Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the required modules have been installed in the system # BEGIN { my @import_modules = (...1149 days ago
Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read name dpkg -s $name &> /dev/null...1040 days ago
984 days ago
Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D955 days ago
Inreractive SCP / File transfer !
...ile (files) / Directory using scp" #next line check if entered value is not null,...ext line finishes while loop done #next line check if entered value is not null,...variable filename filename='null' #next line check if entered value is null, and...944 days ago
Perl onliner to check the ids in two files !
perl -lane 'BEGIN{open(A,"ids2.txt"); while(){chomp; $k{$_}++}} if (defined($k{$F[0]})) {print "$_\t$F[0]\t1"} else {print "$_\tNA\t0"}; ' ids1.txt > aaa.xls921 days ago
913 days ago
Install Install Gffcompare on Ubuntu / Linux
...ompare-0.9.8.Linux_x86_64.tar.gz # make symlink ln -s ~/workspace/bin/gffcompare-0.9.8.Linux_x86_64/gffcompare ~/workspace/bin/gffcompare # check Installation ~/workspace/bin...817 days ago
Raku script to find overlaps between two bed files !
#!/usr/bin/env raku # Check if the correct number of arguments are provided...elds1[1]; my $end1 = @fields1[2]; # Check for overlaps with intervals i...; my $end2 = @fields2[2]; # Check for chromosome match and over...88 days ago
Perl script to find overlaps between two bed files !
#!/usr/bin/perl use strict; use warnings; # Check if the correct number of arguments are provided if (@ARGV != 2) { die "Usage: $0 file1.bed file2.bed\n"; } # Read the contents of the two BED files my $file1 = shift @ARGV; my $file2 = shift @ARGV; open my $fh1, '88 days ago