From 3a504aa3e927cda929896256d1b382d20424c19c Mon Sep 17 00:00:00 2001
From: Sanjay Kumar Srikakulam <sanjaysrikakulam@gmail.com>
Date: Wed, 21 Aug 2024 10:31:59 +0000
Subject: [PATCH 1/2] remove singularity no-mount tmp option for
 funannotate_predict

this is set default by Galaxy. We override it here so this job can use the host's /tmp file system bind mounted into the container. This fixes the write permission error as well as the NFS resource busy error
---
 .gitignore                 | 1 +
 files/galaxy/tpv/tools.yml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index cd036c3c2..40506ee96 100644
--- a/.gitignore
+++ b/.gitignore
@@ -34,3 +34,4 @@ dx_applets/.DS_Store
 #.gitignore
 #roles/*
 #*.code-workspace
+*.vscode/
\ No newline at end of file
diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml
index 11f2b8a78..4a20efd6f 100644
--- a/files/galaxy/tpv/tools.yml
+++ b/files/galaxy/tpv/tools.yml
@@ -1338,6 +1338,7 @@ tools:
       _GALAXY_JOB_TMP_DIR: '/tmp'
     params:
       singularity_run_extra_arguments: "--env GENEMARK_PATH=/usr/local/tools/genemark/etp.for_braker/bin/gmes/"
+      singularity_no_mount: null
     scheduling:
       require:
         - singularity

From 663440f31cd8a0266af4dae48201840973840800 Mon Sep 17 00:00:00 2001
From: Sanjay Kumar Srikakulam <sanjaysrikakulam@gmail.com>
Date: Wed, 21 Aug 2024 10:48:42 +0000
Subject: [PATCH 2/2] lint fix

---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 40506ee96..31e90f156 100644
--- a/.gitignore
+++ b/.gitignore
@@ -34,4 +34,4 @@ dx_applets/.DS_Store
 #.gitignore
 #roles/*
 #*.code-workspace
-*.vscode/
\ No newline at end of file
+*.vscode/