2 && make
make[2]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/seqtk-trinity-0.0.2'
gcc -g -Wall -O2 -Wno-unused-function seqtk.c -o seqtk-trinity -lz -lm
seqtk.c: In function ‘stk_comp’:
seqtk.c:444:16: warning: variable ‘lc’ set but not used [-Wunused-but-set-variable]
int la, lb, lc, na, nb, nc, cnt[11];
^
make[2]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/seqtk-trinity-0.0.2'
mv seqtk-trinity-0.0.2/seqtk-trinity ./BIN/.
tar -zxvf "ParaFly-0.1.0".tar.gz && \
cd "ParaFly-0.1.0" && sh ./configure --prefix=`pwd` && make install && \
cp bin/ParaFly ../BIN/
ParaFly-0.1.0/
ParaFly-0.1.0/LICENSE
ParaFly-0.1.0/Makefile
ParaFly-0.1.0/Makefile.am
ParaFly-0.1.0/Makefile.in
ParaFly-0.1.0/README.md
ParaFly-0.1.0/aclocal.m4
ParaFly-0.1.0/bin/
ParaFly-0.1.0/bin/ParaFly
ParaFly-0.1.0/config.h
ParaFly-0.1.0/config.h.in
ParaFly-0.1.0/config.log
ParaFly-0.1.0/config.status
ParaFly-0.1.0/configure
ParaFly-0.1.0/configure.ac
ParaFly-0.1.0/depcomp
ParaFly-0.1.0/install-sh
ParaFly-0.1.0/missing
ParaFly-0.1.0/src/
ParaFly-0.1.0/src/.deps/
ParaFly-0.1.0/src/.deps/ParaFly.Po
ParaFly-0.1.0/src/.deps/argProcessor.Po
ParaFly-0.1.0/src/Makefile
ParaFly-0.1.0/src/Makefile.am
ParaFly-0.1.0/src/Makefile.in
ParaFly-0.1.0/src/ParaFly.cpp
ParaFly-0.1.0/src/argProcessor.cpp
ParaFly-0.1.0/src/argProcessor.hpp
ParaFly-0.1.0/stamp-h1
ParaFly-0.1.0/test/
ParaFly-0.1.0/test/Makefile
ParaFly-0.1.0/test/cmds.txt
ParaFly-0.1.0/test/rand_exit.pl
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[2]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0'
Making install in src
make[3]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0/src'
g++ -DHAVE_CONFIG_H -I. -I.. -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -MT ParaFly.o -MD -MP -MF .deps/ParaFly.Tpo -c -o ParaFly.o ParaFly.cpp
mv -f .deps/ParaFly.Tpo .deps/ParaFly.Po
g++ -DHAVE_CONFIG_H -I. -I.. -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -MT argProcessor.o -MD -MP -MF .deps/argProcessor.Tpo -c -o argProcessor.o argProcessor.cpp
mv -f .deps/argProcessor.Tpo .deps/argProcessor.Po
g++ -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -o ParaFly ParaFly.o argProcessor.o
make[4]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0/src'
test -z "/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0/bin" || /bin/mkdir -p "/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0/bin"
/usr/bin/install -c ParaFly '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0/bin'
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0/src'
make[3]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0/src'
make[3]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0'
make[4]: Entering directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0'
make[3]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0'
make[2]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins/ParaFly-0.1.0'
ln -sf Trimmomatic-0.36 Trimmomatic
make[1]: Leaving directory '/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity-plugins'
sh ./util/support_scripts/trinity_install_tests.sh
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Performing Unit Tests of Build

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Inchworm: has been Installed Properly
Chrysalis: has been Installed Properly
QuantifyGraph: has been Installed Properly
GraphFromFasta: has been Installed Properly
ReadsToTranscripts: has been Installed Properly
parafly: has been Installed Properly
➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗
➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity

###############################################################################
#

______ ____ ____ ____ ____ ______ __ __
| || \ | || \ | || || | |
| || D ) | | | _ | | | | || | |
|_| |_|| / | | | | | | | |_| |_|| ~ |
| | | \ | | | | | | | | | |___, |
| | | . \ | | | | | | | | | | |
|__| |__|\_||____||__|__||____| |__| |____/

#
#
# Required:
#
# --seqType :type of reads: ('fa' or 'fq')
#
# --max_memory :suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc)
# provided in Gb of RAM, ie. '--max_memory 10G'
#
# If paired reads:
# --left :left reads, one or more file names (separated by commas, no spaces)
# --right :right reads, one or more file names (separated by commas, no spaces)
#
# Or, if unpaired reads:
# --single :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: --run_as_paired )
#
# Or,
# --samples_file tab-delimited text file indicating biological replicate relationships.
# ex.
# cond_A cond_A_rep1 A_rep1_left.fq A_rep1_right.fq
# cond_A cond_A_rep2 A_rep2_left.fq A_rep2_right.fq
# cond_B cond_B_rep1 B_rep1_left.fq B_rep1_right.fq
# cond_B cond_B_rep2 B_rep2_left.fq B_rep2_right.fq
#
# # if single-end instead of paired-end, then leave the 4th column above empty.
#
####################################
## Misc: #########################
#
# --SS_lib_type :Strand-specific RNA-Seq read orientation.
# if paired: RF or FR,
# if single: F or R. (dUTP method = RF)
# See web documentation.
#
# --CPU :number of CPUs to use, default: 2
# --min_contig_length :minimum assembled contig length to report
# (def=200)
#
# --long_reads :fasta file containing error-corrected or circular consensus (CCS) pac bio reads
# (** note: experimental parameter **, this functionality continues to be under development)
#
# --genome_guided_bam :genome guided mode, provide path to coordinate-sorted bam file.
# (see genome-guided param section under --show_full_usage_info)
#
# --jaccard_clip :option, set if you have paired reads and
# you expect high gene density with UTR
# overlap (use FASTQ input file format
# for reads).
# (note: jaccard_clip is an expensive
# operation, so avoid using it unless
# necessary due to finding excessive fusion
# transcripts w/o it.)
#
# --trimmomatic :run Trimmomatic to quality trim reads
# see '--quality_trimming_params' under full usage info for tailored settings.
#
#
# --no_normalize_reads :Do *not* run in silico normalization of reads. Defaults to max. read coverage of 50.
# see '--normalize_max_read_cov' under full usage info for tailored settings.
# (note, as of Sept 21, 2016, normalization is on by default)
#
# --no_distributed_trinity_exec :do not run Trinity phase 2 (assembly of partitioned reads), and stop after generating command list.
#
#
# --output :name of directory for output (will be
# created if it doesn't already exist)
# default( your current working directory: "/home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir"
# note: must include 'trinity' in the name as a safety precaution! )
#
# --workdir :where Trinity phase-2 assembly computation takes place (defaults to --output setting).
# (can set this to a node-local drive or RAM disk)
#
# --full_cleanup :only retain the Trinity fasta file, rename as ${output_dir}.Trinity.fasta
#
# --cite :show the Trinity literature citation
#
# --verbose :provide additional job status info during the run.
#
# --version :reports Trinity version (Trinity-v2.6.6) and exits.
#
# --show_full_usage_info :show the many many more options available for running Trinity (expert usage).
#
#
###############################################################################
#
# *Note, a typical Trinity command might be:
#
# Trinity --seqType fq --max_memory 50G --left reads_1.fq --right reads_2.fq --CPU 6
#
#
# and for Genome-guided Trinity:
#
# Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G
# --genome_guided_max_intron 10000 --CPU 6
#
# see: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/sample_data/test_Trinity_Assembly/
# for sample data and 'runMe.sh' for example Trinity execution
#
# For more details, visit: http://trinityrnaseq.github.io
#
###############################################################################

chromoMap-An R package for Interactive visualization and mapping of human chromosomes

Rahul Nayak — Mon, 25 Jun 2018 17:22:24 -0500

chromoMap is an R package that provides interactive, configurable and elegant graphics visualization of the human chromosomes allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. Because of the enormous size of the chromosomes, it is impractical to visualize each element on the same plot. But chromoMap plots provide a magnified view for each of chromosome location to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order (You will see in the demos below). Not ony that, the plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

https://cran.r-project.org/web/packages/chromoMap/index.html

Install ImageMagick from Unix Source

Jit — Wed, 20 Jun 2018 11:22:43 -0500

ImageMagick builds on a variety of Unix and Unix-like operating systems including Linux, Solaris, FreeBSD, Mac OS X, and others. A compiler is required and fortunately almost all modern Unix systems have one. Download ImageMagick.tar.gzfrom www.imagemagick.org or a mirrors and verify its message digest.

Unpack the distribution with this command:

tar xvzf ImageMagick.tar.gz

Next configure and compile ImageMagick. Note the pkg-config script is required so that ImageMagick can find certain optional delegate libraries on your system. To configure, type:

$ cd ImageMagick-7.0.8
$ ./configure
$ make

If ImageMagick configured and compiled without complaint, you are ready to install it on your system. Administrator privileges are required to install. To install, type

sudo make install

You may need to configure the dynamic linker run-time bindings:

sudo ldconfig /usr/local/lib

Finally, verify the ImageMagick install worked properly, type

/usr/local/bin/convert logo: logo.gif

For a more comprehensive test, run the ImageMagick validation suite. Ghostscript is a prerequisite, otherwise the EPS, PS, and PDF tests will fail.

make check

Congratulations, you have a working ImageMagick distribution and you are ready to use ImageMagick to convert, compose, or edit your images or perhaps you'll want to use one of the Application Program Interfaces for C, C++, Perl, and others.

The above instructions will satisfy a great number of ImageMagick users, but we suspect a few will have additional questions or problems to consider. For example, what does one do if ImageMagick fails to configure or compile? Or what if you don't have administrator privileges and what if you don't want to install ImageMagick in the default /../usr/local folder? You will find the answer to these questions, and more, in Advanced Unix Source Installation.

jitendra@jitendra-UNLOCK-INSTALL[Downloads] git clone https://github.com/ImageMagick/ImageMagick.git []
Cloning into 'ImageMagick'...
remote: Counting objects: 124593, done.
remote: Compressing objects: 100% (77/77), done.
remote: Total 124593 (delta 94), reused 94 (delta 64), pack-reused 124452
Receiving objects: 100% (124593/124593), 76.94 MiB | 24.07 MiB/s, done.
Resolving deltas: 100% (106498/106498), done.
Checking connectivity... done.
jitendra@jitendra-UNLOCK-INSTALL[Downloads] cd ImageMagick []
jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] make []
make: *** No targets specified and no makefile found. Stop.
jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] ./configure []
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '1000' is supported by ustar format... yes
checking whether GID '1000' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
configuring ImageMagick 7.0.8-3
checking whether build environment is sane... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gcc option to accept ISO C99... none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking how to run the C preprocessor... gcc -E
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking how to print strings... printf
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
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checking CFLAGS for maximum warnings... -Wall
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... (cached) /bin/sed
checking for gawk... (cached) gawk
checking if malloc debugging is wanted... no
checking for __attribute__... yes
checking for C compiler vendor... gnu
checking for gcc architecture flag...
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checking for x86 cpuid 1 output... 306a9:3100800:7fbae3ff:bfebfbff
checking whether C compiler accepts -mtune=ivybridge... yes
checking for gcc architecture flag... -mtune=ivybridge
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checking pkg-config is at least version 0.20... yes
checking size of size_t... 8
checking for C compiler vendor... (cached) gnu
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checking CFLAGS for maximum warnings... (cached) -Wall
checking if LD -Wl,--version-script works... yes
checking for linker lazyload option... none
checking whether gcc is Clang... no
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checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for gcc option to support OpenMP... -fopenmp
checking for pthread_join using gcc -pthread ... yes
checking whether gcc is Clang... (cached) no
checking for joinable pthread attribute... (cached) PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... (cached) no
checking for PTHREAD_PRIO_INHERIT... (cached) yes
checking whether we are using the Microsoft C compiler... no
checking CL/cl.h usability... no
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checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking how to truncate binary pipes... /bin/dd bs=4096 count=1
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checking if mt is a manifest tool... no
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checking if gcc supports -fno-rtti -fno-exceptions... no
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checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether gcc needs -traditional... no
checking for ANSI C header files... (cached) yes
checking whether to enable assertions... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking arm/limits.h usability... no
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checking errno.h usability... yes
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checking xlocale.h presence... yes
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checking for stdbool.h that conforms to C99... yes
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checking for working volatile... yes
checking for preprocessor stringizing operator... yes
checking whether stat file-mode macros are broken... no
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for struct tm.tm_zone... yes
checking whether #! works in shell scripts... yes
checking whether char is unsigned... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for C/C++ restrict keyword... __restrict
checking for working volatile... (cached) yes
checking whether byte ordering is bigendian... no
checking for int8_t... yes
checking for int16_t... yes
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checking for int64_t... yes
checking for unsigned long long int... yes
checking for long long int... yes
checking for intmax_t... yes
checking for intptr_t... yes
checking for long double... yes
checking for long double with more range or precision than double... yes
checking for long long int... (cached) yes
checking for mbstate_t... yes
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checking for uid_t in sys/types.h... yes
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checking for unsigned long long int... (cached) yes
checking for locale_t... yes
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checking size of float_t... 4
checking size of double_t... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of signed short... 2
checking size of unsigned short... 2
checking size of signed int... 4
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checking size of signed long... 8
checking size of unsigned long... 8
checking size of signed long long... 8
checking size of unsigned long long... 8
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checking size of ssize_t... 8
checking size of unsigned int*... 8
checking for signed 8-bit type... signed char
checking for unsigned 8-bit type... unsigned char
checking for signed 16-bit type... signed short
checking for unsigned 16-bit type... unsigned short
checking for signed 32-bit type... signed int
checking for unsigned 32-bit type... unsigned int
checking for signed 64-bit type... signed long
checking for unsigned 64-bit type... unsigned long
checking for unsigned maximum type... unsigned long
checking for pointer difference type... unsigned long
checking whether our compiler supports __func__... yes
checking whether closedir returns void... no
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
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checking vfork.h usability... no
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checking for fork... yes
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checking for working fork... yes
checking for working vfork... (cached) yes
checking for working memcmp... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
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checking for sys/socket.h... (cached) yes
checking types of arguments for select... int,fd_set *,struct timeval *
checking return type of signal handlers... void
checking for working strtod... yes
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checking whether strerror_r returns char *... yes
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checking for library containing socket... none required
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checking for clock... yes
checking for clock_getres... yes
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checking for ctime_r... yes
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checking for fork... (cached) yes
checking for ftime... yes
checking for ftruncate... yes
checking for getc_unlocked... yes
checking for getcwd... yes
checking for getpid... yes
checking for getexecname... no
checking for getdtablesize... yes
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checking for getrlimit... yes
checking for getrusage... yes
checking for gettimeofday... yes
checking for gmtime_r... yes
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checking for j0... yes
checking for j1... yes
checking for lltostr... no
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checking for lstat... yes
checking for memmove... yes
checking for memset... yes
checking for mkstemp... yes
checking for munmap... yes
checking for nanosleep... yes
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checking for _NSGetExecutablePath... no
checking for pclose... yes
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checking for poll... yes
checking for popen... yes
checking for _popen... no
checking for posix_fadvise... yes
checking for posix_fallocate... yes
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checking for posix_memalign... yes
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checking for seekdir... yes
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checking for socket... yes
checking for sqrt... yes
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checking for strchr... yes
checking for strrchr... yes
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checking for strpbrk... yes
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checking for strstr... yes
checking for strtod... (cached) yes
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checking for strtoul... yes
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checking for sigemptyset... yes
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checking for library containing clock_gettime... none required
checking whether clock_gettime supports CLOCK_REALTIME... yes
checking whether pread is declared... yes
checking whether pwrite is declared... yes
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checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking whether the compiler recognizes bool as a built-in type... yes
checking whether the compiler implements namespaces... yes
checking if g++ supports namespace std... yes
checking whether the compiler supports ISO C++ standard library... yes
checking for g++ option to support OpenMP... -fopenmp
checking whether C++ compiler is sufficient for Magick++... yes
checking for X11 configure files...
checking for GOMP_parallel_start in -lgomp... yes
-------------------------------------------------------------
checking for BZLIB...
checking bzlib.h usability... no
checking bzlib.h presence... no
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checking for BZ2_bzDecompress in -lbz2... no
checking if BZLIB package is complete... no
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
-------------------------------------------------------------
checking for X11...
checking for shmctl... yes
checking for XShmAttach in -lXext... yes
checking for XShapeCombineMask in -lXext... yes
checking for XtSetEventDispatcher in -lXt... yes
-------------------------------------------------------------
checking for ZLIB... yes
-------------------------------------------------------------
checking for DPS...
checking DPS/dpsXclient.h usability... no
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checking for XDPSPixelsPerPoint in -ldpstk... no
checking if DPS package is complete... no
-------------------------------------------------------------
checking for fftw3... no
-------------------------------------------------------------
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checking flif.h usability... no
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-------------------------------------------------------------
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checking fpxlib.h usability... no
checking fpxlib.h presence... no
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checking for FPX_OpenImageByFilename in -lfpx... no
checking if FlashPIX package is complete... no
-------------------------------------------------------------
checking for ddjvuapi... no
-------------------------------------------------------------
checking for FONTCONFIG... yes
-------------------------------------------------------------
checking for FREETYPE... yes
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checking for RAQM... no
-------------------------------------------------------------
checking for GVC... no
-------------------------------------------------------------
checking for HEIF... no
-------------------------------------------------------------
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checking jbig.h usability... yes
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checking if JBIG package is complete... yes
-------------------------------------------------------------
checking for JPEG...
checking jconfig.h usability... yes
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checking jerror.h usability... yes
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checking jmorecfg.h usability... yes
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checking for jpeglib.h... yes
checking for jpeg_read_header in -ljpeg... yes
checking for JPEG library is version 6b or later... yes
checking if JPEG package is complete... yes
-------------------------------------------------------------
checking for LCMS2... no
-------------------------------------------------------------
checking for LIBOPENJP2... no
-------------------------------------------------------------
checking for LQR... no
-------------------------------------------------------------
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-------------------------------------------------------------
checking for OPENEXR... no
-------------------------------------------------------------
checking for PANGO... yes
checking for PANGO... yes
-------------------------------------------------------------
checking for PNG... yes
-------------------------------------------------------------
checking for RAW_R... no
-------------------------------------------------------------
checking for TIFF...
checking tiff.h usability... yes
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checking tiffio.h presence... yes
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checking for TIFFOpen in -ltiff... yes
checking for TIFFClientOpen in -ltiff... yes
checking for TIFFIsByteSwapped in -ltiff... yes
checking for TIFFReadRGBATile in -ltiff... yes
checking for TIFFReadRGBAStrip in -ltiff... yes
checking if TIFF package is complete... yes
checking tiffconf.h usability... yes
checking tiffconf.h presence... yes
checking for tiffconf.h... yes
checking for TIFFIsCODECConfigured... yes
checking for TIFFMergeFieldInfo... yes
checking for TIFFIsBigEndian... yes
checking for TIFFReadEXIFDirectory... yes
checking for TIFFSetErrorHandlerExt... yes
checking for TIFFSetTagExtender... yes
checking for TIFFSetWarningHandlerExt... yes
checking for TIFFSwabArrayOfTriples... yes
-------------------------------------------------------------
checking for WEBP... no
checking for WEBPMUX... no
checking for WMF support ...
checking for libwmf/ipa.h... no
checking if WMF package is complete ... no
-------------------------------------------------------------
checking for XML... yes
-------------------------------------------------------------
checking for ImageMagick delegate programs...
checking for bpgdec... bpgdec
checking for bpgenc... bpgenc
checking for blender... blender
checking for xdg-open... /usr/bin/xdg-open
checking for ufraw-batch... ufraw-batch
checking for soffice... /usr/bin/soffice
checking for dvips... /usr/bin/dvips
checking for magick... magick
checking for magick... magick
checking for xterm... /usr/bin/xterm
checking for dot... /usr/bin/dot
checking for hp2xx... hp2xx
checking for html2ps... html2ps
checking for ilbmtoppm... /usr/bin/ilbmtoppm
checking for ppmtoilbm... /usr/bin/ppmtoilbm
checking for JxrDecApp... JxrDecApp
checking for JxrEncApp... JxrEncApp
checking for lepton... lepton
checking for lp... /usr/bin/lp
checking for lpr... /usr/bin/lpr
checking for gimp... /usr/bin/gimp
checking for magick... magick
checking for avconv... avconv
checking for ffmpeg... (cached) avconv
checking for avconv... avconv
checking for ffmpeg... (cached) avconv
checking for mrsidgeodecode... mrsidgeodecode
checking for mv... /bin/mv
checking for pcl6... pcl6
checking for gsx... no
checking for gsc... no
checking for gs... /usr/bin/gs
checking for rm... /bin/rm
checking for rsvg-convert... rsvg-convert
checking for inkscape... inkscape
checking for uniconvertor... uniconvertor
checking for dwebp... dwebp
checking for cwebp... cwebp
checking for curl... /usr/bin/curl
checking for gxps... gxps
checking for Apple fonts directory... not found!
checking for Dejavu fonts directory... not found!
checking for Ghostscript fonts directory... /usr/share/fonts/type1/gsfonts/
checking for URW-base35 fonts directory... not found!
checking for Windows fonts directory... not found!
checking for gnutar... no
checking for gtar... no
checking for tar... tar
checking for perl... perl
checking for rpmbuild... no
checking for rpm... no
checking for 7za... 7za
checking for zip... zip
-------------------------------------------------------------
checking for Ghostscript...
checking for Ghostscript version... 9.18
checking for gs color device... pnmraw
checking for gs alpha device... pngalpha
checking for gs CMYK device... pamcmyk32
checking for gs mono device... pbmraw
checking for gs PDF writing device... pdfwrite
checking for gs PS writing device... ps2write
checking for gs EPS writing device... eps2write
-------------------------------------------------------------
Update ImageMagick configuration
checking that generated files are newer than configure... done
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating common.shi
config.status: creating config/configure.xml
config.status: creating config/delegates.xml
config.status: creating config/ImageMagick.rdf
config.status: creating config/MagickCore.dox
config.status: creating config/MagickWand.dox
config.status: creating config/Magick++.dox
config.status: creating config/type-apple.xml
config.status: creating config/type-dejavu.xml
config.status: creating config/type-ghostscript.xml
config.status: creating config/type-urw-base35.xml
config.status: creating config/type-windows.xml
config.status: creating config/type.xml
config.status: creating ImageMagick.spec
config.status: creating Magick++/bin/Magick++-config
config.status: creating MagickCore/ImageMagick.pc
config.status: creating Magick++/lib/Magick++.pc
config.status: creating MagickCore/MagickCore-config
config.status: creating MagickCore/MagickCore.pc
config.status: creating MagickCore/version.h
config.status: creating Makefile
config.status: creating magick.sh
config.status: creating PerlMagick/check.sh
config.status: creating PerlMagick/default/Magick.pm
config.status: creating PerlMagick/Makefile.PL
config.status: creating PerlMagick/default/Makefile.PL
config.status: creating PerlMagick/quantum/Makefile.PL
config.status: creating PerlMagick/quantum/quantum.pm
config.status: creating PerlMagick/quantum/quantum.xs
config.status: creating PerlMagick/quantum/typemap
config.status: creating utilities/animate.1
config.status: creating utilities/compare.1
config.status: creating utilities/composite.1
config.status: creating utilities/conjure.1
config.status: creating utilities/convert.1
config.status: creating utilities/display.1
config.status: creating utilities/identify.1
config.status: creating utilities/ImageMagick.1
config.status: creating utilities/import.1
config.status: creating utilities/magick.1
config.status: creating utilities/magick-script.1
config.status: creating utilities/mogrify.1
config.status: creating utilities/montage.1
config.status: creating utilities/stream.1
config.status: creating MagickWand/MagickWand-config
config.status: creating MagickWand/MagickWand.pc
config.status: creating config/config.h
config.status: executing MagickCore/magick-baseconfig.h commands
config.status: creating MagickCore/magick-baseconfig.h - prefix MAGICKCORE for config/config.h defines
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default commands
config.status: executing magick.sh.in commands
config.status: executing MagickCore-config.in commands
config.status: executing MagickWand-config.in commands
config.status: executing Magick++-config.in commands
config.status: executing PerlMagick/check.sh.in commands
configure:
==============================================================================
ImageMagick is configured as follows. Please verify that this configuration
matches your expectations.
Host system type: x86_64-pc-linux-gnu
Build system type: x86_64-pc-linux-gnu
Option Value
------------------------------------------------------------------------------
Shared libraries --enable-shared=yes yes
Static libraries --enable-static=yes yes
Build utilities --with-utilities=yes yes

/usr/bin/install -c -m 644 ./www/api/MagickCore/tab_l.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/tab_r.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/tabs.css /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/token_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/token_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/token_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/tree.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/type_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/type_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/type_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/version_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/version_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/version_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
mkdir -p -- /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/animate_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/animate_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/animate_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/annotated.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/classes.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/compare_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/compare_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/compare_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/composite_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/composite_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/composite_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/conjure_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/conjure_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/conjure_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/deprecate_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/deprecate_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/deprecate_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/dir_101f7ac0a894e32543a314e85b2e1524.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/dirs.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/display_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/display_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/display_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/doxygen.css /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/doxygen.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawing-wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawing-wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawing-wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawtest_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/files.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2blank.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2doc.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2folderclosed.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2folderopen.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2lastnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2link.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2mlastnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2mnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2node.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2plastnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2pnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2vertline.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/functions.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/functions_vars.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x61.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x62.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x63.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x64.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x65.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x67.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x69.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x6d.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x6e.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x6f.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x70.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x71.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x72.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x73.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x74.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x75.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x77.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x78.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_defs.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_enum.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_eval.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x63.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x64.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x67.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x69.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x6d.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x6e.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x70.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x72.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x73.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_type.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_vars.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/import_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/import_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/import_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/index.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-image_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-image_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-image_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-property_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-property_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-property_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick__wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/MagickWand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick__wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/MagickWand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/main.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
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/usr/bin/install -c -m 644 ./www/api/MagickWand/montage_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/montage_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/montage_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-iterator_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
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/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-iterator_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__CompositeOptions.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__DrawingWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__DrawVTable.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__MagickWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__PixelIterator.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__PixelWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/studio_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/studio_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tab_b.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tab_l.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tab_r.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tabs.css /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tree.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wandtest_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/bin/mkdir -p '/usr/local/share/doc/ImageMagick-7'
/usr/bin/install -c -m 644 LICENSE ChangeLog NEWS.txt '/usr/local/share/doc/ImageMagick-7'
/bin/mkdir -p '/usr/local/include/ImageMagick-7/Magick++'
/usr/bin/install -c -m 644 Magick++/lib/Magick++/Blob.h Magick++/lib/Magick++/CoderInfo.h Magick++/lib/Magick++/Color.h Magick++/lib/Magick++/Drawable.h Magick++/lib/Magick++/Exception.h Magick++/lib/Magick++/Functions.h Magick++/lib/Magick++/Geometry.h Magick++/lib/Magick++/Image.h Magick++/lib/Magick++/Include.h Magick++/lib/Magick++/Montage.h Magick++/lib/Magick++/Pixels.h Magick++/lib/Magick++/ResourceLimits.h Magick++/lib/Magick++/SecurityPolicy.h Magick++/lib/Magick++/Statistic.h Magick++/lib/Magick++/STL.h Magick++/lib/Magick++/TypeMetric.h '/usr/local/include/ImageMagick-7/Magick++'
/bin/mkdir -p '/usr/local/include/ImageMagick-7'
/usr/bin/install -c -m 644 Magick++/lib/Magick++.h '/usr/local/include/ImageMagick-7'
/bin/mkdir -p '/usr/local/share/man/man1'
/usr/bin/install -c -m 644 MagickCore/MagickCore-config.1 MagickWand/MagickWand-config.1 Magick++/bin/Magick++-config.1 utilities/ImageMagick.1 utilities/animate.1 utilities/compare.1 utilities/composite.1 utilities/conjure.1 utilities/convert.1 utilities/display.1 utilities/identify.1 utilities/import.1 utilities/magick.1 utilities/magick-script.1 utilities/mogrify.1 utilities/montage.1 utilities/stream.1 '/usr/local/share/man/man1'
/bin/mkdir -p '/usr/local/lib/pkgconfig'
/usr/bin/install -c -m 644 MagickCore/ImageMagick.pc MagickCore/MagickCore.pc MagickCore/ImageMagick-7.Q16HDRI.pc MagickCore/MagickCore-7.Q16HDRI.pc MagickWand/MagickWand.pc MagickWand/MagickWand-7.Q16HDRI.pc Magick++/lib/Magick++.pc Magick++/lib/Magick++-7.Q16HDRI.pc '/usr/local/lib/pkgconfig'
make[2]: Leaving directory '/home/jitendra/Downloads/ImageMagick'
make[1]: Leaving directory '/home/jitendra/Downloads/ImageMagick'
jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] []