Add GATK to snpeff docker image

genialis · Aug 29, 2024 · ef17c1b · ef17c1b
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diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -5,6 +5,15 @@ Change Log
 All notable changes to this project are documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
+==========
+2024-08-29
+==========
+
+Changed
+-------
+- Add GATK (v4.2.4.1) to
+  ``public.ecr.aws/genialis/resolwebio/snpeff:3.1.0`` Docker image
+
 
 ==========
 2024-08-08

diff --git a/resolwe_docker_images/snpeff/Dockerfile b/resolwe_docker_images/snpeff/Dockerfile
@@ -1,3 +1,5 @@
 FROM public.ecr.aws/genialis/resolwebio/base:ubuntu-22.04-14112023
 
 LABEL maintainer="Resolwe Bioinformatics authors https://github.com/genialis/resolwe-bio"
+
+RUN ln -s /usr/bin/python3 /usr/bin/python
diff --git a/resolwe_docker_images/snpeff/README.md b/resolwe_docker_images/snpeff/README.md
@@ -7,3 +7,4 @@ Included bioinformatics tools
 -----------------------------
 * SnpEff (5.1)
 * Tabix (1.13+ds)
+* GATK (4.2.4.1)
diff --git a/resolwe_docker_images/snpeff/build.env b/resolwe_docker_images/snpeff/build.env
@@ -1,3 +1,3 @@
 BASE_IMAGE=public.ecr.aws/genialis/resolwebio/base:ubuntu-22.04-14112023
 REPOSITORY=resolwebio/snpeff
-TAG=3.0.0
+TAG=3.1.0
diff --git a/resolwe_docker_images/snpeff/packages-manual.txt b/resolwe_docker_images/snpeff/packages-manual.txt
@@ -1 +1,2 @@
 snpeff
+gatk
diff --git a/resolwe_docker_images/snpeff/packages-manual/gatk.sh b/resolwe_docker_images/snpeff/packages-manual/gatk.sh
@@ -0,0 +1,15 @@
+#!/bin/bash -e
+
+. /var/cache/build/packages-manual/common.sh
+
+download_and_verify \
+    broadinstitute \
+    gatk \
+    4.2.4.1 \
+    2dc007f534cca1e29253864601e480ce24ce376b4b2bbd7a491571f9ecedc2e2 \
+    https://github.com/broadinstitute/gatk/releases/download/\${version}/gatk-\${version}.zip \
+    gatk-\${version}
+
+add_binary_path \
+    broadinstitute \
+    gatk
diff --git a/resolwe_docker_images/snpeff/packages-python3.txt b/resolwe_docker_images/snpeff/packages-python3.txt
@@ -0,0 +1,11 @@
+# Top-level packages.
+pandas==2.0.3 --hash=sha256:ba619e410a21d8c387a1ea6e8a0e49bb42216474436245718d7f2e88a2f8d7c0
+
+# Pandas dependencies.
+python_dateutil==2.8.2 --hash=sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9
+pytz==2023.3 --hash=sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb
+tzdata==2023.3 --hash=sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda
+openpyxl==3.1.2 --hash=sha256:f91456ead12ab3c6c2e9491cf33ba6d08357d802192379bb482f1033ade496f5
+et_xmlfile==1.1.0 --hash=sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada
+numpy==1.25.2 --hash=sha256:f08f2e037bba04e707eebf4bc934f1972a315c883a9e0ebfa8a7756eabf9e357
+