Package: SRA-Tools

About: Short Read Archive data retrieval and format conversion tools.

Version: 2.5.7

Added: 2016-01-19

Updated: 2016-01-19

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)
  • copies .sra file to scratch and writes .fastq 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_rec)
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 $(SRA_file_prefix).sra

transfer_executable      = False
should_transfer_files    = YES
when_to_transfer_output  = ON_EXIT
transfer_input_files     = /path/to/$(SRA_file_prefix).sra



###############################################################################################
## Need to edit info here: Variables
###############################################################################################
run_type                 = fastqdump
SRA_file_prefix          = [SRA name prefix]
cpu_req                  = [Number of processors i.e. 1]
memory_req               = [RAM request i.e. 1G]
disk_req                 = [scratch disk size request 3G]


queue