From 23c8298010159cbaafa866763977baca6a25905a Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sun, 6 Aug 2023 21:29:08 +0200
Subject: [PATCH 1/4] make pulling container optional

---
 .github/workflows/pr.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 39b2e429..74ffe3d0 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -318,8 +318,10 @@ jobs:
       run: ln -s $(which apptainer) $(dirname apptainer)/singularity
     - name: Install containers
       run: |
-        singularity pull --dir /tmp docker://continuumio/anaconda3
-        singularity pull --dir /tmp docker://rocker/tidyverse
+        if [ grep scripting ${{ needs.setup.outputs.repository-list }} ]; then
+          singularity pull --dir /tmp docker://continuumio/anaconda3
+          singularity pull --dir /tmp docker://rocker/tidyverse
+        fi
 
     - name: Planemo test
       uses: galaxyproject/planemo-ci-action@v1

From e855937ae44f1ed48ef128637acd81f89917a956 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sun, 6 Aug 2023 21:30:38 +0200
Subject: [PATCH 2/4] bumps

---
 tools/longorf/longORF.xml   | 2 +-
 tools/scripting/general.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/longorf/longORF.xml b/tools/longorf/longORF.xml
index 1b58b6ca..bedcc250 100644
--- a/tools/longorf/longORF.xml
+++ b/tools/longorf/longORF.xml
@@ -1,4 +1,4 @@
-<tool id="longORF" name="Obtain longest ORFs" version="0.2.0">
+<tool id="longORF" name="Obtain longest ORFs" version="0.3.0">
     <description> in six-frame translations</description>
     <command><![CDATA[
         python $__tool_directory__/getLongestORF.py $input $output_longestORF $output_ORFs
diff --git a/tools/scripting/general.xml b/tools/scripting/general.xml
index 89844ab1..9deea2ca 100644
--- a/tools/scripting/general.xml
+++ b/tools/scripting/general.xml
@@ -1,4 +1,4 @@
-<tool id="singularity_scriptrunner" name="scriptrunner" version="0.1" profile="22.05">
+<tool id="singularity_scriptrunner" name="scriptrunner" version="0.1.1" profile="22.05">
     <description>singularity</description>
     <creator>
         <person givenName="Matthias" familyName="Bernt" email="m.bernt@ufz.de" />

From ab554efc7e7c4b4d64af42a227628968adb447c7 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sun, 6 Aug 2023 21:47:26 +0200
Subject: [PATCH 3/4] try fix

---
 .github/workflows/pr.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 74ffe3d0..3db76cc2 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -318,7 +318,8 @@ jobs:
       run: ln -s $(which apptainer) $(dirname apptainer)/singularity
     - name: Install containers
       run: |
-        if [ grep scripting ${{ needs.setup.outputs.repository-list }} ]; then
+        echo "${{ needs.setup.outputs.repository-list }}" > repository_list.txt
+        if grep -q scripting repository_list.txt; then
           singularity pull --dir /tmp docker://continuumio/anaconda3
           singularity pull --dir /tmp docker://rocker/tidyverse
         fi

From 3da19cab8875724d98039d37ac26c72ad2cc7d89 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Mon, 7 Aug 2023 12:00:12 +0200
Subject: [PATCH 4/4] Update tools/scripting/general.xml

---
 tools/scripting/general.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/scripting/general.xml b/tools/scripting/general.xml
index 9deea2ca..89844ab1 100644
--- a/tools/scripting/general.xml
+++ b/tools/scripting/general.xml
@@ -1,4 +1,4 @@
-<tool id="singularity_scriptrunner" name="scriptrunner" version="0.1.1" profile="22.05">
+<tool id="singularity_scriptrunner" name="scriptrunner" version="0.1" profile="22.05">
     <description>singularity</description>
     <creator>
         <person givenName="Matthias" familyName="Bernt" email="m.bernt@ufz.de" />