Mercurial > repos > jjohnson > encyclopedia_searchtolib

changeset 7:29309591ca3e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit dd611a143e4e003a5fb085cdf93ae477cc5ea0b1"
author jjohnson
date Wed, 26 Aug 2020 14:45:18 -0400
parents 7efddaece152
children aad27385a532
files encyclopedia_searchtolib.xml
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/encyclopedia_searchtolib.xml	Fri Aug 21 16:13:47 2020 -0400
+++ b/encyclopedia_searchtolib.xml	Wed Aug 26 14:45:18 2020 -0400
@@ -12,7 +12,7 @@
         @LINK_LIB_INPUT@
         for SCAN_FILE in `ls -1 inputs/*`; do 
         echo "\$SCAN_FILE" &&
-        EncyclopeDIA -Djava.awt.headless=true -Xmx20g 
+        EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g 
         #if not $library
             -walnut
         #end if
@@ -29,7 +29,7 @@
         @SEARCH_OPTIONS@ | tee -a search2lib.log
         ; done && 
         for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
-        EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
+        EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport
         #if not $library
             -pecan
         #end if