Support additional studies

BimberLab · Jan 28, 2025 · 4173962 · 4173962
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commit 4173962
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Showing 3 changed files with 14 additions and 10 deletions.
diff --git a/SequenceAnalysis/pipeline_code/sequence_tools_install.sh b/SequenceAnalysis/pipeline_code/sequence_tools_install.sh
@@ -985,15 +985,15 @@ then
     rm -Rf $LKTOOLS_DIR/blast_formatter
     rm -Rf $LKTOOLS_DIR/makeblastdb
 
-    wget $WGET_OPTS ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz
-    gunzip ncbi-blast-2.2.31+-x64-linux.tar.gz
-    tar -xf ncbi-blast-2.2.31+-x64-linux.tar
-    gzip ncbi-blast-2.2.31+-x64-linux.tar
-
-    install ./ncbi-blast-2.2.31+/bin/blastn $LKTOOLS_DIR/blastn
-    install ./ncbi-blast-2.2.31+/bin/blast_formatter $LKTOOLS_DIR/blast_formatter
-    install ./ncbi-blast-2.2.31+/bin/makeblastdb $LKTOOLS_DIR/makeblastdb
-    install ./ncbi-blast-2.2.31+/bin/makembindex $LKTOOLS_DIR/makembindex
+    wget $WGET_OPTS ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/ncbi-blast-2.16.0+-x64-linux.tar.gz
+    gunzip ncbi-blast-2.16.0+-x64-linux.tar.gz
+    tar -xf ncbi-blast-2.16.0+-x64-linux.tar
+    gzip ncbi-blast-2.16.0+-x64-linux.tar
+
+    install ./ncbi-blast-2.16.0+/bin/blastn $LKTOOLS_DIR/blastn
+    install ./ncbi-blast-2.16.0+/bin/blast_formatter $LKTOOLS_DIR/blast_formatter
+    install ./ncbi-blast-2.16.0+/bin/makeblastdb $LKTOOLS_DIR/makeblastdb
+    install ./ncbi-blast-2.16.0+/bin/makembindex $LKTOOLS_DIR/makembindex
 else
     echo "Already installed"
 fi

diff --git a/singlecell/resources/chunks/StudyMetadata.R b/singlecell/resources/chunks/StudyMetadata.R
@@ -21,6 +21,10 @@ for (datasetId in names(seuratObjects)) {
         seuratObj <- Rdiscvr::ApplyPC531Metadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
     } else if (studyName == 'AcuteNx') {
         seuratObj <- Rdiscvr::ApplyAcuteNxMetadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
+    } else if (studyName == 'EC') {
+        seuratObj <- Rdiscvr::ApplyEC_Metadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
+    } else if (studyName == 'PPG_Stims') {
+        seuratObj <- Rdiscvr::ApplyPPG_Stim_Metadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
     } else {
         stop(paste0('Unknown study: ', studyName))
     }

diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/StudyMetadata.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/StudyMetadata.java
@@ -24,7 +24,7 @@ public Provider()
                     {{
                         put("multiSelect", false);
                         put("allowBlank", false);
-                        put("storeValues", "PC475;PC531;TB;Malaria;AcuteNx");
+                        put("storeValues", "PC475;PC531;TB;Malaria;AcuteNx;EC;PPG_Stims");
                         put("delimiter", ";");
                     }}, null, null, false, false),
                     SeuratToolParameter.create("errorIfUnknownIdsFound", "Error If Unknown Ids Found", "If true, the job will fail if the seurat object contains ID not present in the metadata", "checkbox", null, true)