How do I submit a bio perl job via qsub?
There are two ways. One is to qsub the perl program directly. The other is to qsub a script that runs the perl script. This latter method is easier. Method 1: • qsub -S /usr/bin/perl test_bio.pl Method 2: • qsub test_bio.sh • chmod +x test_bio.sh (done only once). If test_bio.sh is located in a directory other than the home directory, then: • qsub ~/whatever_path/test_bio.sh The contents of test_bio.sh are: —- cut here —– (yes just two lines) • # • perl test_bio.pl —- cut here —– The contents of test_bio.pl are: —- cut here —– • #!/usr/bin/perl • use lib “/sw/lib/perl5”; • use lib “/sw/lib/perl5/darwin”; • use lib “/RemotePerl”; • # The PERL5LIB environment variable should already be set to: • # • # PERL5LIB=”/sw/lib/perl5:/sw/lib/perl5/darwin:/RemotePerl/” • # • # If not, you must set this in .bashrc or .tcshrc or .cshrc for your login.
