Quote file paths used in bash scripts

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GxfSorter.java

@@ -51,8 +51,8 @@ public File sortGff(File input, @Nullable File output) throws PipelineJobExcepti
             writer.println("#!/bin/bash");
             writer.println("set -x");
             writer.println("set -e");
-            writer.println("GFF=" + input.getPath());
-            writer.println("OUT_GFF=" + outputFile.getPath());
+            writer.println("GFF='" + input.getPath() + "'");
+            writer.println("OUT_GFF='" + outputFile.getPath() + "'");
 
             String cat = inputIsGzip ? "zcat" : "cat";
             writer.println(cat + " $GFF | awk '{ if ($1 ~ \"^#\" ) print $0; else exit; }' > $OUT_GFF");
@@ -85,8 +85,8 @@ public File sortGtf(File input, @Nullable File output) throws PipelineJobExcepti
             writer.println("#!/bin/bash");
             writer.println("set -x");
             writer.println("set -e");
-            writer.println("GTF=" + input.getPath());
-            writer.println("OUT_GTF=" + outputFile.getPath());
+            writer.println("GTF='" + input.getPath() + "'");
+            writer.println("OUT_GTF='" + outputFile.getPath() + "'");
 
             String cat = inputIsGzip ? "zcat" : "cat";
             writer.println(cat + " $GTF | awk '{ if ($1 ~ \"^#\" ) print $0; else exit; }' > $OUT_GTF");

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java

@@ -503,7 +503,7 @@ else if (!samples.equals(header.getGenotypeSamples()))
         for (File vcf : files)
         {
             String cat = vcf.getName().toLowerCase().endsWith(".gz") ? "zcat" : "cat";
-            bashCommands.add(cat + " " + vcf.getPath() + " | grep -v '^#';");
+            bashCommands.add(cat + " '" + vcf.getPath() + "' | grep -v '^#';");
         }
 
         try
@@ -523,7 +523,7 @@ else if (!samples.equals(header.getGenotypeSamples()))
                     threads = Math.max(1, threads - 1);
                 }
 
-                writer.write("} | bgzip -f" + (compressionLevel == null ? "" : " --compress-level 9") + (threads == null ? "" : " --threads " + threads) + " > " + outputGzip.getPath() + "\n");
+                writer.write("} | bgzip -f" + (compressionLevel == null ? "" : " --compress-level 9") + (threads == null ? "" : " --threads " + threads) + " > '" + outputGzip.getPath() + "'\n");
             }
 
             SimpleScriptWrapper wrapper = new SimpleScriptWrapper(log);
@@ -560,7 +560,7 @@ public static Set<String> getContigsInVcf(File vcf) throws PipelineJobException
             {
                 writer.println("#!/bin/bash");
                 String cat = vcf.getPath().toLowerCase().endsWith(".gz") ? "zcat" : "cat";
-                writer.println(cat + " " + vcf.getPath() + " | grep -v '#' | awk ' { print $1 } ' | sort | uniq");
+                writer.println(cat + " '" + vcf.getPath() + "' | grep -v '#' | awk ' { print $1 } ' | sort | uniq");
             }
 
             SimpleScriptWrapper wrapper = new SimpleScriptWrapper(null);