Update xengsort Docker image:

* bump the tool to version 2.0.5
* support building using GHA

.github/workflows/docker_build.yml

@@ -15,6 +15,7 @@ on:
           - 'base'
           - 'common'
           - 'snpeff'
+          - 'xengsort'
 
 env:
   REGISTRY: ${{ vars.REGISTRY }}

docs/CHANGELOG.rst

@@ -6,6 +6,16 @@ All notable changes to this project are documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
 
+==========
+2024-05-03
+==========
+
+Changed
+-------
+- Upgrade xengsort to version 2.0.5 in 
+  ``public.ecr.aws/genialis/resolwebio/xengsort:2.0.0`` Docker image
+
+
 ==========
 2024-04-08
 ==========

resolwe_docker_images/xengsort/Dockerfile

@@ -1,4 +1,5 @@
-FROM public.ecr.aws/genialis/resolwebio/common:3.2.0
+FROM public.ecr.aws/genialis/resolwebio/common:4.1.1
 
-MAINTAINER Resolwe Bioinformatics authors https://github.com/genialis/resolwe-bio
+LABEL maintainer="Resolwe Bioinformatics authors https://github.com/genialis/resolwe-bio"
 
+RUN pip3 install -U pip

resolwe_docker_images/xengsort/README.md

@@ -2,10 +2,10 @@
 
 The image is based on the [`public.ecr.aws/genialis/resolwebio/common`](
 https://gallery.ecr.aws/genialis/resolwebio/common) image, derived from the
-`ubuntu-20.04` version of [`public.ecr.aws/genialis/base`](
+`ubuntu-22.04` version of [`public.ecr.aws/genialis/base`](
 https://gallery.ecr.aws/genialis/resolwebio/base) image.
 
 Included bioinformatics tools:
 ------------------------------
-* Xengsort (1.1.0)
+* Xengsort (2.0.5)
 * ntCard (1.2.2)

resolwe_docker_images/xengsort/build.env

@@ -0,0 +1,3 @@
+BASE_IMAGE=public.ecr.aws/genialis/resolwebio/common:4.1.1
+REPOSITORY=resolwebio/xengsort
+TAG=2.0.0

resolwe_docker_images/xengsort/packages-manual.txt

@@ -1,2 +1 @@
-xengsort
-ntcard
+ntcard

resolwe_docker_images/xengsort/packages-python3.txt

@@ -1,7 +1,14 @@
-# Required by xengsort.
-numpy==1.21.6 --hash=sha256:4aa48afdce4660b0076a00d80afa54e8a97cd49f457d68a4342d188a09451c1a
-numba==0.55.1 --hash=sha256:6d0042371880fa56ed58be27502b11a08bff0b6335f0ebde82af1a7aef5e1287
-h5py==3.6.0 --hash=sha256:542781d50e1182b8fb619b1265dfe1c765e18215f818b0ab28b2983c28471325
+xengsort==2.0.5 --hash=sha256:42e2c819ba38d6682d499fdd605fa2cf1586ce741d85babeb2cb100a53d170ce
 
-# Required by numba.
-llvmlite==0.38.0 --hash=sha256:48558fddce5ff351f9de98beff35888aa351598e5635b3b91d67ec9e10d458cc
+# Requirements
+numpy==1.26.4 --hash=sha256:ffa75af20b44f8dba823498024771d5ac50620e6915abac414251bd971b4529f
+numba==0.59.1 --hash=sha256:525ef3f820931bdae95ee5379c670d5c97289c6520726bc6937a4a7d4230ba24
+jsonargparse==4.28.0 --hash=sha256:9dcda241349547e8035c630d51de73b8b4ba67bdc2b014d7f76734d404e82518
+pytest==8.2.0 --hash=sha256:1733f0620f6cda4095bbf0d9ff8022486e91892245bb9e7d5542c018f612f233
+exceptiongroup==1.2.1 --hash=sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad
+llvmlite==0.42.0 --hash=sha256:763f8d8717a9073b9e0246998de89929071d15b47f254c10eef2310b9aac033d
+tomli==2.0.1 --hash=sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc
+iniconfig==2.0.0 --hash=sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374
+packaging==24.0 --hash=sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5
+pluggy==1.5.0 --hash=sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669
+PyYAML==6.0.1 --hash=sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515