Explicitly set tmp dir for fasterq-dump (#5863)

galaxyproject · Mar 14, 2024 · cb858cb · cb858cb
1 parent bc6ba57
commit cb858cb
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/tools/sra-tools/fasterq_dump.xml b/tools/sra-tools/fasterq_dump.xml
@@ -2,6 +2,7 @@
     <description>format from NCBI SRA</description>
     <macros>
         <import>macros.xml</import>
+        <token name="VERSION_SUFFIX">1</token>
     </macros>
     <expand macro="edam_ontology"/>
     <expand macro="bio_tools"/>
@@ -13,7 +14,9 @@
     @CONFIGURE_RETRY@
     @SET_ACCESSIONS@
     while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
-        fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
+        fasterq-dump "\$acc"
+        -e \${GALAXY_SLOTS:-1}
+        -t \${TMPDIR}
         --seq-defline '$adv.seq_defline'
         --qual-defline '+'
         $adv.split