Package: SRA-Tools¶
About: Short Read Archive data retrieval and format conversion tools.
Version: 2.8.2-5
Added: 2016-01-19
Updated: 2018-01-08
Installation directory: /shares/bioinfo/bin
Source directory: /shares/bioinfo/installs/ncbi/sra-tools
Link: SRA-Tools
fastq-dump¶
Example fastq-dump HTCondor job file¶
- requests resources (CPUs, RAM, scratch)
- downloads .sra file from the SRA and writes .fastq.gz outputs to scratch (faster than writing to NFS)
- all output file(s) are automatically transferred to working directory at end of job
###############################################################################################
## Housekeeping
###############################################################################################
universe = vanilla
getenv = true
accounting_group = $ENV(CONDOR_GROUP)
request_cpus = $(cpu_req)
request_memory = $(memory_req)
request_disk = $(disk_req)
notification = Complete
condor_output = /path/to/condor/output/dir
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 & arguments
###############################################################################################
executable = /shares/bioinfo/bin/fastq-dump
arguments = -I --split-files --gzip $(SRA_record)
transfer_executable = False
should_transfer_files = YES
when_to_transfer_output = ON_EXIT
###############################################################################################
## Need to edit info here: Variables
###############################################################################################
run_type = fastqdump
SRA_record = [SRA record ID i.e. SRR390728]
cpu_req = [Number of processors i.e. 1]
memory_req = [RAM request i.e. 1G]
disk_req = [scratch disk size request 3G]
queue