From cb858cbf5d9e307b663105f674f1acaa4f90a1fb Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Thu, 14 Mar 2024 16:00:45 +0100
Subject: [PATCH] Explicitly set tmp dir for fasterq-dump (#5863)

---
 tools/sra-tools/fasterq_dump.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tools/sra-tools/fasterq_dump.xml b/tools/sra-tools/fasterq_dump.xml
index d954ecc3089..9493cb4307c 100644
--- 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