Merge 25.11 to develop

mGAP/resources/web/mGAP/DownloadWindow.js

@@ -54,9 +54,10 @@ Ext4.define('mGAP.window.DownloadWindow', {
 
                 LDK.Assert.assertNotEmpty('Missing objectId variantCatalogReleases', results.rows[0].objectId);
 
-                var releaseVcf = results.rows[0].objectId + '/' + results.rows[0]['vcfId/dataid/Name'];
-                var urlFasta = results.rows[0]['vcfId/library_id/fasta_file/Name'];
-                var sitesOnlyVcf = results.rows[0].objectId + '/' + results.rows[0]['sitesOnlyVcfId/dataid/Name'];
+                var releaseVcfWithGUID = results.rows[0].objectId + '/' + results.rows[0]['vcfId/dataid/Name'];
+                var sitesOnlyVcfWithGUID = results.rows[0].objectId + '/' + results.rows[0]['sitesOnlyVcfId/dataid/Name'];
+                var genomeFasta = results.rows[0]['vcfId/library_id/fasta_file/Name'];
+                var genomeDict = genomeFasta.replace(/fasta$/, 'dict')
 
                 const getFileName = function(path){
                     path = path.split('/');
@@ -66,16 +67,16 @@ Ext4.define('mGAP.window.DownloadWindow', {
                 var toAdd = [{
                     html: 'Due to the large file size, the preferred option is to download using wget or curl on the command line, such as the exmaples below. Nonetheless, you also are able to paste the URLs into your browser and download through this way as well, although it will be slower and possibly not able to resume if your connection is disrupted.<br><br>' +
                             'Use these to download the VCF and index. Note, -C will allow file resume if the download is disrupted:<br>' +
-                            '<pre>curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/' + releaseVcf + '<br>' +
-                            'curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/' + releaseVcf + '.tbi</pre>' +
-                            (sitesOnlyVcf ?
+                            '<pre>curl -C - -o ' + getFileName(releaseVcfWithGUID) + ' https://mgapdownload.ohsu.edu/' + releaseVcfWithGUID + '<br>' +
+                            'curl -C - -o ' + getFileName(releaseVcfWithGUID) + '.tbi' + ' https://mgapdownload.ohsu.edu/' + releaseVcfWithGUID + '.tbi</pre>' +
+                            (sitesOnlyVcfWithGUID ?
                             'or a VCF without genotypes (considerably smaller):<br>' +
-                            '<pre>curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/' + sitesOnlyVcf + '<br>' +
-                            'curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/' + sitesOnlyVcf + '.tbi</pre>' : '') +
+                            '<pre>curl -C - -o ' + getFileName(sitesOnlyVcfWithGUID) + ' https://mgapdownload.ohsu.edu/' + sitesOnlyVcfWithGUID + '<br>' +
+                            'curl -C - -o ' + getFileName(sitesOnlyVcfWithGUID) + '.tbi' + ' https://mgapdownload.ohsu.edu/' + sitesOnlyVcfWithGUID + '.tbi</pre>' : '') +
                             'and genome:<br>' +
-                            '<pre>curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/genomes/' + urlFasta + '<br>' +
-                            'curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/genomes/' + urlFasta + '.fai<br>' +
-                            'curl -C - -o ' + getFileName(releaseVcf) + ' https://mgapdownload.ohsu.edu/genomes/' + urlFasta.replace(/fasta$/, 'dict') + '</pre>'
+                            '<pre>curl -C - -o ' + getFileName(genomeFasta) + ' https://mgapdownload.ohsu.edu/genomes/' + genomeFasta + '<br>' +
+                            'curl -C - -o ' + getFileName(genomeFasta) + '.fai' + ' https://mgapdownload.ohsu.edu/genomes/' + genomeFasta + '.fai<br>' +
+                            'curl -C - -o ' + getFileName(genomeDict) + ' https://mgapdownload.ohsu.edu/genomes/' + genomeDict + '</pre>'
                 },{
                     html: '<br><b>mGAP is an NIH funded project.  If you use these data in a publication, we ask that you please include R24 OD021324 in the acknowledgements.</b>',
                     border: false,

primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java

@@ -69,9 +69,9 @@ private boolean isSequenceAlignmentTask(PipelineJob job)
         return (job.getActiveTaskId() != null && job.getActiveTaskId().getNamespaceClass().getName().endsWith("SequenceAlignmentTask"));
     }
 
-    private boolean isCacheAlignerIndexesTask(PipelineJob job)
+    private boolean isCacheOrPrepareAlignerIndexesTask(PipelineJob job)
     {
-        return (job.getActiveTaskId() != null && job.getActiveTaskId().getNamespaceClass().getName().endsWith("CacheAlignerIndexesTask"));
+        return (job.getActiveTaskId() != null && (job.getActiveTaskId().getNamespaceClass().getName().endsWith("CacheAlignerIndexesTask") || job.getActiveTaskId().getNamespaceClass().getName().endsWith("PrepareAlignerIndexesTask")));
     }
 
     private boolean isSequenceSequenceOutputHandlerTask(PipelineJob job)
@@ -188,7 +188,7 @@ public Integer getMaxRequestMemory(PipelineJob job)
             return 96;
         }
 
-        if (isCacheAlignerIndexesTask(job))
+        if (isCacheOrPrepareAlignerIndexesTask(job))
         {
             int mem = getAlignerIndexMem(job);
             job.getLogger().debug("setting memory to: " + mem);

tcrdb/resources/schemas/tcrdb.xml

@@ -129,7 +129,7 @@
                 <columnTitle>Clonotype</columnTitle>
             </column>
             <column columnName="activationFrequency">
-                <columnTitle>Activated Freq</columnTitle>
+                <columnTitle>Activated Freq (of parent population)</columnTitle>
             </column>
             <column columnName="backgroundFrequency">
                 <columnTitle>Background Freq</columnTitle>