Update location of genome symlinks in mGAP

Author: bbimber

mGAP/resources/web/mGAP/DownloadWindow.js

@@ -68,9 +68,9 @@ Ext4.define('mGAP.window.DownloadWindow', {
                             '<pre>wget https://mgapdownload.ohsu.edu/' + sitesOnlyVcf + '<br>' +
                             'wget https://mgapdownload.ohsu.edu/' + sitesOnlyVcf + '.tbi</pre>' : '') +
                             'and genome:<br>' +
-                            '<pre>wget https://mgapdownload.ohsu.edu/' + urlFasta + '<br>' +
-                            'wget https://mgapdownload.ohsu.edu/' + urlFasta + '.fai<br>' +
-                            'wget https://mgapdownload.ohsu.edu/' + urlFasta.replace(/fasta$/, 'dict') + '</pre>'
+                            '<pre>wget https://mgapdownload.ohsu.edu/genomes/' + urlFasta + '<br>' +
+                            'wget https://mgapdownload.ohsu.edu/genomes/' + urlFasta + '.fai<br>' +
+                            'wget https://mgapdownload.ohsu.edu/genomes/' + urlFasta.replace(/fasta$/, 'dict') + '</pre>'
                 },{
                     html: '<br><b>mGAP is an NIH funded project.  If you use these data in a publication, we ask that you please include R24OD021324 in the acknowledgements.</b>',
                     border: false,

mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java

@@ -121,9 +121,9 @@ private void checkMGapFiles(Logger log, User u)
             try
             {
                 ReferenceGenome rg = SequenceAnalysisService.get().getReferenceGenome(genomeId, u);
-                checkSymlink(log, rg.getSourceFastaFile(), null, commandsToRun);
-                checkSymlink(log, new File(rg.getSourceFastaFile().getPath() + ".fai"), null, commandsToRun);
-                checkSymlink(log, new File(rg.getSourceFastaFile().getPath().replace(".fasta", ".dict")), null, commandsToRun);
+                checkSymlink(log, rg.getSourceFastaFile(), "genomes", commandsToRun);
+                checkSymlink(log, new File(rg.getSourceFastaFile().getPath() + ".fai"), "genomes", commandsToRun);
+                checkSymlink(log, new File(rg.getSourceFastaFile().getPath().replace(".fasta", ".dict")), "genomes", commandsToRun);
             }
             catch (PipelineJobException e)
             {