From 82c2db3a79d2855053cb4f59ae107df7b17f9e11 Mon Sep 17 00:00:00 2001 From: eby Date: Mon, 3 Oct 2022 15:33:34 -0700 Subject: [PATCH] Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm --- docs/v20/index.html | 11 +++- docs/v20/test.md | 11 +++- .../invalid_mix_species1_test.yml | 45 +++++++++++++++ .../invalid_mix_species2_test.yml | 47 +++++++++++++++ .../valid_same_vers_with_chip_test.yml | 52 +++++++++++++++++ .../version_check/valid_same_version_test.yml | 51 +++++++++++++++++ .../valid_warn_mix_vers_with_chip1_test.yml | 57 +++++++++++++++++++ .../valid_warn_mix_vers_with_chip2_test.yml | 57 +++++++++++++++++++ .../valid_warn_mix_version_test.yml | 55 ++++++++++++++++++ manifest | 15 ++--- release.properties | 8 +-- 11 files changed, 392 insertions(+), 17 deletions(-) create mode 100644 gpunit_functionality/version_check/invalid_mix_species1_test.yml create mode 100644 gpunit_functionality/version_check/invalid_mix_species2_test.yml create mode 100644 gpunit_functionality/version_check/valid_same_vers_with_chip_test.yml create mode 100644 gpunit_functionality/version_check/valid_same_version_test.yml create mode 100644 gpunit_functionality/version_check/valid_warn_mix_vers_with_chip1_test.yml create mode 100644 gpunit_functionality/version_check/valid_warn_mix_vers_with_chip2_test.yml create mode 100644 gpunit_functionality/version_check/valid_warn_mix_version_test.yml diff --git a/docs/v20/index.html b/docs/v20/index.html index ba1db19..30c2756 100644 --- a/docs/v20/index.html +++ b/docs/v20/index.html @@ -1,7 +1,7 @@ - GSEA (v20.3.x) + GSEA (v20.4.x) @@ -15,7 +15,7 @@
-

GSEA (v20.3.x) GP Logo

+

GSEA (v20.4.x) GP Logo

@@ -33,7 +33,7 @@

GSEA (v20.3.x)

-

GSEA Version: 4.2.1

+

GSEA Version: 4.3.x

@@ -409,6 +409,11 @@

Version Comments

+ + 20.4.0 + 2022-10-2 + Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm. + 20.3.6 2022-9-15 diff --git a/docs/v20/test.md b/docs/v20/test.md index 6745eb3..d17f485 100644 --- a/docs/v20/test.md +++ b/docs/v20/test.md @@ -1,4 +1,4 @@ -# GSEA (v20.3.x) +# GSEA (v20.4.x) Gene Set Enrichment Analysis @@ -14,7 +14,7 @@ for GSEA questions. team](http://software.broadinstitute.org/cancer/software/genepattern/contact) for GenePattern issues. -**GSEA Version:** 4.2.1 +**GSEA Version:** 4.3._x_ ## Description @@ -476,6 +476,11 @@ Java +20.4.0 +2022-10-2 +Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm. + + 20.3.6 2022-9-15 Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available @@ -607,7 +612,7 @@ Java -Copyright © 2003-2021 Broad Institute, Inc., Massachusetts Institute of +Copyright © 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. diff --git a/gpunit_functionality/version_check/invalid_mix_species1_test.yml b/gpunit_functionality/version_check/invalid_mix_species1_test.yml new file mode 100644 index 0000000..6df8b25 --- /dev/null +++ b/gpunit_functionality/version_check/invalid_mix_species1_test.yml @@ -0,0 +1,45 @@ +# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. +#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 +module: GSEA +name: GSEA invalid_mix_species1_test +description: Test the GSEA version check with files of mixed species no collapsing; expect an error. Note that we need to use remote files to trigger the check. +params: + expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_collapsed_symbols.gct" + gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt", + "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Mm/m1.all.v2022.1.Mm.symbols.gmt" ] + number.of.permutations: "10" + phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" + target.profile: "" + permutation.type: "phenotype" + collapse.dataset: "No_Collapse" + #chip.platform.file: + output.file.name: ".zip" + scoring.scheme: "weighted" + metric.for.ranking.genes: "Signal2Noise" + gene.list.sorting.mode: "real" + gene.list.ordering.mode: "descending" + max.gene.set.size: "500" + min.gene.set.size: "15" + collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe" + normalization.mode: "meandiv" + randomization.mode: "no_balance" + omit.features.with.no.symbol.match: "true" + median.for.class.metrics: "false" + number.of.markers: "100" + # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results + random.seed: "149" + create.svgs: "false" + create.gcts: "false" + save.random.ranked.lists: "false" + plot.graphs.for.the.top.sets.of.each.phenotype: "20" + make.detailed.gene.set.report: "false" + selected.gene.sets: "" + dev.mode: "true" + alt.delim: "" + create.zip: "false" +assertions: + jobStatus: fail + files: + "stderr.txt": + diffCmd: ../grepMessages.sh + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/invalid_mix_species1_test/stderrMatches.txt" diff --git a/gpunit_functionality/version_check/invalid_mix_species2_test.yml b/gpunit_functionality/version_check/invalid_mix_species2_test.yml new file mode 100644 index 0000000..6c7736b --- /dev/null +++ b/gpunit_functionality/version_check/invalid_mix_species2_test.yml @@ -0,0 +1,47 @@ +# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. +#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 +module: GSEA +name: GSEA invalid_mix_species2_test +description: Test the GSEA version check with files of mixed species no collapsing; expect an error. Note that we need to use remote files to trigger the check. +params: + expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_hgu133a.gct" + gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt" ] + number.of.permutations: "10" + phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" + target.profile: "" + permutation.type: "phenotype" + collapse.dataset: "Collapse" + chip.platform.file: "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/mouse/Human_AFFY_HG_U133_Mouse_Orthologs_MSigDB.v2022.1.Mm.chip" + # Modifying the ZIP name here so that the diffCmd can find the RNK inside. We could modify the diffCmd + # to be able to find it, but that makes the code somewhat complicated. + output.file.name: "Diabetes_hgu133a_collapsed_to_symbols.zip" + scoring.scheme: "weighted" + metric.for.ranking.genes: "Signal2Noise" + gene.list.sorting.mode: "real" + gene.list.ordering.mode: "descending" + max.gene.set.size: "500" + min.gene.set.size: "15" + collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes" + normalization.mode: "meandiv" + randomization.mode: "no_balance" + omit.features.with.no.symbol.match: "true" + median.for.class.metrics: "false" + number.of.markers: "100" + # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results + random.seed: "149" + create.svgs: "false" + create.gcts: "false" + save.random.ranked.lists: "false" + plot.graphs.for.the.top.sets.of.each.phenotype: "20" + make.detailed.gene.set.report: "false" + selected.gene.sets: "" + dev.mode: "true" + alt.delim: "" + create.zip: "true" +assertions: + jobStatus: fail + files: + "stderr.txt": + diffCmd: ../grepMessages.sh + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/invalid_mix_species2_test/stderrMatches.txt" + \ No newline at end of file diff --git a/gpunit_functionality/version_check/valid_same_vers_with_chip_test.yml b/gpunit_functionality/version_check/valid_same_vers_with_chip_test.yml new file mode 100644 index 0000000..f8709b1 --- /dev/null +++ b/gpunit_functionality/version_check/valid_same_vers_with_chip_test.yml @@ -0,0 +1,52 @@ +# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. +#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 +module: GSEA +name: GSEA valid_same_vers_with_chip_test +description: Test the GSEA version check with files of matching version with collapsing. Note that we need to use remote files to trigger the check. +params: + expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_hgu133a.gct" + gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt" ] + number.of.permutations: "10" + phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" + target.profile: "" + permutation.type: "phenotype" + collapse.dataset: "Collapse" + chip.platform.file: "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Human_AFFY_HG_U133_MSigDB.v2022.1.Hs.chip" + # Modifying the ZIP name here so that the diffCmd can find the RNK inside. We could modify the diffCmd + # to be able to find it, but that makes the code somewhat complicated. + output.file.name: "Diabetes_hgu133a_collapsed_to_symbols.zip" + scoring.scheme: "weighted" + metric.for.ranking.genes: "Signal2Noise" + gene.list.sorting.mode: "real" + gene.list.ordering.mode: "descending" + max.gene.set.size: "500" + min.gene.set.size: "15" + collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes" + normalization.mode: "meandiv" + randomization.mode: "no_balance" + omit.features.with.no.symbol.match: "true" + median.for.class.metrics: "false" + number.of.markers: "100" + # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results + random.seed: "149" + create.svgs: "false" + create.gcts: "false" + save.random.ranked.lists: "false" + plot.graphs.for.the.top.sets.of.each.phenotype: "20" + make.detailed.gene.set.report: "false" + selected.gene.sets: "" + dev.mode: "true" + alt.delim: "" + create.zip: "true" +assertions: + jobStatus: success + files: + "results.edb": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_vers_with_chip_test/results.edb" + "gene_sets.gmt": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_vers_with_chip_test/gene_sets.gmt" + "Diabetes_hgu133a_collapsed_to_symbols.rnk": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_vers_with_chip_test/Diabetes_hgu133a_collapsed_to_symbols.rnk" diff --git a/gpunit_functionality/version_check/valid_same_version_test.yml b/gpunit_functionality/version_check/valid_same_version_test.yml new file mode 100644 index 0000000..c65edfc --- /dev/null +++ b/gpunit_functionality/version_check/valid_same_version_test.yml @@ -0,0 +1,51 @@ +# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. +#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 +module: GSEA +name: GSEA valid_same_version_test +description: Test the GSEA version check with files of matching version and no collapsing. Note that we need to use remote files to trigger the check. +params: + expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_collapsed_symbols.gct" + gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt", + "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/c1.all.v2022.1.Hs.symbols.gmt" ] + number.of.permutations: "10" + phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" + target.profile: "" + permutation.type: "phenotype" + collapse.dataset: "No_Collapse" + #chip.platform.file: + output.file.name: ".zip" + scoring.scheme: "weighted" + metric.for.ranking.genes: "Signal2Noise" + gene.list.sorting.mode: "real" + gene.list.ordering.mode: "descending" + max.gene.set.size: "500" + min.gene.set.size: "15" + collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe" + normalization.mode: "meandiv" + randomization.mode: "no_balance" + omit.features.with.no.symbol.match: "true" + median.for.class.metrics: "false" + number.of.markers: "100" + # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results + random.seed: "149" + create.svgs: "false" + create.gcts: "false" + save.random.ranked.lists: "false" + plot.graphs.for.the.top.sets.of.each.phenotype: "20" + make.detailed.gene.set.report: "false" + selected.gene.sets: "" + dev.mode: "true" + alt.delim: "" + create.zip: "false" +assertions: + jobStatus: success + files: + "results.edb": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_version_test/results.edb" + "gene_sets.gmt": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_version_test/gene_sets.gmt" + "Diabetes_collapsed_symbols.rnk": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_version_test/Diabetes_collapsed_symbols.rnk" diff --git a/gpunit_functionality/version_check/valid_warn_mix_vers_with_chip1_test.yml b/gpunit_functionality/version_check/valid_warn_mix_vers_with_chip1_test.yml new file mode 100644 index 0000000..de5aacd --- /dev/null +++ b/gpunit_functionality/version_check/valid_warn_mix_vers_with_chip1_test.yml @@ -0,0 +1,57 @@ +# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. +#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 +module: GSEA +name: GSEA valid_warn_mix_vers_with_chip1_test +description: Test the GSEA version check with files of mixed versions with collapsing; should warn but complete. Note that we need to use remote files to trigger the check. +params: + expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_hgu133a.gct" + gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.5.1/h.all.v7.5.1.symbols.gmt", + "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/c1.all.v2022.1.Hs.symbols.gmt" ] + number.of.permutations: "10" + phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" + target.profile: "" + permutation.type: "phenotype" + collapse.dataset: "Collapse" + chip.platform.file: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Human_AFFY_HG_U133_MSigDB.v2022.1.Hs.chip" ] + # Modifying the ZIP name here so that the diffCmd can find the RNK inside. We could modify the diffCmd + # to be able to find it, but that makes the code somewhat complicated. + output.file.name: "Diabetes_hgu133a_collapsed_to_symbols.zip" + scoring.scheme: "weighted" + metric.for.ranking.genes: "Signal2Noise" + gene.list.sorting.mode: "real" + gene.list.ordering.mode: "descending" + max.gene.set.size: "500" + min.gene.set.size: "15" + collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes" + normalization.mode: "meandiv" + randomization.mode: "no_balance" + omit.features.with.no.symbol.match: "true" + median.for.class.metrics: "false" + number.of.markers: "100" + # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results + random.seed: "149" + create.svgs: "false" + create.gcts: "false" + save.random.ranked.lists: "false" + plot.graphs.for.the.top.sets.of.each.phenotype: "20" + make.detailed.gene.set.report: "false" + selected.gene.sets: "" + dev.mode: "true" + alt.delim: "" + create.zip: "true" +assertions: + jobStatus: success + files: + "results.edb": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip1_test/results.edb" + "gene_sets.gmt": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip1_test/gene_sets.gmt" + "Diabetes_hgu133a_collapsed_to_symbols.rnk": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip1_test/Diabetes_hgu133a_collapsed_to_symbols.rnk" + "stdout.txt": + diffCmd: ../grepMessages.sh + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/ valid_warn_mix_vers_with_chip1_test/stdoutMatches.txt" + \ No newline at end of file diff --git a/gpunit_functionality/version_check/valid_warn_mix_vers_with_chip2_test.yml b/gpunit_functionality/version_check/valid_warn_mix_vers_with_chip2_test.yml new file mode 100644 index 0000000..7b2ea1f --- /dev/null +++ b/gpunit_functionality/version_check/valid_warn_mix_vers_with_chip2_test.yml @@ -0,0 +1,57 @@ +# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. +#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 +module: GSEA +name: GSEA valid_warn_mix_vers_with_chip2_test +description: Test the GSEA version check with files of mixed versions with collapsing; should warn but complete. Note that we need to use remote files to trigger the check. +params: + expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_hgu133a.gct" + gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt", + "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/c1.all.v2022.1.Hs.symbols.gmt" ] + number.of.permutations: "10" + phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" + target.profile: "" + permutation.type: "phenotype" + collapse.dataset: "Collapse" + chip.platform.file: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Human_AFFY_HG_U133_MSigDB.v7.5.1.chip" ] + # Modifying the ZIP name here so that the diffCmd can find the RNK inside. We could modify the diffCmd + # to be able to find it, but that makes the code somewhat complicated. + output.file.name: "Diabetes_hgu133a_collapsed_to_symbols.zip" + scoring.scheme: "weighted" + metric.for.ranking.genes: "Signal2Noise" + gene.list.sorting.mode: "real" + gene.list.ordering.mode: "descending" + max.gene.set.size: "500" + min.gene.set.size: "15" + collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes" + normalization.mode: "meandiv" + randomization.mode: "no_balance" + omit.features.with.no.symbol.match: "true" + median.for.class.metrics: "false" + number.of.markers: "100" + # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results + random.seed: "149" + create.svgs: "false" + create.gcts: "false" + save.random.ranked.lists: "false" + plot.graphs.for.the.top.sets.of.each.phenotype: "20" + make.detailed.gene.set.report: "false" + selected.gene.sets: "" + dev.mode: "true" + alt.delim: "" + create.zip: "true" +assertions: + jobStatus: success + files: + "results.edb": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip2_test/results.edb" + "gene_sets.gmt": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip2_test/gene_sets.gmt" + "Diabetes_hgu133a_collapsed_to_symbols.rnk": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip2_test/Diabetes_hgu133a_collapsed_to_symbols.rnk" + "stdout.txt": + diffCmd: ../grepMessages.sh + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip2_test/stdoutMatches.txt" + \ No newline at end of file diff --git a/gpunit_functionality/version_check/valid_warn_mix_version_test.yml b/gpunit_functionality/version_check/valid_warn_mix_version_test.yml new file mode 100644 index 0000000..9d5c90c --- /dev/null +++ b/gpunit_functionality/version_check/valid_warn_mix_version_test.yml @@ -0,0 +1,55 @@ +# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. +#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 +module: GSEA +name: GSEA valid_warn_mix_version_test +description: Test the GSEA version check with files of mixed versions and no collapsing; should warn but complete. Note that we need to use remote files to trigger the check. +params: + expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_collapsed_symbols.gct" + gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt", + "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.5.1/c1.all.v7.5.1.symbols.gmt" ] + number.of.permutations: "10" + phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" + target.profile: "" + permutation.type: "phenotype" + collapse.dataset: "No_Collapse" + #chip.platform.file: + output.file.name: ".zip" + scoring.scheme: "weighted" + metric.for.ranking.genes: "Signal2Noise" + gene.list.sorting.mode: "real" + gene.list.ordering.mode: "descending" + max.gene.set.size: "500" + min.gene.set.size: "15" + collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe" + normalization.mode: "meandiv" + randomization.mode: "no_balance" + omit.features.with.no.symbol.match: "true" + median.for.class.metrics: "false" + number.of.markers: "100" + # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results + random.seed: "149" + create.svgs: "false" + create.gcts: "false" + save.random.ranked.lists: "false" + plot.graphs.for.the.top.sets.of.each.phenotype: "20" + make.detailed.gene.set.report: "false" + selected.gene.sets: "" + dev.mode: "true" + alt.delim: "" + create.zip: "false" +assertions: + jobStatus: success + files: + "results.edb": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_version_test/results.edb" + "gene_sets.gmt": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_version_test/gene_sets.gmt" + "Diabetes_collapsed_symbols.rnk": + diffCmd: diff -q --strip-trailing-cr + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_version_test/Diabetes_collapsed_symbols.rnk" + "stdout.txt": + diffCmd: ../grepMessages.sh + diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_version_test/stdoutMatches.txt" + \ No newline at end of file diff --git a/manifest b/manifest index 195b648..196fa8a 100644 --- a/manifest +++ b/manifest @@ -3,7 +3,7 @@ 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_4.2.3/gsea-cli.sh GSEA -res -cls -collapse -mode -norm -nperm -permute -rnd_type -scoring_scheme -metric -sort -order -include_only_symbols -make_sets -median -num -plot_top_x -rnd_seed -save_rnd_lists -set_max -set_min -gmx_list -create_svgs -create_gcts -target_profile -dev_mode -zip_report true -run_as_genepattern true +commandLine=/opt/gsea/GSEA_4.3.2/gsea-cli.sh GSEA -res -cls -collapse -mode -norm -nperm -permute -rnd_type -scoring_scheme -metric -sort -order -include_only_symbols -make_sets -median -num -plot_top_x -rnd_seed -save_rnd_lists -set_max -set_min -gmx_list -create_svgs -create_gcts -target_profile -dev_mode -zip_report true -run_as_genepattern true cpuType=any taskDoc=doc.html description=Gene Set Enrichment Analysis. If you are using GSEA on RNA-seq data, please read these guidelines. @@ -11,7 +11,8 @@ fileFormat=zip language=Java name=GSEA os=any -job.docker.image=genepattern/gsea_4.2.3\:0.1 +job.docker.image=genepattern/gsea_4.3.2\:0.1 +job.memory=4Gb p1_MODE=IN p1_TYPE=FILE @@ -28,8 +29,8 @@ 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_choiceDir= +p2_choiceDir=https://www.gsea-msigdb.org/gsea/msigdb/gp_modules_gmt.json p2_default_value= p2_description=Gene sets database from GSEA website. Upload a gene set if your gene set is not listed as a choice from MSigDB. p2_fileFormat=gmt;gmx;grp @@ -109,8 +110,8 @@ p7_value=phenotype;gene_set p8_MODE=IN p8_TYPE=FILE -p8_choiceDir=ftp\://ftp.broadinstitute.org/pub/gsea/annotations_versioned/ -p8_choiceDirFilter=*v2022.1.Hs.chip +p8_choiceDir=https://www.gsea-msigdb.org/gsea/msigdb/gp_modules_chip.json +p8_choiceDir= p8_default_value= p8_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. p8_fileFormat=chip @@ -417,6 +418,6 @@ serializedModel= taskType=Pathway Analysis categories=gsea;pathway analysis userid=eby@broadinstitute.org -version=Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available +version=Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm. publicationDate=10/05/2018 04\:51 diff --git a/release.properties b/release.properties index f225896..3d79f7b 100644 --- a/release.properties +++ b/release.properties @@ -1,5 +1,5 @@ -#Thu, 15 Sep 2022 17:35:02 -0700 +#Mon, 03 Oct 2022 15:31:07 -0700 LSID.noVersion=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00072 -release.version=20.3 -build.number=6 -build.timestamp=Thu, 15 Sep 2022 17\:35\:02 -0700 +release.version=20.4 +build.number=0 +build.timestamp=Mon, 3 Oct 2022 15\:31\:07 -0700