From 1614f791c19e2be6339eff1cdfe9103f3bdee798 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 5 Nov 2013 13:46:06 -0600 Subject: [PATCH] Enhance tophats to utilize GALAXY_SLOTS configuration when available. --- tools/ngs_rna/tophat2_wrapper.xml | 2 +- tools/ngs_rna/tophat_color_wrapper.xml | 2 +- tools/ngs_rna/tophat_wrapper.xml | 3 +-- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/tools/ngs_rna/tophat2_wrapper.xml b/tools/ngs_rna/tophat2_wrapper.xml index b9492252710..e42839567fb 100644 --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -28,7 +28,7 @@ tophat2 ## Change this to accommodate the number of threads you have available. - --num-threads 4 + --num-threads \${GALAXY_SLOTS:-4} ## Set params. #if $params.settingsType == "full": diff --git a/tools/ngs_rna/tophat_color_wrapper.xml b/tools/ngs_rna/tophat_color_wrapper.xml index 399d2c9c46c..8698fddc6e9 100644 --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -6,7 +6,7 @@ tophat_wrapper.py ## Change this to accommodate the number of threads you have available. - --num-threads="4" + --num-threads="\${GALAXY_SLOTS:-4}" ## base- or color-space --color-space diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml index a8961fe98a4..ef4bab1fc66 100644 --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -10,8 +10,7 @@ tophat_wrapper.py ## Change this to accommodate the number of threads you have available. - --num-threads="4" - + --num-threads="\${GALAXY_SLOTS:-4}" ## Provide outputs. --junctions-output=$junctions --hits-output=$accepted_hits