From 9482f08b75f6e752e61be5593c496b7109f51d56 Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Tue, 1 Mar 2016 13:13:41 +0100
Subject: [PATCH] disabled chmod when building star index
---
dge_workflow/dge_utils.sh | 2 +-
dge_workflow/star_align.sh | 5 ++---
2 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index ef37e33..bbe3d05 100755
--- a/dge_workflow/dge_utils.sh
+++ b/dge_workflow/dge_utils.sh
@@ -494,7 +494,7 @@ dge_create_star_index(){
jl submit --wait -t 5 -q medium -n "${project}_star_index" "$cmd"
## prevent further modification
- chmod -w $(dirname ${star_index})
+# chmod -w $(dirname ${star_index})
mailme "created star index for $igenome"
}
diff --git a/dge_workflow/star_align.sh b/dge_workflow/star_align.sh
index d8ae2cf..bbe4d00 100755
--- a/dge_workflow/star_align.sh
+++ b/dge_workflow/star_align.sh
@@ -12,13 +12,12 @@ Options:
--pc-only Use protein coding genes only for mapping and quantification
'
-
#eval $(echo "$usage" | ~/bin/docopts/docopts -h - -A dopts : "$@")
#echo "$usage" | ~/bin/docopts/docopts -h - : "$@"
#echo "$usage" | ~/bin/docopts/docopts -h - : "hallo dfds"
#eval $(echo $usage | ~/bin/docopts/docopts -h - : "$@")
#eval(exit 64)
-eval "$(echo "$usage" | ~/bin/docopts/docopts -h - : "$@")"
+eval "$(echo "$usage" | /projects/bioinfo/holger/bin/docopts/docopts -h - : "$@")"
# v0.7 style
#eval $(echo "$usage" | /home/brandl/bin/docopts_v0.7/docopts "hallo")
@@ -144,7 +143,7 @@ dge_bam_correlate . &
#mysub "${project}__feature_counts" "featureCounts -t exon -g gene_id -a ${gtfFile} -o gene_counts.txt $(ls *bam) -T 5" -q medium | blockScript
## create tophat mapping report
-spin.R ${NGS_TOOLS}/dge_workflow/star_qc.R .
+rend.R ${NGS_TOOLS}/dge_workflow/star_qc.R .
## Condense counts into matrix
--
GitLab