diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 583decfd1..6fddca0d6 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -4,4 +4,4 @@ updates: - package-ecosystem: "github-actions" directory: "/" schedule: - interval: "daily" \ No newline at end of file + interval: "weekly" diff --git a/SequenceAnalysis/pipeline_code/extra_tools_install.sh b/SequenceAnalysis/pipeline_code/extra_tools_install.sh index 5ba95e5dd..bfb71465b 100755 --- a/SequenceAnalysis/pipeline_code/extra_tools_install.sh +++ b/SequenceAnalysis/pipeline_code/extra_tools_install.sh @@ -350,3 +350,32 @@ then else echo "Already installed" fi + + +echo "" +echo "" +echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%" +echo "Install hifiasm" +echo "" +cd $LKSRC_DIR +if [[ ! -e ${LKTOOLS_DIR}/primer3_core || ! -z $FORCE_REINSTALL ]]; +then + echo "Cleaning up previous installs" + rm -Rf $LKTOOLS_DIR/hifiasm* + rm -Rf $LKTOOLS_DIR/yak* + rm -Rf hifiasm* + rm -Rf yak* + + git clone https://github.com/chhylp123/hifiasm + cd hifiasm + make + install hifiasm $LKTOOLS_DIR/ + cd ../ + + git clone https://github.com/lh3/yak + cd yak + make + install yak $LKTOOLS_DIR/ +else + echo "Already installed" +fi diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/sequence_readsets/SRA Info.qview.xml b/SequenceAnalysis/resources/queries/sequenceanalysis/sequence_readsets/SRA Info.qview.xml index 10a6f3edf..9678d647b 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/sequence_readsets/SRA Info.qview.xml +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/sequence_readsets/SRA Info.qview.xml @@ -20,6 +20,7 @@ + diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java index 43ee9c486..bb48598f6 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java @@ -14,7 +14,6 @@ import org.junit.Assert; import org.junit.Test; import org.labkey.api.collections.IntHashMap; -import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.SimpleFilter; diff --git a/cluster/src/org/labkey/cluster/pipeline/ClusterPipelineJob.java b/cluster/src/org/labkey/cluster/pipeline/ClusterPipelineJob.java index 2ff235f9c..f48dafea2 100644 --- a/cluster/src/org/labkey/cluster/pipeline/ClusterPipelineJob.java +++ b/cluster/src/org/labkey/cluster/pipeline/ClusterPipelineJob.java @@ -169,8 +169,6 @@ public Task createTask(PipelineJob job) @Override public RecordedActionSet run() throws PipelineJobException { - job.setStatus(TaskStatus.running, "I am running!"); - ((ClusterPipelineJob)getJob()).getRunnable().run(getJob().getLogger()); return new RecordedActionSet(); diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 47717a897..b968b65f6 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -3213,9 +3213,9 @@ } }, "node_modules/@labkey/components": { - "version": "6.72.0", - "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/components/-/@labkey/components-6.72.0.tgz", - "integrity": "sha512-ouYWpvQBF0GZ/j/ErGRcAOHTAwkGP/fSA4hDKaql59U1kMGI7gZdoHZNb5aX0YWX+FLor8FDqLXz9WWmkykEWw==", + "version": "6.72.1", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/components/-/@labkey/components-6.72.1.tgz", + "integrity": "sha512-ef3/BCqUrUHXIkkdTqcnhM1usj80GvR+SfTSEwi30pyIkiUVMDToqnbpzdKXR84cN+ZrwT4b98+YE79G9R4qyw==", "dependencies": { "@hello-pangea/dnd": "18.0.1", "@labkey/api": "1.44.0", @@ -4224,7 +4224,8 @@ "node_modules/@types/pako": { "version": "2.0.4", "resolved": "https://registry.npmjs.org/@types/pako/-/pako-2.0.4.tgz", - "integrity": "sha512-VWDCbrLeVXJM9fihYodcLiIv0ku+AlOa/TQ1SvYOaBuyrSKgEcro95LJyIsJ4vSo6BXIxOKxiJAat04CmST9Fw==" + "integrity": "sha512-VWDCbrLeVXJM9fihYodcLiIv0ku+AlOa/TQ1SvYOaBuyrSKgEcro95LJyIsJ4vSo6BXIxOKxiJAat04CmST9Fw==", + "license": "MIT" }, "node_modules/@types/parse-json": { "version": "4.0.2", @@ -6705,6 +6706,7 @@ "version": "6.4.0", "resolved": "https://registry.npmjs.org/fast-png/-/fast-png-6.4.0.tgz", "integrity": "sha512-kAqZq1TlgBjZcLr5mcN6NP5Rv4V2f22z00c3g8vRrwkcqjerx7BEhPbOnWCPqaHUl2XWQBJQvOT/FQhdMT7X/Q==", + "license": "MIT", "dependencies": { "@types/pako": "^2.0.3", "iobuffer": "^5.3.2", @@ -6714,7 +6716,8 @@ "node_modules/fast-png/node_modules/pako": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/pako/-/pako-2.1.0.tgz", - "integrity": "sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug==" + "integrity": "sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug==", + "license": "(MIT AND Zlib)" }, "node_modules/fast-uri": { "version": "3.0.1", @@ -7700,7 +7703,8 @@ "node_modules/iobuffer": { "version": "5.4.0", "resolved": "https://registry.npmjs.org/iobuffer/-/iobuffer-5.4.0.tgz", - "integrity": "sha512-DRebOWuqDvxunfkNJAlc3IzWIPD5xVxwUNbHr7xKB8E6aLJxIPfNX3CoMJghcFjpv6RWQsrcJbghtEwSPoJqMA==" + "integrity": "sha512-DRebOWuqDvxunfkNJAlc3IzWIPD5xVxwUNbHr7xKB8E6aLJxIPfNX3CoMJghcFjpv6RWQsrcJbghtEwSPoJqMA==", + "license": "MIT" }, "node_modules/ipaddr.js": { "version": "2.2.0", @@ -8088,11 +8092,12 @@ } }, "node_modules/jspdf": { - "version": "3.0.4", - "resolved": "https://registry.npmjs.org/jspdf/-/jspdf-3.0.4.tgz", - "integrity": "sha512-dc6oQ8y37rRcHn316s4ngz/nOjayLF/FFxBF4V9zamQKRqXxyiH1zagkCdktdWhtoQId5K20xt1lB90XzkB+hQ==", + "version": "3.0.3", + "resolved": "https://registry.npmjs.org/jspdf/-/jspdf-3.0.3.tgz", + "integrity": "sha512-eURjAyz5iX1H8BOYAfzvdPfIKK53V7mCpBTe7Kb16PaM8JSXEcUQNBQaiWMI8wY5RvNOPj4GccMjTlfwRBd+oQ==", + "license": "MIT", "dependencies": { - "@babel/runtime": "^7.28.4", + "@babel/runtime": "^7.26.9", "fast-png": "^6.2.0", "fflate": "^0.8.1" }, @@ -8696,9 +8701,9 @@ "dev": true }, "node_modules/node-forge": { - "version": "1.3.1", - "resolved": "https://registry.npmjs.org/node-forge/-/node-forge-1.3.1.tgz", - "integrity": "sha512-dPEtOeMvF9VMcYV/1Wb8CPoVAXtp6MKMlcbAt4ddqmGqUJ6fQZFXkNZNkNlfevtNkGtaSoXf/vNNNSvgrdXwtA==", + "version": "1.3.2", + "resolved": "https://registry.npmjs.org/node-forge/-/node-forge-1.3.2.tgz", + "integrity": "sha512-6xKiQ+cph9KImrRh0VsjH2d8/GXA4FIMlgU4B757iI1ApvcyA9VlouP0yZJha01V+huImO+kKMU7ih+2+E14fw==", "dev": true, "engines": { "node": ">= 6.13.0" diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java index 87b18cc8d..471b89a7f 100644 --- a/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java +++ b/singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java @@ -52,6 +52,7 @@ import java.io.File; import java.io.IOException; import java.nio.file.Files; +import java.nio.file.Path; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; @@ -637,12 +638,23 @@ public enum Chemistry public File getInclusionListFile(Logger logger) throws PipelineJobException { - File exe = new CellRangerWrapper(logger).getExe(); + File exe = new CellRangerWrapper(logger).getExe().getAbsoluteFile(); + logger.debug("cellranger executable: " + exe.getPath()); if (Files.isSymbolicLink(exe.toPath())) { try { - exe = Files.readSymbolicLink(exe.toPath()).toFile(); + Path exePath = Files.readSymbolicLink(exe.toPath()); + logger.debug("cellranger symlink target: " + exePath); + if (!exePath.isAbsolute()) + { + File parent = exe.getParentFile(); + exePath = parent.toPath().resolve(exePath); + logger.debug("resolved symlink target: " + exePath); + } + + exe = exePath.toFile(); + logger.debug("cellranger resolved symlink target: " + exe.getPath()); } catch (IOException e) { @@ -650,7 +662,7 @@ public File getInclusionListFile(Logger logger) throws PipelineJobException } } - File il = new File(exe.getParentFile(), "lib/python/cellranger/barcodes/" + _inclusionListFile); + File il = new File(exe.getParentFile(), "../lib/python/cellranger/barcodes/" + _inclusionListFile); if (!il.exists()) { throw new PipelineJobException("Unable to find file: " + il.getPath());