diff --git a/bin/pfastq-dump b/bin/pfastq-dump index 97d7525..5ce05ef 100644 --- a/bin/pfastq-dump +++ b/bin/pfastq-dump @@ -4,11 +4,11 @@ set -e # pfastq-dump version -VERSION="0.1.2" +VERSION="0.1.3" # default arguments -TMPDIR="$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )" -OUTDIR="${TMPDIR}" +TMPDIR="$( pwd -P )" +OUTDIR="$( pwd -P )" NTHREADS=1 # functions for version and help @@ -174,6 +174,9 @@ check_binary_location(){ check_binary_location "sra-stat" check_binary_location "fastq-dump" +echo "tmpdir: ${TMPDIR}" +echo "outdir: ${OUTDIR}" + if [[ ! -z "${SRAID}" ]]; then spot_count=`calc_spot_count "${SRAID}"` parallel_fastq_dump "${SRAID}" "${spot_count}"