Package: Bowtie2¶
About: Short-read alignment program.
Version: 2.2.9
Added: 2016-04-21
Updated: 2016-04-21
Installation directory: /bioinfo/bin
Source directory: /bioinfo/installs/bowtie2-2.2.9
Link: Bowtie2
bowtie2¶
Example bowtie2 HTCondor job file¶
- requests resources (CPUs, RAM, scratch)
- transfers pair1 and pair2 into scratch
- all output file(s) are automatically transferred to working directory at end of job
universe = vanilla
getenv = true
condor_output = /path/to/condor/output/dir/
request_cpus = $(cpu_req)
request_memory = $(memory_req)
request_disk = $(disk_req)
notification = Complete
ID = $(Cluster).$(Process)
output = $(condor_output)$(run_type).$(ID).out
error = $(condor_output)$(run_type).$(ID).err
log = $(condor_output)$(run_type).$(ID).log
###################
executable = /bioinfo/bin/bowtie2
arguments = -q --threads $(cpu_req) -x /path/to/genome.fa -1 pair1.reads.fastq.qz -2 pair2.reads.fastq.gz -S alignment.sam
transfer_executable = False
should_transfer_files = YES
when_to_transfer_output = ON_EXIT
transfer_input_files = [full/path/to/pair1.reads.fastq.gz,full/path/to/pair2.reads.fastq.gz]
## Need to edit info here ##
run_type = bowtie2
cpu_req = [Number of processors]
memory_req = [RAM request i.e. 1G]
disk_req = [scratch disk size request 3G]
############################
queue