Add bash script to output directory

ebi-pf-team · Nov 5, 2024 · 197a012 · 197a012
1 parent 734ba81
commit 197a012
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Showing 3 changed files with 10 additions and 52 deletions.
diff --git a/core/precalcmatches/berkeley/assembly.xml b/core/precalcmatches/berkeley/assembly.xml
@@ -2,13 +2,9 @@
     <id>dist</id>
     <formats>
         <format>dir</format>
-        <!--<format>zip</format>-->
-        <format>tar.gz</format>
     </formats>
     <includeBaseDirectory>false</includeBaseDirectory>
     <fileSets>
-
-
         <fileSet>
             <directory>target</directory>
             <outputDirectory></outputDirectory>
@@ -17,26 +13,14 @@
             </includes>
             <fileMode>0755</fileMode>
         </fileSet>
-
-
         <fileSet>
-            <directory>target</directory>
-            <outputDirectory></outputDirectory>
-            <includes>
-                <include>*.jar</include>
-            </includes>
-        </fileSet>
-
-
-        <fileSet>
-            <directory></directory>
-            <outputDirectory></outputDirectory>
+            <directory>${basedir}</directory>
+            <outputDirectory>/</outputDirectory>
             <includes>
                 <include>*.sh</include>
             </includes>
             <fileMode>0755</fileMode>
         </fileSet>
-
     </fileSets>
     <dependencySets>
         <dependencySet>

diff --git a/core/precalcmatches/berkeley/build.sh b/core/precalcmatches/berkeley/build.sh
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+dirname=$(dirname "$0")
+java -XX:+UseParallelGC \
+     -XX:ParallelGCThreads=8 \
+     -XX:+UseCompressedOops \
+     -Xms16000M -Xmx32000M \
+     -jar "${dirname}/berkeley-db-builder.jar" "$@"
diff --git a/core/precalcmatches/berkeley/buildFromIprscan.sh b/core/precalcmatches/berkeley/buildFromIprscan.sh