Results for "Command lines"
Bio-Scripts
Install Python locally on shared Linux server !
...o put the #related output of make command, by default it is in the /usr...By the default, if we type python command, it will use the default pyth...hrc_profile and add the following lines: export PATH=$HOME/python/Py...nstall pip. #Run the following command to install pip as a local u...2098 days ago
- ...PROPERTIES/FILE gatk forwards commands to GATK and adds some sugar...--spark-submit-command may be specified to control t...e, and host reads PathSeqPipelineSpark C...calibration on Spark BQSRPipelineSpark...
2075 days ago
- ➜ upgrade_oh_my_zsh Updating Oh My Zsh remote: Counting objects: 484, done. remote: Compressing objects: 100%...plugins/coffee/_coffee | 4 +- plugins/command-not-found/comma...
2075 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail --------------------------------------------------...0.18.0-h1310cd9_1 bioconda pbcommand: 1.1.1-py27h24b...####################| Time: 0:00:00 21.90 MB/s pbcomma...2034 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'git-s...sers/j/n/jnarayan/FALCON-examples/.git-sym') git: 'check-ignore' is not a git comma...
2034 days ago
Installing Platypus on Ubuntu !
(py27) ➜ Tools git:(master) ✗ git clone https://github.com/andyrimmer/Platypus.git...ider upgrading via the 'pip install --upgrade pip' command. (py27) ➜ Platypus git:(m...tabix.c: At top level: cc1: warning: unrecognized comma...2019 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: done...py_0 22 KB bioconda pbcommand-1.1.1 |...1310cd9_1 bioconda pbcommand: 1.1.1-py27_2...########################## | 100% pbcomma...1990 days ago
Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1615 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### co...ej.sam ### viewing bam files (view command) samtool view sal_sej.bam |...identifying genome variants (mpileup command) # -g : output is bcf (binar..."bcftools" to see current version and comma...1603 days ago
Perl script to remove duplicated lines !
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; while( $next_line = ) { #print "current line: $_ -- next line: $next_line$/"...1560 days ago
