universe=vanilla

executable=/bin/sh

log=bismark_methylation_extractor-1x5p27mers.$(Process).log
output=bismark_methylation_extractor-1x5p27mers.$(Process).out
error=bismark_methylation_extractor-1x5p27mers.$(Process).err

request_cpus = 8
request_memory = 4000
request_disk = 0

Requirements = (Machine == "pongo.cacr.caltech.edu" || Machine == "myogenin.cacr.caltech.edu" || Machine == "mondom.cacr.caltech.edu" || Machine == "bostau.caltech.edu" || Machine == "wold-clst-3.woldlab" || Machine == "wold-clst-4.woldlab" )

arguments="-c  '/woldlab/castor/home/georgi/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /woldlab/castor/home/georgi/genomes/sacCer3/bismarck_indexes L101-dSMF-S_cerevisiae-200U_per_25M_cells.1x5p27mers.Bismark_v0.19.0.bowtie1.sacCer3.bam'"
queue
arguments="-c  '/woldlab/castor/home/georgi/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /woldlab/castor/home/georgi/genomes/sacCer3/bismarck_indexes L102-dSMF-S_cerevisiae-100U_per_25M_cells.1x5p27mers.Bismark_v0.19.0.bowtie1.sacCer3.bam'"
queue
arguments="-c  '/woldlab/castor/home/georgi/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /woldlab/castor/home/georgi/genomes/sacCer3/bismarck_indexes L103-dSMF-S_cerevisiae-50U_per_25M_cells.1x5p27mers.Bismark_v0.19.0.bowtie1.sacCer3.bam'"
queue
arguments="-c  '/woldlab/castor/home/georgi/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /woldlab/castor/home/georgi/genomes/sacCer3/bismarck_indexes L104-dSMF-S_cerevisiae-10U_per_25M_cells.1x5p27mers.Bismark_v0.19.0.bowtie1.sacCer3.bam'"
queue
arguments="-c  '/woldlab/castor/home/georgi/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /woldlab/castor/home/georgi/genomes/sacCer3/bismarck_indexes L105-dSMF-S_cerevisiae-2U_per_25M_cells.1x5p27mers.Bismark_v0.19.0.bowtie1.sacCer3.bam'"
queue
arguments="-c  '/woldlab/castor/home/georgi/programs/Bismark_v0.19.0/bismark_methylation_extractor -s --no_overlap --comprehensive --merge_non_CpG --gzip --multicore 16 --bedGraph --cytosine_report --CX --genome_folder /woldlab/castor/home/georgi/genomes/sacCer3/bismarck_indexes L106-dSMF-S_cerevisiae-0U_per_25M_cells.1x5p27mers.Bismark_v0.19.0.bowtie1.sacCer3.bam'"
queue