Updated for MSigDB 7.2. Changed to use a dedicated Docker container.

Changed to use a new dedicated Docker container. The corresponding Dockerfile is in the gsea-desktop repo. The build has been changed since we no longer need to download a GSEA bundle to be included in the module's ZIP bundle (still need to update this to deal with local test builds, however). The MSigDB 7.2 update is very much like the usual, except some new collections have been added.
GSEA-MSigDB · Sep 23, 2020 · e2b90b5 · e2b90b5
1 parent 41fb0dd
commit e2b90b5
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diff --git a/build.xml b/build.xml
@@ -2,7 +2,7 @@
 <!--
   Copyright (c) 2003-2020 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California.  All rights reserved.
 -->
-<project basedir="" default="devLocalModule" name="GSEA">
+<project basedir="" default="devReleaseModule" name="GSEA">
     <target name="init">
         <tstamp>
             <format property="publish.time" pattern="MM/dd/yyyy HH:mm " />
@@ -13,7 +13,6 @@
         <property name="test.version" value="999999999"/>
         <property name="dest.dir" value="build" />
         <mkdir dir="build" />
-        <property name="dataBroadBaseUrl" value="https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/4.1" />
     </target>
 
     <target name="init_devrelease" depends="init" description="internal target used by other init_devrelease_* targets; do not use directly">
@@ -23,36 +22,16 @@
         <property name="prereleasingModule" value="false" />
         <property name="quality.level" value="development" />
     </target>
-
-    <target name="init_devrelease_snapshotDesktop" depends="init_devrelease" 
-        description="Init properties for a Dev module build with the GSEA Desktop Snapshot bundle">
-        <!-- Override the default URL and release tag to point to the Snapshot -->
-        <property name="desktop.release.tag" value="snapshot" />
-    </target>
-
+
+	<!-- Note: we formerly had support for building with a local bundle.  We no longer have that
+	     at this time with our switch to Docker, though we will want to bring back something similar
+	     at some point (as support for local images).
+	-->
+
     <target name="init_devrelease_prodDesktop" depends="init_devrelease"
         description="Init properties for a Dev module build with the GSEA Desktop Production bundle">
     </target>
 
-    <target name="init_devrelease_local" depends="init_devrelease"
-        description="Init properties for a Dev module build with a local build of the GSEA Desktop">
-        <!-- Include the extra libs needed for a Java 11 build.  These are required for modularity dependencies. -->
-        <condition property="check_GSEA_REPO_HOME"> <isset property="env.GSEA_REPO_HOME" /> </condition>
-        <fail unless="${check_GSEA_REPO_HOME}" message="Please set the GSEA_REPO_HOME environment variable to your local GSEA Git repository location." />
-
-        <!-- Make sure a Java 11 build exists in the repo -->
-        <condition property="check_GSEA_build_exists">
-            <resourceexists> <file file="${env.GSEA_REPO_HOME}/build_java11/GSEA-dist" /> </resourceexists> 
-        </condition>
-        <fail unless="${check_GSEA_build_exists}" message="Please perform a Java 11 build in GSEA_REPO_HOME." />
-
-        <!-- Only pick up disable-prefs.jar from the module repo.  All other jars come from the Desktop build -->
-        <zipfileset id="lib_jars" dir="lib" includes="disable-prefs.jar" prefix="modules" />
-        <zipfileset id="lib_patch_jars" dir="${env.GSEA_REPO_HOME}/build_java11/GSEA-dist/lib" includes="*.jar" prefix="lib" />
-        <zipfileset id="module_jars" dir="${env.GSEA_REPO_HOME}/build_java11/GSEA-dist/modules" includes="*.jar" prefix="modules" />
-        <zipfileset id="cli_scripts" dir="${env.GSEA_REPO_HOME}/scripts/java11" includes="gsea.args,gsea-cli.sh" prefix="" filemode="755" />
-    </target>
-
     <!-- Bump the build number and set the quality flag if we're doing a prerelease or release -->
     <target name="init_prerelease" depends="init" 
         description="Init properties for a Prerelease module build with the GSEA Desktop Production bundle">
@@ -69,23 +48,7 @@
     </target>
 
     <target name="clean">
-        <delete>
-            <fileset dir="build" includes="manifest,*DEV_BUILD*" />
-        </delete>
-    </target>
-
-    <target name="getDesktopBundle" depends="init">
-        <property name="bundleBaseUrl" value="${dataBroadBaseUrl}" />
-        <property name="desktop.release.tag" value="${desktop.prod.version}" />
-        <property name="bundleUrl" value="${bundleBaseUrl}/GSEA_${desktop.release.tag}.zip" />
-        <get src="${bundleUrl}" dest="${dest.dir}" skipexisting="true" />
-        <unzip src="${dest.dir}/GSEA_${desktop.release.tag}.zip" dest="${dest.dir}/desktop" overwrite="false" />
-
-        <!-- Only pick up disable-prefs.jar from the module repo.  All other jars come from the Desktop build -->
-        <zipfileset id="lib_jars" dir="lib" includes="disable-prefs.jar" prefix="modules" />
-        <zipfileset id="lib_patch_jars" dir="${dest.dir}/desktop/GSEA_${desktop.release.tag}/lib" includes="*.jar" prefix="lib" />
-        <zipfileset id="module_jars" dir="${dest.dir}/desktop/GSEA_${desktop.release.tag}/modules" includes="*.jar" prefix="modules" />
-        <zipfileset id="cli_scripts" dir="${dest.dir}/desktop/GSEA_${desktop.release.tag}/" includes="gsea.args,gsea-cli.sh" prefix="" filemode="755" />
+        <delete dir="build" />
     </target>
 
     <target name="update-release-props" depends="init">
@@ -104,22 +67,14 @@
         <zip destfile="${dest.dir}/${ant.project.name}_v${full.version}.zip" whenempty="fail" defaultexcludes="true" duplicate="preserve">
             <fileset dir="." includes="*.html, *.json, LICENSE*.txt, release.properties" />
             <fileset dir="${dest.dir}" includes="manifest" />
-            <zipfileset refid="lib_jars" />
-            <zipfileset refid="module_jars" />
-            <zipfileset refid="lib_patch_jars" />
-            <zipfileset refid="cli_scripts" />
         </zip>
     </target>
 
-    <target name="devLocalModule" depends="init_devrelease_local,load-release-props,create-zip" />
-
-    <target name="devSnapshotModule" depends="init_devrelease_snapshotDesktop,getDesktopBundle,load-release-props,create-zip" />
-
-    <target name="devReleaseModule" depends="init_devrelease_prodDesktop,getDesktopBundle,load-release-props,create-zip" />
+    <target name="devReleaseModule" depends="init_devrelease_prodDesktop,load-release-props,create-zip" />
 
-    <target name="prereleaseModule" depends="init_prerelease,getDesktopBundle,update-release-props,load-release-props,create-zip" />
+    <target name="prereleaseModule" depends="init_prerelease,update-release-props,load-release-props,create-zip" />
 
-    <target name="releaseModule" depends="init_release,getDesktopBundle,update-release-props,load-release-props,create-zip" />
+    <target name="releaseModule" depends="init_release,update-release-props,load-release-props,create-zip" />
 
     <target name="addLSIDtoManifest" depends="init,getLSID">
         <tstamp>
@@ -154,4 +109,4 @@
         </condition>
         <echo>${LSID.key} = ${LSID}</echo>
     </target>
-</project>
+</project>
diff --git a/docs/v20/index.html b/docs/v20/index.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- saved from url=(0083)http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/GSEA/18 -->
 <html class=""><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-  <title>GSEA (v20.1.x)</title>
+  <title>GSEA (v20.2.x)</title>
   <link href="./application.css" media="all" rel="stylesheet">
   <script src="./application.js"></script><style>.cke{visibility:hidden;}</style><style type="text/css"></style>
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -15,7 +15,7 @@
 
 	<div class="gp-content-header fluid">
 	<div class="container">
-		<h1>GSEA (v20.1.x) <a style="float: right" href="https://www.genepattern.org"><img alt="GP Logo" src="gplogo.png" /></a></h1>
+		<h1>GSEA (v20.2.x) <a style="float: right" href="https://www.genepattern.org"><img alt="GP Logo" src="gplogo.png" /></a></h1>
 	</div>
 </div>
 <div class="container">
@@ -410,6 +410,11 @@ <h2>Version Comments</h2>
 					</tr>
 				</thead>
 				<tbody>
+                        <tr>
+                            <td>20.2.0</td>
+                            <td>2020-9-23</td>
+                            <td>Updated to MSigDB v7.2. Updated to use dedicated Docker container.</td>
+                        </tr>
                         <tr>
                             <td>20.1.0</td>
                             <td>2020-7-30</td>

diff --git a/docs/v20/test.md b/docs/v20/test.md
@@ -1,4 +1,4 @@
-# GSEA (v20.1.x)
+# GSEA (v20.2.x)
 
 Gene Set Enrichment Analysis
 
@@ -476,6 +476,11 @@ Java
 </tr>
 </thead>
 <tbody>
+<tr class="odd">
+<td align="left">20.2.0</td>
+<td align="left">2020-9-23</td>
+<td align="left">Updated to MSigDB v7.2. Updated to use dedicated Docker container.</td>
+</tr>
 <tr class="even">
 <td align="left">20.1.0</td>
 <td align="left">2020-7-30</td>

diff --git a/lib/disable-prefs.jar b/lib/disable-prefs.jar
diff --git a/manifest b/manifest
@@ -4,15 +4,15 @@
 JVMLevel=11
 LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00072\:999999999
 author=Aravind Subramanian, Pablo Tamayo, David Eby; Broad Institute
-commandLine=/bin/sh <libdir>/gsea-cli.sh GSEA -res <expression.dataset> -cls <phenotype.labels> -collapse <collapse.dataset> -mode <collapsing.mode.for.probe.sets.with.more.than.one.match> -norm <normalization.mode> -nperm <number.of.permutations> -permute <permutation.type> -rnd_type <randomization.mode> -scoring_scheme <scoring.scheme> -metric <metric.for.ranking.genes> -sort <gene.list.sorting.mode> -order <gene.list.ordering.mode> -include_only_symbols <omit.features.with.no.symbol.match> -make_sets <make.detailed.gene.set.report> -median <median.for.class.metrics> -num <number.of.markers> -plot_top_x <plot.graphs.for.the.top.sets.of.each.phenotype> -rnd_seed <random.seed> -save_rnd_lists <save.random.ranked.lists> -set_max <max.gene.set.size> -set_min <min.gene.set.size> <chip.platform.file> -gmx_list <gene.sets.database> -create_svgs <create.svgs> -create_gcts <create.gcts> -target_profile <target.profile>  <selected.gene.sets> <output.file.name> <alt.delim> -dev_mode <dev.mode> -zip_report <create.zip> -run_as_genepattern true
+commandLine=/opt/gsea/GSEA_4.1.0/gsea-cli.sh GSEA -res <expression.dataset> -cls <phenotype.labels> -collapse <collapse.dataset> -mode <collapsing.mode.for.probe.sets.with.more.than.one.match> -norm <normalization.mode> -nperm <number.of.permutations> -permute <permutation.type> -rnd_type <randomization.mode> -scoring_scheme <scoring.scheme> -metric <metric.for.ranking.genes> -sort <gene.list.sorting.mode> -order <gene.list.ordering.mode> -include_only_symbols <omit.features.with.no.symbol.match> -make_sets <make.detailed.gene.set.report> -median <median.for.class.metrics> -num <number.of.markers> -plot_top_x <plot.graphs.for.the.top.sets.of.each.phenotype> -rnd_seed <random.seed> -save_rnd_lists <save.random.ranked.lists> -set_max <max.gene.set.size> -set_min <min.gene.set.size> <chip.platform.file> -gmx_list <gene.sets.database> -create_svgs <create.svgs> -create_gcts <create.gcts> -target_profile <target.profile>  <selected.gene.sets> <output.file.name> <alt.delim> -dev_mode <dev.mode> -zip_report <create.zip> -run_as_genepattern true
 cpuType=any
 taskDoc=doc.html
 description=Gene Set Enrichment Analysis.  <strong>If you are using GSEA on RNA-seq data, please read <a href="http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA" target="_blank">these guidelines</a>.</strong>
 fileFormat=zip
 language=Java
 name=GSEA
 os=any
-job.docker.image=genepattern/docker-openjdk_11\:0.1
+job.docker.image=genepattern/gsea_4.1.0\:0.1
 
 
 p1_MODE=IN
@@ -40,7 +40,7 @@ p2_optional=
 p2_prefix=
 p2_prefix_when_specified=
 p2_type=java.io.File
-p2_value=ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c1.all.v7.1.symbols.gmt\=c1.all.v7.1.symbols.gmt [Positional];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.all.v7.1.symbols.gmt\=c2.all.v7.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cgp.v7.1.symbols.gmt\=c2.cgp.v7.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.v7.1.symbols.gmt\=c2.cp.v7.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.biocarta.v7.1.symbols.gmt\=c2.cp.biocarta.v7.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.kegg.v7.1.symbols.gmt\=c2.cp.kegg.v7.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.pid.v7.1.symbols.gmt\=c2.cp.pid.v7.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.reactome.v7.1.symbols.gmt\=c2.cp.reactome.v7.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.all.v7.1.symbols.gmt\=c3.all.v7.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.mir.v7.1.symbols.gmt\=c3.mir.v7.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.tft.v7.1.symbols.gmt\=c3.tft.v7.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.all.v7.1.symbols.gmt\=c4.all.v7.1.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.cgn.v7.1.symbols.gmt\=c4.cgn.v7.1.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.cm.v7.1.symbols.gmt\=c4.cm.v7.1.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.all.v7.1.symbols.gmt\=c5.all.v7.1.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.bp.v7.1.symbols.gmt\=c5.bp.v7.1.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.cc.v7.1.symbols.gmt\=c5.cc.v7.1.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.mf.v7.1.symbols.gmt\=c5.mf.v7.1.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c6.all.v7.1.symbols.gmt\=c6.all.v7.1.symbols.gmt [Oncogenic Signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c7.all.v7.1.symbols.gmt\=c7.all.v7.1.symbols.gmt [Immunologic signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/h.all.v7.1.symbols.gmt\=h.all.v7.1.symbols.gmt [Hallmarks]
+p2_value=ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c1.all.v7.2.symbols.gmt\=c1.all.v7.2.symbols.gmt [Positional];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.all.v7.2.symbols.gmt\=c2.all.v7.2.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cgp.v7.2.symbols.gmt\=c2.cgp.v7.2.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.v7.2.symbols.gmt\=c2.cp.v7.2.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.biocarta.v7.2.symbols.gmt\=c2.cp.biocarta.v7.2.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.kegg.v7.2.symbols.gmt\=c2.cp.kegg.v7.2.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.pid.v7.2.symbols.gmt\=c2.cp.pid.v7.2.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.reactome.v7.2.symbols.gmt\=c2.cp.reactome.v7.2.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.wikipathways.v7.2.symbols.gmt\=c2.cp.wikipathways.v7.2.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.all.v7.2.symbols.gmt\=c3.all.v7.2.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.mir.v7.2.symbols.gmt\=c3.mir.v7.2.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.mir.mirdb.v7.2.symbols.gmt\=c3.mir.mirdb.v7.2.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.mir.mir_legacy.v7.2.symbols.gmt\=c3.mir.mir_legacy.v7.2.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.tft.v7.2.symbols.gmt\=c3.tft.v7.2.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.tft.gtrd.v7.2.symbols.gmt\=c3.tft.gtrd.v7.2.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.tft.tft_legacy.v7.2.symbols.gmt\=c3.tft.tft_legacy.v7.2.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.all.v7.2.symbols.gmt\=c4.all.v7.2.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.cgn.v7.2.symbols.gmt\=c4.cgn.v7.2.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.cm.v7.2.symbols.gmt\=c4.cm.v7.2.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.all.v7.2.symbols.gmt\=c5.all.v7.2.symbols.gmt [Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.go.v7.2.symbols.gmt\=c5.go.v7.2.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.go.bp.v7.2.symbols.gmt\=c5.go.bp.v7.2.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.go.cc.v7.2.symbols.gmt\=c5.go.cc.v7.2.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.go.mf.v7.2.symbols.gmt\=c5.go.mf.v7.2.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.hpo.v7.2.symbols.gmt\=c5.hpo.v7.2.symbols.gmt [Human Phenotype Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c6.all.v7.2.symbols.gmt\=c6.all.v7.2.symbols.gmt [Oncogenic Signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c7.all.v7.2.symbols.gmt\=c7.all.v7.2.symbols.gmt [Immunologic signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c8.all.v7.2.symbols.gmt\=c8.all.v7.2.symbols.gmt [cell type signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/h.all.v7.2.symbols.gmt\=h.all.v7.2.symbols.gmt [Hallmarks]
 
 p3_MODE=
 p3_TYPE=Integer
@@ -430,6 +430,6 @@ serializedModel=
 taskType=Gene List Selection
 category=
 [email protected]
-version=Updated to use the GSEA v4.1.0 code base.
+version=Updated to MSigDB v7.2. Updated to use dedicated Docker container.
 
 publicationDate=10/05/2018 04\:51 
diff --git a/release.properties b/release.properties
@@ -1,5 +1,5 @@
-#Thu, 30 Jul 2020 16:06:26 -0700
+#Wed, 23 Sep 2020 12:44:11 +0900
 LSID.noVersion=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00072
-release.version=20.1
+release.version=20.2
 build.number=0
-build.timestamp=Thu, 30 Jul 2020 16\:06\:26 -0700
+build.timestamp=Wed, 23 Sep 2020 12\:44\:11 +0900