Results for "benchmarking and designing tools"
Bio-Scripts
...6:41-- https://github.com/samtools/ht...s/lzma_stub.h htslib-1.9/os/rand.c htslib-1.9/plugin.c htslib-....in htslib-1.9/configure ➜ Tools git:(master) ✗ cd htslib-1.9...onfig.h echo '#define HAVE_DRAND48 1' >> config.h gcc -g -Wall...-I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gc...2018 days ago
Installing Platypus on Ubuntu !
(py27) ➜ Tools git:(master) ✗ git clone https://github.com/andyrimmer/Platypus.git...o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/file...ip install --upgrade pip' command. (py27) ➜ Platypus git:(mas...ter release! File: /home/urbe/Tools/Platypus/src/cython/fastafile...2018 days ago
Setting up falconUnzip conda environments for genome assembly !
...bioconda bcftools:...bioconda pbcommand: 1.1.1-py27_2...conda-forge samtools: 1.9-h8ee4bcc_...rmation on License, Copyright and Disclaimer...# # PacBio(R) tools distributed via Bioconda are:...1989 days ago
- Download page https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_....1+-x64-linux.tar.gz # add BLAST location to system PATH export PATH=$HOME/tools/BLAST/ncbi-blast-2.8.1+/bin:$...
1761 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::S...for my $i ( 1 .. $n_processes ) { $pm->start and next;...-outfile=$fn $seq --AUGUSTUS_CONFIG_PATH=/home/urbe/Tools/Alienomics_v1.1/augustus.2.5....1685 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paire...rectly compatible with any downstream tools, so it's necessary to put t...ng. The --split-files part of the command ensur...s we get two files, one for the first and second mate in each pair. We'll...1558 days ago
Commands to install conda in Ubuntu !
...SD License: Redistribution and use in source and binary forms, with or without...f_5 ... installing: more-itertools-6.0.0-py37_0 ... installing:...0.46-py37_0 ... installing: pandocfilters-1.4.2-py37_1 ... inst...-py37_1 ... installing: setuptools-40.8.0-py37_0 ... installing...1510 days ago
- (base) jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ docker build -t autocontampr . Sending build context to Docker daemon 9.024MB Step 1/16 : FROM ubuntu:14.04 --...
1441 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICAR...1336 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen s...
1214 days ago
