Updated to Human MSigDB v2022.1.Hs.

Direct support for Mouse MSigDB 2022.1.Mm is not yet available

Author: davideby

docs/v7/index.html

@@ -280,6 +280,11 @@ <h2>Version Comments</h2>
 					</tr>
 				</thead>
 				<tbody>
+                        <tr>
+                            <td>7.3.6</td>
+                            <td>2022-9-15</td>
+                            <td>Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available</td>
+                        </tr>
                         <tr>
                             <td>7.3.5</td>
                             <td>2022-3-2</td>

docs/v7/test.md

@@ -290,6 +290,11 @@ Java
 </tr>
 </thead>
 <tbody>
+<tr class="even">
+<td align="left">7.3.6</td>
+<td align="left">2022-9-15</td>
+<td align="left">Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available</td>
+</tr>
 <tr class="odd">
 <td align="left">7.3.5</td>
 <td align="left">2022-3-22</td>

manifest

@@ -10,7 +10,7 @@ fileFormat=
 language=Java
 name=GSEAPreranked
 os=any
-job.docker.image=genepattern/gsea_4.2.3\:0.1
+job.docker.image=genepattern/gsea_4.2.3\:local
 
 p1_MODE=IN
 p1_TYPE=FILE
@@ -27,6 +27,8 @@ p1_value=
 
 p2_MODE=IN
 p2_TYPE=FILE
+p2_choiceDir=ftp\://ftp.broadinstitute.org/pub/gsea/msigdb/human/gene_sets
+p2_choiceDirFilter=*v2022.1.Hs.symbols.gmt
 p2_default_value=
 p2_description=Gene sets database from GSEA website.
 p2_fileFormat=gmt;gmx;grp
@@ -37,7 +39,7 @@ 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.v7.5.1.symbols.gmt\=c1.all.v7.5.1.symbols.gmt [Positional];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.all.v7.5.1.symbols.gmt\=c2.all.v7.5.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cgp.v7.5.1.symbols.gmt\=c2.cgp.v7.5.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.v7.5.1.symbols.gmt\=c2.cp.v7.5.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.biocarta.v7.5.1.symbols.gmt\=c2.cp.biocarta.v7.5.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.kegg.v7.5.1.symbols.gmt\=c2.cp.kegg.v7.5.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.pid.v7.5.1.symbols.gmt\=c2.cp.pid.v7.5.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.reactome.v7.5.1.symbols.gmt\=c2.cp.reactome.v7.5.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.wikipathways.v7.5.1.symbols.gmt\=c2.cp.wikipathways.v7.5.1.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.all.v7.5.1.symbols.gmt\=c3.all.v7.5.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.mir.v7.5.1.symbols.gmt\=c3.mir.v7.5.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.mir.mirdb.v7.5.1.symbols.gmt\=c3.mir.mirdb.v7.5.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.mir.mir_legacy.v7.5.1.symbols.gmt\=c3.mir.mir_legacy.v7.5.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.tft.v7.5.1.symbols.gmt\=c3.tft.v7.5.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.tft.gtrd.v7.5.1.symbols.gmt\=c3.tft.gtrd.v7.5.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.tft.tft_legacy.v7.5.1.symbols.gmt\=c3.tft.tft_legacy.v7.5.1.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.all.v7.5.1.symbols.gmt\=c4.all.v7.5.1.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.cgn.v7.5.1.symbols.gmt\=c4.cgn.v7.5.1.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.cm.v7.5.1.symbols.gmt\=c4.cm.v7.5.1.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.all.v7.5.1.symbols.gmt\=c5.all.v7.5.1.symbols.gmt [Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.go.v7.5.1.symbols.gmt\=c5.go.v7.5.1.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.go.bp.v7.5.1.symbols.gmt\=c5.go.bp.v7.5.1.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.go.cc.v7.5.1.symbols.gmt\=c5.go.cc.v7.5.1.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.go.mf.v7.5.1.symbols.gmt\=c5.go.mf.v7.5.1.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.hpo.v7.5.1.symbols.gmt\=c5.hpo.v7.5.1.symbols.gmt [Human Phenotype Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c6.all.v7.5.1.symbols.gmt\=c6.all.v7.5.1.symbols.gmt [Oncogenic Signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c7.all.v7.5.1.symbols.gmt\=c7.all.v7.5.1.symbols.gmt [Immunologic signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c7.immunesigdb.v7.5.1.symbols.gmt\=c7.immunesigdb.v7.5.1.symbols.gmt [Immunologic signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c7.vax.v7.5.1.symbols.gmt\=c7.vax.v7.5.1.symbols.gmt [Immunologic signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c8.all.v7.5.1.symbols.gmt\=c8.all.v7.5.1.symbols.gmt [cell type signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/h.all.v7.5.1.symbols.gmt\=h.all.v7.5.1.symbols.gmt [Hallmarks]
+p2_value=
 
 p3_MODE=
 p3_TYPE=Integer
@@ -68,7 +70,7 @@ p4_value=No_Collapse;Collapse;Remap_Only
 p5_MODE=IN
 p5_TYPE=FILE
 p5_choiceDir=ftp\://ftp.broadinstitute.org/pub/gsea/annotations_versioned/
-p5_choiceDirFilter=*.v7.5.1.chip
+p5_choiceDirFilter=*.v2022.1.Hs.chip
 p5_default_value=
 p5_description=DNA Chip (array) annotation file from GSEA website.  Upload your own chip file if the one corresponding to your DNA Microarray platform is not listed in the drop-down menu.  A chip file is only required if collapse dataset is set to true.
 p5_fileFormat=chip
@@ -273,4 +275,4 @@ taskDoc=doc.html
 taskType=Pathway Analysis
 categories=gsea;pathway analysis
 userid=eby@broadinstitute.org
-version=Removed Log4J entirely from the code base.  Fixed weighted_p1.5 computation.  Added min dataset size warnings.
+version=Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available

release.properties

@@ -1,5 +1,5 @@
-#Wed, 02 Mar 2022 11:25:04 -0800
+#Thu, 15 Sep 2022 17:35:39 -0700
 LSID.noVersion=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00317
 release.version=7.3
-build.number=5
-build.timestamp=Wed, 2 Mar 2022 11\:25\:04 -0800
+build.number=6
+build.timestamp=Thu, 15 Sep 2022 17\:35\:39 -0700