BOL: All

Install htop on ubuntu

Jit — Sun, 01 Mar 2020 23:33:28 -0600

jit@jit-HP-Pro-3335-MT:~/Downloads/annotated$ sudo apt  install htop
[sudo] password for jit: 
Sorry, try again.
[sudo] password for jit: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
  htop
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 80.0 kB of archives.
After this operation, 221 kB of additional disk space will be used.
Get:1 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 htop amd64 2.1.0-3 [80.0 kB]
Fetched 80.0 kB in 1s (122 kB/s)
Selecting previously unselected package htop.
(Reading database ... 193509 files and directories currently installed.)
Preparing to unpack .../htop_2.1.0-3_amd64.deb ...
Unpacking htop (2.1.0-3) ...
Setting up htop (2.1.0-3) ...
Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.2) ...
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ...
Processing triggers for mime-support (3.60ubuntu1) ...

Install vcftools on Ubuntu

Jit — Sun, 01 Mar 2020 23:27:29 -0600

jit@jit-HP-Pro-3335-MT:~/Downloads/annotated$ sudo apt install vcftools
[sudo] password for jit: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
  vcftools
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 452 kB of archives.
After this operation, 1,459 kB of additional disk space will be used.
Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 vcftools amd64 0.1.15-1 [452 kB]
Fetched 452 kB in 1s (449 kB/s)  
Selecting previously unselected package vcftools.
(Reading database ... 193392 files and directories currently installed.)
Preparing to unpack .../vcftools_0.1.15-1_amd64.deb ...
Unpacking vcftools (0.1.15-1) ...
Setting up vcftools (0.1.15-1) ...
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...

#MORE at https://vcftools.github.io/perl_module.html

# Calculate stats separately for the filter field, quality and non-indels vcf-stats file.vcf.gz -f FILTER,QUAL=10:200,INFO/INDEL=False -p out/


# Calculate stats for all samples vcf-stats file.vcf.gz -f FORMAT/DP=10:200 -p out/

# Calculate stats only for the sample NA00001 vcf-stats file.vcf.gz -f SAMPLE/NA00001/DP=1:200 -p out/

vcf-stats file.vcf.gz > perl.dump

Install Parrot Virtual Machine !

Jit — Wed, 19 Feb 2020 06:21:29 -0600

#Parrot is a virtual machine designed to efficiently compile and execute bytecode for dynamic languages

jit@jit-HP-Pro-3335-MT:~/Downloads/parrot-8.1.0$ wget ftp://ftp.parrot.org/pub/parrot/releases/supported/8.1.0/parrot-8.1.0.tar.gz

jit@jit-HP-Pro-3335-MT:~/Downloads/parrot-8.1.0$ tar -zxvf parrot-8.1.0.tar.gz parrot-8.1.0/

jit@jit-HP-Pro-3335-MT:~/Downloads/parrot-8.1.0$ cd parrot-8.1.0/

jit@jit-HP-Pro-3335-MT:~/Downloads/parrot-8.1.0$ perl Configure.pl 
Parrot Version 8.1.0 Configure 2.0
Copyright (C) 2001-2015, Parrot Foundation.

Hello, I'm Configure. My job is to poke and prod your system to figure out
how to build Parrot. The process is completely automated, unless you passed in
the `--ask' flag on the command line, in which case I'll prompt you for a few
pieces of info.

Since you're running this program, you obviously have Perl 5--I'll be pulling
some defaults from its configuration.
do "lib/Parrot/Config/Generated.pm" failed, '.' is no longer in @INC; did you mean do "./lib/Parrot/Config/Generated.pm"? at Configure.pl line 84.
Deleting gcov-generated files
Deleting cover-generated html files

init::manifest -      Check MANIFEST.....................................done.
init::defaults -      Set Configure's default values.....................done.
init::install -       Set up installation paths..........................done.
init::hints -         Load platform and local hints files................done.
inter::progs -        Determine what C compiler and linker to use........done.
inter::make -         Is make installed...................................yes.
inter::lex -          Is lex installed................................skipped.
inter::yacc -         Is yacc installed...............................skipped.
auto::gcc -           Is your C compiler actually gcc................yes, 7.4.
auto::glibc -         Is GNU libc installed...............................yes.
auto::backtrace -     Does libc have the backtrace* functions.............yes.
auto::msvc -          Is your C compiler actually Visual C++..........skipped.
auto::attributes -    Detect compiler attributes.........................done.
auto::arch -          Determine CPU architecture and type, and OS........done.
auto::cpu -           Generate CPU specific stuff........................done.
init::optimize -      Enable optimization..................................no.
inter::shlibs -       Determine flags for building shared libraries.....-fPIC.
inter::libparrot -    Should parrot link against a shared library.........yes.
inter::types -        What types should Parrot use.......................done.
auto::ops -           Which opcode files should be compiled in...........done.
auto::pmc -           Which pmc files should be compiled in..............done.
auto::headers -       Probe for C headers................................done.
auto::sizes -         Determine some sizes...............................done.
auto::byteorder -     Compute native byteorder for wordsize.....little-endian.
auto::va_ptr -        Test the type of va_ptr........................register.
auto::format -        What formats should be used for sprintf............done.
auto::isreg -         Does your C library have a working S_ISREG..........yes.
auto::llvm -          Is minimum version of LLVM installed............skipped.
auto::inline -        Does your compiler support inline....................no.
auto::gc -            Determine allocator to use..........................gms.
auto::memalign -      Does your C library support memalign................yes.
auto::signal -        Determine some signal stuff........................done.
auto::socklen_t -     Determine whether there is socklen_t................yes.
auto::stat -          Detect stat type....................................bsd.
auto::neg_0 -         Determine whether negative zero can be printed......yes.
auto::env -           Does your C library have setenv / unsetenv.........both.
auto::timespec -      Does your system has timespec.......................yes.
auto::infnan -        Is standard C Inf/NaN handling present..............yes.
auto::thread -        Does your system have threads.......................yes.
auto::gmp -           Does your platform support GMP.......................no.
auto::readline -      Does your platform support readline.................yes.
auto::pcre -          Does your platform support pcre...............yes, 8.39.
auto::opengl -        Does your platform support OpenGL....................no.
auto::zlib -          Does your platform support zlib.....................yes.
auto::gettext -       Does your configuration include gettext.............yes.
auto::snprintf -      Test for snprintf..............................yes, C99.
auto::mathl -         Test for long math support..........................yes.
auto::perldoc -       Is perldoc installed.................................no.
auto::coverage -      Are coverage analysis tools installed...Negative repeat count does nothing at lib/Parrot/Configure.pm line 481.
lacking cover gcov2perl.
auto::pod2man -       Is pod2man installed................................yes.
auto::ctags -         Is (exuberant) ctags installed.......................no.
auto::icu -           Is ICU installed..............................yes, 60.2.
auto::libffi -        Is libffi installed.....................no, failed test.
auto::ipv6 -          Determine IPV6 capabilities.........................yes.
auto::platform -      Generate a list of platform object files...........done.
auto::alignof -       Determine offsetof values for our types.........skipped.
auto::expect -        Does your compiler support __builtin_expect.........yes.
auto::warnings -      Detect supported compiler warnings.................done.
gen::config_h -       Generate C headers.................................done.
gen::core_pmcs -      Generate core pmc list.............................done.
gen::opengl -         Generating OpenGL bindings......................skipped.
gen::makefiles -      Generate makefiles and other build files...........done.
gen::config_pm -      Record configuration data for later retrieval......done.
Okay, we're done!

You can now use `make' to build your Parrot.
After that, you can use `make test' to run the test suite.

Happy Hacking,
        The Parrot Team

jit@jit-HP-Pro-3335-MT:~/Downloads/parrot-8.1.0$ make

jit@jit-HP-Pro-3335-MT:~/Downloads/parrot-8.1.0$ ./parrot -h
parrot [Options]  []
  Options:
    -h --help
    -V --version
    -I --include add path to include search
    -L --library add path to library search
       --hash-seed F00F  specify hex value to use as hash seed
    -X --dynext add path to dynamic extension search
   
    -R --runcore fast|slow|bounds
    -R --runcore trace|profiling|subprof
    -t --trace [flags]
   
    -D --parrot-debug[=HEXFLAGS]
       --help-debug
    -w --warnings
    -G --no-gc
    -g --gc ms2|gms|ms|inf set GC type
       
       --gc-dynamic-threshold=percentage    maximum memory wasted by GC
       --gc-min-threshold=KB
       
       --gc-nursery-size=percent of sysmem  size of gen0 (default 2)
       --gc-debug
       --leak-test|--destroy-at-end
    -. --wait    Read a keystroke before starting
       --runtime-prefix
   
    -v --verbose
    -E --pre-process-only
    -o --output=FILE
       --output-pbc
    -O --optimize[=LEVEL]
    -a --pasm
    -c --pbc
    -r --run-pbc
    -y --yydebug
    -d --imcc-debug[=HEXFLAGS] (see --help-debug)
   
see docs/running.pod for more

Bash oneliner to extract all ids from a multifasta file

biogeek — Tue, 18 Feb 2020 08:06:09 -0600

#List of ids - one per line in allIds.txt

$ awk 'BEGIN{while((getline<"allIds.txt")>0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa

# You can play with this f=!l[$1 ] if wanted to extract or not extract the ids

Install snakemake and activate on conda

biogeek — Tue, 18 Feb 2020 06:33:24 -0600

$ conda create -c bioconda -c conda-forge -n snakemake snakemake
$ conda activate snakemake

Check your Linux OS

Rahul Nayak — Tue, 18 Feb 2020 01:35:23 -0600

(py36) [wsu29@bladeamd-2 lofreq]$ lsb_release -a
LSB Version:	:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID:	CentOS
Description:	CentOS release 6.7 (Final)
Release:	6.7
Codename:	Final

Install printer in Ubuntu !

Jit — Mon, 17 Feb 2020 00:58:34 -0600

jit@jit-HP-Pro-3335-MT:~$ java -version
openjdk version "11.0.6" 2020-01-14
OpenJDK Runtime Environment (build 11.0.6+10-post-Ubuntu-1ubuntu118.04.1)
OpenJDK 64-Bit Server VM (build 11.0.6+10-post-Ubuntu-1ubuntu118.04.1, mixed mode, sharing)
jit@jit-HP-Pro-3335-MT:~$ sudo ufw allow 9191
[sudo] password for jit: 
Rules updated
Rules updated (v6)
jit@jit-HP-Pro-3335-MT:~$ sudo ufw allow 9192
Rules updated
Rules updated (v6)
jit@jit-HP-Pro-3335-MT:~$ sudo apt-get install python3-smbc
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
  python3-smbc
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 16.8 kB of archives.
After this operation, 69.6 kB of additional disk space will be used.
Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python3-smbc amd64 1.0.15.6-1build2 [16.8 kB]
Fetched 16.8 kB in 1s (18.6 kB/s) 
Selecting previously unselected package python3-smbc.
(Reading database ... 192946 files and directories currently installed.)
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Unpacking python3-smbc (1.0.15.6-1build2) ...
Setting up python3-smbc (1.0.15.6-1build2) ...
jit@jit-HP-Pro-3335-MT:~$ sudo apt-get install smbclient
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  python-ldb python-samba python-tdb samba-common samba-common-bin
Suggested packages:
  python-gpgme heimdal-clients cifs-utils
The following NEW packages will be installed:
  python-ldb python-samba python-tdb samba-common samba-common-bin smbclient
0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
Need to get 2,912 kB of archives.
After this operation, 18.5 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
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Get:2 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 smbclient amd64 2:4.7.6+dfsg~ubuntu-0ubuntu2.15 [352 kB]
Get:3 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-ldb amd64 2:1.2.3-1ubuntu0.1 [30.9 kB]
Get:4 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 python-tdb amd64 1.3.15-2 [11.1 kB]
Get:5 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-samba amd64 2:4.7.6+dfsg~ubuntu-0ubuntu2.15 [1,926 kB]
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Preconfiguring packages ...
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Setting up python-tdb (1.3.15-2) ...
Setting up samba-common (2:4.7.6+dfsg~ubuntu-0ubuntu2.15) ...

Creating config file /etc/samba/smb.conf with new version
Setting up smbclient (2:4.7.6+dfsg~ubuntu-0ubuntu2.15) ...
Setting up python-ldb:amd64 (2:1.2.3-1ubuntu0.1) ...
Setting up python-samba (2:4.7.6+dfsg~ubuntu-0ubuntu2.15) ...
Setting up samba-common-bin (2:4.7.6+dfsg~ubuntu-0ubuntu2.15) ...
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...

Install python-numpy python-scipy python-matplotlib on Ubuntu !

Rahul Nayak — Sat, 15 Feb 2020 05:57:22 -0600

$MT:~/Downloads/chaos$ sudo apt-get install python-numpy python-scipy python-matplotlib
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  blt fonts-lyx libjs-jquery-ui python-backports.functools-lru-cache python-cycler python-dateutil python-decorator
  python-matplotlib-data python-olefile python-pil python-subprocess32 python-tk python-tz tk8.6-blt2.5
  ttf-bitstream-vera
Suggested packages:
  blt-demo libjs-jquery-ui-docs python-cycler-doc dvipng ffmpeg inkscape ipython python-cairocffi python-configobj
  python-excelerator python-gobject python-matplotlib-doc python-nose python-qt4 python-sip python-tornado python-traits
  python-wxgtk3.0 texlive-extra-utils texlive-latex-extra ttf-staypuft python-numpy-dbg python-numpy-doc python-pil-doc
  python-pil-dbg python-scipy-doc tix python-tk-dbg
The following NEW packages will be installed:
  blt fonts-lyx libjs-jquery-ui python-backports.functools-lru-cache python-cycler python-dateutil python-decorator
  python-matplotlib python-matplotlib-data python-numpy python-olefile python-pil python-scipy python-subprocess32
  python-tk python-tz tk8.6-blt2.5 ttf-bitstream-vera
0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded.
Need to get 21.1 MB/21.1 MB of archives.
After this operation, 83.2 MB of additional disk space will be used.
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Get:2 http://in.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 fonts-lyx all 2.2.4-0ubuntu0.18.04.1 [155 kB]
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Get:15 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-pil amd64 5.1.0-1ubuntu0.2 [329 kB]          
Get:16 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python-scipy amd64 0.19.1-2ubuntu1 [9,689 kB]           
Fetched 21.1 MB in 14s (1,460 kB/s)                                                                                      
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Setting up python-numpy (1:1.13.3-2ubuntu1) ...
Setting up python-dateutil (2.6.1-1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-4) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-5) ...
Setting up python-olefile (0.45.1-1) ...
Setting up ttf-bitstream-vera (1.10-8) ...
Setting up python-decorator (4.1.2-1) ...
Setting up python-subprocess32 (3.2.7-3) ...
Setting up python-pil:amd64 (5.1.0-1ubuntu0.2) ...
Setting up blt (2.5.3+dfsg-4) ...
Setting up fonts-lyx (2.2.4-0ubuntu0.18.04.1) ...
Setting up python-matplotlib-data (2.1.1-2ubuntu3) ...
Setting up python-scipy (0.19.1-2ubuntu1) ...
Setting up python-matplotlib (2.1.1-2ubuntu3) ...
Setting up python-tk (2.7.17-1~18.04) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
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Install gnuplot in Ubuntu !

Rahul Nayak — Sat, 15 Feb 2020 05:38:06 -0600

$MT:~/Downloads/cgr-perl$ sudo apt-get install gnuplot
[sudo] password for jit: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  aglfn gnuplot-data gnuplot-qt libdouble-conversion1 libqt5core5a libqt5dbus5 libqt5gui5
  libqt5network5 libqt5printsupport5 libqt5svg5 libqt5widgets5 libwxbase3.0-0v5 libwxgtk3.0-0v5
  libxcb-xinerama0 qt5-gtk-platformtheme qttranslations5-l10n
Suggested packages:
  gnuplot-doc qt5-image-formats-plugins qtwayland5
The following NEW packages will be installed:
  aglfn gnuplot gnuplot-data gnuplot-qt libdouble-conversion1 libqt5core5a libqt5dbus5
  libqt5gui5 libqt5network5 libqt5printsupport5 libqt5svg5 libqt5widgets5 libwxbase3.0-0v5
  libwxgtk3.0-0v5 libxcb-xinerama0 qt5-gtk-platformtheme qttranslations5-l10n
0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded.
Need to get 15.8 MB/15.8 MB of archives.
After this operation, 65.0 MB of additional disk space will be used.
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Get:13 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 gnuplot-qt amd64 5.2.2+dfsg1-2ubuntu1 [1,013 kB]
Get:14 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 gnuplot all 5.2.2+dfsg1-2ubuntu1 [3,816 B]
Get:15 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 qt5-gtk-platformtheme amd64 5.9.5+dfsg-0ubuntu2.5 [117 kB]
Get:16 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 qttranslations5-l10n all 5.9.5-0ubuntu1 [1,485 kB]
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update-alternatives: using /usr/bin/gnuplot-qt to provide /usr/bin/gnuplot (gnuplot) in auto mode
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To convert just one specific read group to fastq

Rahul Nayak — Fri, 14 Feb 2020 03:35:22 -0600

# Stop script on error.
set -uex

# The SRR BioProject number for the sequencing data.
PROJECT=PRJNA257197

# The number of datasets to subselect from the project.
N=5

# Get the project run information.
esearch -db sra -query $PROJECT  | efetch -format runinfo > runinfo.txt

# Select the first N elements. Keep only valid SRR numbers.
cat runinfo.txt | cut -f 1 -d , | grep SRR | head -$N > selected.txt

# Store the data in the reads folder.
mkdir -p reads

# Download the SRR data for each
cat selected.txt | parallel fastq-dump -O reads -X 1000 --split-files {}

# Create a directory for bam files
mkdir -p bam

# Generate a separate BAM file for each SAMPLE.
cat selected.txt | parallel "picard FastqToSam F1=reads/{}_1.fastq F2=reads/{}_1.fastq O=bam/{}.bam  RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} QUIET=true 2>> log.txt"

# Merge all the BAM files into one.
samtools merge -f all.bam bam/*.bam

# Investigate the readgroups in the header.
echo ""
echo "SAM file header:"
samtools view -H all.bam

echo ""
echo "Number of alignments with read group: GROUP-SRR1972919"
samtools view -c -r GROUP-SRR1972919 all.bam

# Reverting the process is to extract reads, tagged with readgroups to paired files.
samtools fastq -t -1 all1.fq -2 all2.fq all.bam

# To convert just one specific read group.
samtools view -r GROUP-SRR1972919 all.bam | samtools fastq -t -1 all_SRR1972919_1.fq -2 all_SRR1972919_2fq -