From 13f54c1d3fd7c8ea0294f0b6ae81eedfca6e1ea5 Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Tue, 26 May 2015 09:25:08 -0700 Subject: [PATCH] use rsync instead of wget --- fpkm_from_srr | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/fpkm_from_srr b/fpkm_from_srr index dab329d..a7ab6e0 100755 --- a/fpkm_from_srr +++ b/fpkm_from_srr @@ -26,14 +26,14 @@ function set_up_the_run { mkdir -p "$FROM_SRR_SRR"; set -e; (cd $FROM_SRR_SRR; - wget -O ${FROM_SRR_SRR}.sra ftp://ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/${FROM_SRR_SRR:0:6}/${FROM_SRR_SRR}/${FROM_SRR_SRR}.sra; + rsync -avP rsync://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/${FROM_SRR_SRR:0:6}/${FROM_SRR_SRR}/${FROM_SRR_SRR}.sra; ); qsub -q budget -v FROM_SRR_SRR,FROM_SRR_GTF,FROM_SRR_REF -S /bin/bash -d $(pwd) -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0" }; if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then - if [ -z "$FROM_SRR_SRR" ]; then + if [ -n "$FROM_SRR_SRR" ]; then actually_run_the_alignment; exit 0; fi; -- 2.39.2