@@ -0,0 +1,828 @@
+__author__ = 'olga'%0A%0Afrom glob import iglob, glob%0Afrom gscripts.qtools._Submitter import Submitter%0Aimport sys%0Aimport os%0A%0Aspecies = sys.argv%5B1%5D%0Atry:%0A    jobname = sys.argv%5B2%5D + %22_cufflinks_%22 + species%0Aexcept IndexError:%0A    jobname = %22cufflinks_%22 + species%0A%0Acommands = %5B%5D%0A%0Aif species == 'hg19':%0A    gtf = '/projects/ps-yeolab/genomes/hg19/gencode_v17/gencode.v17.annotation.gtf'%0A%0Afor bam in iglob('*.sorted.bam'):%0A    commands.append('cufflinks --GTF %7B0%7D --GTF-guide  '%0A                    '--multi-read-correct --num-threads 8 %7B1%7D'.format(%0A        gtf, bam%0A    ))%0A%0Asub = Submitter(queue_type='PBS', sh_file=jobname + '.sh',%0A                command_list=commands,%0A                job_name=jobname)%0Asub.write_sh(submit=True, nodes=1, ppn=8, walltime='0:30:00', use_array=True,%0A             array=True,%0A             max_running=20)

add cufflinks command line (human only so far)