From 164d6bcb6022758445e133dc9a6f3ff597e88b08 Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Tue, 30 Jul 2024 14:33:46 +0200
Subject: [PATCH] fixes error with incorrectly used brackets

---
 files/galaxy/tpv/destinations.yml.j2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/files/galaxy/tpv/destinations.yml.j2 b/files/galaxy/tpv/destinations.yml.j2
index bc075744e..3066fe261 100644
--- a/files/galaxy/tpv/destinations.yml.j2
+++ b/files/galaxy/tpv/destinations.yml.j2
@@ -259,7 +259,7 @@ destinations:
       jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-eu/files/staging"
       persistence_directory: "/opt/pulsar/files/persistent"
       singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR,/storage/praha5-elixir/home/galaxyeu:/home/galaxyeu,/cvmfs/data.galaxyproject.org/managed/:/data/db/data_managers/:ro"
-      singularity_run_extra_arguments: --env "_JAVA_OPTIONS=\"-Xmx{int(mem)}G -Djava.io.tmpdir=$SCRATCHDIR\""
+      singularity_run_extra_arguments: '--env _JAVA_OPTIONS="-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR"'
       submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local=100gb -l walltime=24:00:00 -q galaxyeu@pbs-m1.metacentrum.cz -N pulsar_eu_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
     scheduling:
       require: