Package: Trinity¶
About: De novo transcriptome assembly.
Version: 2.1.1
Added: 2015-10-28
Updated: 2015-10-28
Installation directory: /bioinfo/installs/trinity
Source directory: /bioinfo/installs/trinity
Link: Trinity
trinity¶
Example Trinity HTCondor job file¶
- requests resources (CPUs, RAM, scratch)
- transfers pair1 and pair2 into scratch
- creates a trinity-working-directory (in scratch)
- only the final Trinity.fasta output file is transferred back to the original directory
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/installs/trinity/Trinity
arguments = --seqType fq --CPU $(cpu_req) --max_memory $(memory_req) --output $(output_name)/ --SS_lib_type RF --left left.fastq.gz --right right.fastq.gz
transfer_executable = False
should_transfer_files = YES
transfer_input_files = /full/path/to/left.fastq.gz,/full/path/to/right.fastq.gz
when_to_transfer_output = ON_EXIT
transfer_output_files = $(output_name)/Trinity.fasta
## Need to edit info here ##
run_type = Trinity
output_name = trinity_$(sampleID)
sampleID = [sample ID]
cpu_req = [Number of processors]
memory_req = [RAM request i.e. 20G]
disk_req = [scratch disk size request 3G]
############################
queue