Updated to GSEA 4.2.3

Removed Log4J entirely from the code base.  Fixed weighted_p1.5
computation.  Added min dataset size warnings.

docs/v20/index.html

@@ -409,6 +409,11 @@ <h2>Version Comments</h2>
 					</tr>
 				</thead>
 				<tbody>
+                        <tr>
+                            <td>20.3.5</td>
+                            <td>2022-3-2</td>
+                            <td>Removed Log4J entirely from the code base.  Fixed weighted_p1.5 computation.  Added min dataset size warnings.</td>
+                        </tr>
                         <tr>
                             <td>20.3.4</td>
                             <td>2022-1-20</td>

docs/v20/test.md

@@ -475,6 +475,11 @@ Java
 </tr>
 </thead>
 <tbody>
+<tr class="odd">
+<td align="left">20.3.5</td>
+<td align="left">2022-3-22</td>
+<td align="left">Removed Log4J entirely from the code base.  Fixed weighted_p1.5 computation.  Added min dataset size warnings.</td>
+</tr>
 <tr class="even">
 <td align="left">20.3.4</td>
 <td align="left">2022-1-20</td>

manifest

@@ -3,15 +3,15 @@
 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=/opt/gsea/GSEA_4.2.2/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 true -run_as_genepattern true
+commandLine=/opt/gsea/GSEA_4.2.3/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 true -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/gsea_4.2.2\:0.1
+job.docker.image=genepattern/gsea_4.2.3\:0.1
 
 p1_MODE=IN
 p1_TYPE=FILE
@@ -415,6 +415,6 @@ serializedModel=
 taskType=Pathway Analysis
 categories=gsea;pathway analysis
 [email protected]
-version=Updated Log4J to 2.17.1.
+version=Removed Log4J entirely from the code base.  Fixed weighted_p1.5 computation.  Added min dataset size warnings.
 
 publicationDate=10/05/2018 04\:51 

release.properties

@@ -1,5 +1,5 @@
-#Thu, 20 Jan 2022 20:27:37 -0800
+#Wed, 02 Mar 2022 11:24:56 -0800
 LSID.noVersion=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00072
 release.version=20.3
-build.number=4
-build.timestamp=Thu, 20 Jan 2022 20\:27\:37 -0800
+build.number=5
+build.timestamp=Wed, 2 Mar 2022 11\:24\:56 -0800