Temporarily bump Interval2Maf1 to 32GB for Wilfried

galaxyproject · Jul 14, 2017 · 0638aac · 0638aac
1 parent f9e62c1
commit 0638aac
Showing 1 changed file with 29 additions and 1 deletion.
diff --git a/templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 b/templates/galaxy/usegalaxy.org/config/job_conf.xml.j2
@@ -181,6 +181,10 @@
             <param id="type">python</param>
             <param id="function">dynamic_normal_reserved_16gb</param>
         </destination>
+        <destination id="dynamic_normal_reserved_32gb" runner="dynamic">
+            <param id="type">python</param>
+            <param id="function">dynamic_normal_reserved_32gb</param>
+        </destination>
         <destination id="dynamic_normal_reserved_64gb" runner="dynamic">
             <param id="type">python</param>
             <param id="function">dynamic_normal_reserved_64gb</param>
@@ -278,6 +282,18 @@
            <env exec="mkdir -p $TEMP" />
            <env file="/cvmfs/main.galaxyproject.org/venv/bin/activate" />
         </destination>
+        <destination id="reserved_32gb" runner="slurm">
+           <param id="nativeSpecification">--time=36:00:00 --clusters=roundup --nodes=1 --ntasks=1 --partition=reserved --mem-per-cpu=30720</param>
+           <env id="PATH">/cvmfs/main.galaxyproject.org/deps/_manual/bin:/galaxy/main/linux-x86_64/bin:/galaxy/software/linux-x86_64/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin</env>
+           <env id="LC_ALL">C</env>
+           <env id="FONTCONFIG_FILE">/cvmfs/main.galaxyproject.org/fontconfig/fonts.conf</env>
+           <env id="LD_LIBRARY_PATH">/cvmfs/main.galaxyproject.org/venv/lib</env>
+           <env id="TEMP">$(dirname ${BASH_SOURCE[0]})/_galaxy_tmp</env>
+           <env id="TMPDIR">$TEMP</env>
+           <env id="_JAVA_OPTIONS">-Djava.io.tmpdir=$TEMP -Xmx32256m -Xms256m</env>
+           <env exec="mkdir -p $TEMP" />
+           <env file="/cvmfs/main.galaxyproject.org/venv/bin/activate" />
+        </destination>
         <destination id="reserved_64gb" runner="slurm">
            <param id="nativeSpecification">--time=36:00:00 --clusters=roundup --nodes=1 --ntasks=1 --partition=reserved --mem-per-cpu=61440</param>
            <env id="PATH">/cvmfs/main.galaxyproject.org/deps/_manual/bin:/galaxy/main/linux-x86_64/bin:/galaxy/software/linux-x86_64/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin</env>
@@ -328,6 +344,18 @@
            <env exec="mkdir -p $TEMP" />
            <env file="/cvmfs/main.galaxyproject.org/venv/bin/activate" />
         </destination>
+        <destination id="slurm_normal_32gb" runner="slurm">
+           <param id="nativeSpecification">--time=24:00:00 --nodes=1 --ntasks=1 --partition=multi --mem-per-cpu=30720</param>
+           <env id="PATH">/cvmfs/main.galaxyproject.org/deps/_manual/bin:/galaxy/main/linux-x86_64/bin:/galaxy/software/linux-x86_64/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin</env>
+           <env id="LC_ALL">C</env>
+           <env id="FONTCONFIG_FILE">/cvmfs/main.galaxyproject.org/fontconfig/fonts.conf</env>
+           <env id="LD_LIBRARY_PATH">/cvmfs/main.galaxyproject.org/venv/lib</env>
+           <env id="TEMP">$(dirname ${BASH_SOURCE[0]})/_galaxy_tmp</env>
+           <env id="TMPDIR">$TEMP</env>
+           <env id="_JAVA_OPTIONS">-Djava.io.tmpdir=$TEMP -Xmx32256m -Xms256m</env>
+           <env exec="mkdir -p $TEMP" />
+           <env file="/cvmfs/main.galaxyproject.org/venv/bin/activate" />
+        </destination>
         <destination id="slurm_normal_64gb" runner="slurm">
            <param id="nativeSpecification">--time=24:00:00 --nodes=1 --ntasks=1 --partition=multi --mem-per-cpu=61440</param>
            <env id="PATH">/cvmfs/main.galaxyproject.org/deps/_manual/bin:/galaxy/main/linux-x86_64/bin:/galaxy/software/linux-x86_64/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin</env>
@@ -636,7 +664,7 @@
         <tool id="scatterplot_rpy" destination="dynamic_normal_reserved_16gb"/>
         <tool id="htseq_count" destination="dynamic_normal_reserved_16gb"/>
         <tool id="flanking_features_1" destination="dynamic_normal_reserved_16gb"/>
-        <tool id="Interval2Maf1" destination="dynamic_normal_reserved_16gb"/>
+        <tool id="Interval2Maf1" destination="dynamic_normal_reserved_32gb"/>
         <!-- picard tools may not actually need 16GB. Without -Xmx they were only using 2GB of their allocated memory
         <tool id="picard_AddCommentsToBam" destination="dynamic_normal_reserved_16gb"/>
         <tool id="picard_AddOrReplaceReadGroups" destination="dynamic_normal_reserved_16gb"/>