# HG changeset patch
# User rhpvorderman
# Date 1643799001 0
# Node ID 33412e85e6698560636f39ed5f6fd1bc665167d4
# Parent  7ae6b6b5d890f3797d35951ab06e7af2c154239b
"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"

diff -r 7ae6b6b5d890 -r 33412e85e669 CHANGES.md
--- a/CHANGES.md	Tue Dec 14 12:45:47 2021 +0000
+++ b/CHANGES.md	Wed Feb 02 10:50:01 2022 +0000
@@ -1,3 +1,8 @@
+version 1.1.0
+-------------
++ Add a container requirement to allow using docker or singularity.
++ Add an option to download all files at once contained in a zip file.
+
 version 1.0.2
 -------------
 + Remove some wrongly placed quotes
diff -r 7ae6b6b5d890 -r 33412e85e669 build_container.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build_container.sh	Wed Feb 02 10:50:01 2022 +0000
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+set -e
+DEFAULT_BASE_IMAGE="$1"
+
+python3 create_container_hash.py $DEFAULT_BASE_IMAGE
+mulled-build-files --namespace rhpvorderman build-and-test ./container_hash.tsv --verbose
+
diff -r 7ae6b6b5d890 -r 33412e85e669 complete_immunerepertoire.xml
--- a/complete_immunerepertoire.xml	Tue Dec 14 12:45:47 2021 +0000
+++ b/complete_immunerepertoire.xml	Wed Feb 02 10:50:01 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.1.0.alpha1">
+<tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.1.0">
 	<requirements>
         <requirement type="package" version="2.3">r-gridextra</requirement>
         <requirement type="package" version="3.0.0">r-ggplot2</requirement>
@@ -15,7 +15,7 @@
 		<requirement type="package" version="0.4">unrar</requirement>
 		<requirement type="package" version="16.02">p7zip</requirement>
 		<requirement type="package" version="4.6.0">findutils</requirement>
-   		<container type="docker">quay.io/rhpvorderman/mulled-v2-62aaeb9dad7d9973e676594c3aa69e605c73cd0c:80328e762d48b0d7b11c4fa41a5c09ca43d49db9-0</container>
+   		<container type="docker">quay.io/argalaxy/mulled-v2-62aaeb9dad7d9973e676594c3aa69e605c73cd0c:80328e762d48b0d7b11c4fa41a5c09ca43d49db9-0</container>
 	</requirements>
 	<description> </description>
 	<command interpreter="bash">
diff -r 7ae6b6b5d890 -r 33412e85e669 container_hash.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/container_hash.tsv	Wed Feb 02 10:50:01 2022 +0000
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+r-gridextra=2.3,r-ggplot2=3.0.0,r-plyr=1.8.4,r-data.table=1.11.4,r-reshape2=1.4.3,r-lymphclon=1.3.0,r-stringi=1.2.4,r-stringr=1.3.1,circos=0.69.6,circos-tools=0.23,tar=1.34,unzip=6.0,unrar=0.4,p7zip=16.02,findutils=4.6.0,font-ttf-ubuntu=0.83	bgruening/busybox-bash:latest	0
diff -r 7ae6b6b5d890 -r 33412e85e669 create_container_hash.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_container_hash.py	Wed Feb 02 10:50:01 2022 +0000
@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+
+import sys
+
+from xml.etree import ElementTree
+from xml.etree.ElementTree import Element
+
+DEFAULT_BASE_IMAGE = "bgruening/busybox-bash:latest"
+def main():
+    try:
+        base_image = sys.argv[1]
+    except IndexError:
+        base_image = DEFAULT_BASE_IMAGE
+    tool = ElementTree.parse("complete_immunerepertoire.xml").getroot()
+    requirements: Element = tool.find("requirements")
+    packages = []
+    for req in requirements.findall("requirement"):
+        if req.get("type") == "package":
+            name = req.text
+            version = req.get("version")
+            package_string = f"{name}={version}"
+            packages.append(package_string)
+    with open("container_hash.tsv", mode="wt") as container_hash_file:
+        container_hash_file.write("#targets\tbase_image\timage_build\n")
+        container_hash_file.write(",".join(packages) + f"\t{base_image}\t0\n")
+
+
+if __name__ == "__main__":
+    main()
diff -r 7ae6b6b5d890 -r 33412e85e669 involucro
Binary file involucro has changed
diff -r 7ae6b6b5d890 -r 33412e85e669 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Tue Dec 14 12:45:47 2021 +0000
+++ b/report_clonality/r_wrapper.sh	Wed Feb 02 10:50:01 2022 +0000
@@ -9,6 +9,8 @@
 filterproductive=$7
 clonality_method=$8
 
+ALL_OUTPUTS_ZIP="$outputDir/all_outputs.zip"
+
 dir="$(cd "$(dirname "$0")" && pwd)"
 useD="false"
 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
@@ -334,9 +336,36 @@
 	echo "</div>" >> $outputFile
 fi
 
+
+# Create zip file with all download files
+# Use 7za as it is packaged in the container already.
+cd "$outputDir" || exit 1
+
+7za a -tzip "$ALL_OUTPUTS_ZIP" -- \
+  allUnique.txt VFFrequency.txt VFrequency.txt \
+  JFrequency.txt DReadingFrame.txt CDR3LengthPlot.txt \
+  AAComposition.txt clonalityComplete.txt
+
+if [[ "$useD" == "true" ]] ; then
+  7za a -tzip "$ALL_OUTPUTS_ZIP" -- \
+  DFFrequency.txt DFrequency.txt
+fi
+for sample in $samples; do
+  if [[ "$useD" == "true" ]] ; then
+    7za a -tzip "$ALL_OUTPUTS_ZIP" -- \
+    "HeatmapVD_$sample.txt" "HeatmapDJ_$sample.txt" \
+    "${sample}_VD_circos.txt" "${sample}_DJ_circos.txt"
+  fi
+  7za a -tzip "$ALL_OUTPUTS_ZIP" -- \
+  "HeatmapVJ_$sample.txt" "${sample}_VJ_circos.txt"
+done
+
+cd $dir || exit 1
+
 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
+echo "<tr><td>All outputs below in a zip file</td><td><a href='$ALL_OUTPUTS_ZIP'>Download</a></td></tr>" >> $outputFile
 echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile
 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>" >> $outputFile
 
diff -r 7ae6b6b5d890 -r 33412e85e669 tests/__pycache__/test_imgt.cpython-39-pytest-6.2.5.pyc
Binary file tests/__pycache__/test_imgt.cpython-39-pytest-6.2.5.pyc has changed
diff -r 7ae6b6b5d890 -r 33412e85e669 tests/test_imgt.py
--- a/tests/test_imgt.py	Tue Dec 14 12:45:47 2021 +0000
+++ b/tests/test_imgt.py	Wed Feb 02 10:50:01 2022 +0000
@@ -77,6 +77,12 @@
     docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
                   "-v", f"{sample}:{sample}",
                   "-w", str(working_dir),
+                  # Run as current user which allows deletion of files.
+                  # It also mitigates some security considerations
+                  "-u", f"{os.getuid()}:{os.getgid()}",
+                  # Run with default seccomp profile to mitigate mitigation slowdown
+                  # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html
+                  "--security-opt", "seccomp=unconfined",
                   get_container()] + cmd
     with open(temp_dir / "stderr", "wt") as stderr_file:
         with open(temp_dir / "stdout", "wt") as stdout_file: