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Enhance tophats to utilize GALAXY_SLOTS configuration when available.

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This commit is contained in:
John Chilton
2013-11-05 13:46:06 -06:00
parent cfb194f0a0
commit 1614f791c1
3 changed files with 3 additions and 4 deletions
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tools/ngs_rna/tophat2_wrapper.xml
+1 -1
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@@ -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 $params.settingsType == "full":
tools/ngs_rna/tophat_color_wrapper.xml
+1 -1
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@@ -6,7 +6,7 @@
<command interpreter="python">
tophat_wrapper.py
## Change this to accommodate the number of threads you have available.
--num-threads="4"
--num-threads="\${GALAXY_SLOTS:-4}"
## base- or color-space
--color-space
tools/ngs_rna/tophat_wrapper.xml
+1 -2
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@@ -10,8 +10,7 @@
<command interpreter="python">
tophat_wrapper.py
## Change this to accommodate the number of threads you have available.
--num-threads="4"
--num-threads="\${GALAXY_SLOTS:-4}"
## Provide outputs.
--junctions-output=$junctions
--hits-output=$accepted_hits