feat: add docker container for vcf2cytosure

.github/workflows/docker_build_push.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py36, balsamic, delly]
+        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py36, balsamic, delly, vcf2cytosure]
     steps:
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v1

.github/workflows/docker_build_push_release.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py36, balsamic, delly]
+        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py36, balsamic, delly, vcf2cytosure]
     steps:
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v1

.github/workflows/docker_build_test_pull_request.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py36, balsamic, delly]
+        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py36, balsamic, delly, vcf2cytosure]
     steps:
       - name: Git checkout
         id: git_checkout

BALSAMIC/config/balsamic_env.yaml

@@ -31,4 +31,6 @@ vcf_merge:
 delly:
   - delly
 ascatNgs:
-  -ascat
+  - ascat
+vcf2cytosure:
+  - vcf2cytosure

BALSAMIC/constants/common.py

@@ -79,6 +79,7 @@
     "delly": "delly",
     "ascatNgs": "ascatNgs",
     "sentieon": "sentieon",
+    "vcf2cytosure": "vcf2cytosure",
 }
 
 VALID_OPS = {

BALSAMIC/containers/annotate/annotate.yaml

@@ -10,5 +10,3 @@ dependencies:
   - bioconda::vcfanno=0.3.3
   - anaconda::gxx_linux-64=7.3.0
   - anaconda::pip=20.2.4
-  - pip:
-    - "--editable git+https://github.com/NBISweden/vcf2cytosure@0.5.1#egg=vcf2cytosure"

BALSAMIC/containers/balsamic/Dockerfile

@@ -1,6 +1,6 @@
-FROM continuumio/miniconda3:4.9.2-alpine
+FROM continuumio/miniconda3:4.10.3-alpine
 
-LABEL base_image="continuumio/miniconda3:4.9.2-alpine"
+LABEL base.image="continuumio/miniconda3:4.10.3-alpine"
 LABEL about.home="https://github.com/Clinical-Genomics/BALSAMIC"
 LABEL about.documentation="https://balsamic.readthedocs.io/"
 LABEL about.license="MIT License (MIT)"

BALSAMIC/containers/vcf2cytosure/Dockerfile

@@ -0,0 +1,20 @@
+FROM continuumio/miniconda3:4.10.3-alpine
+
+LABEL base.image="continuumio/miniconda3:4.10.3-alpine"
+LABEL about.home="https://github.com/Clinical-Genomics/BALSAMIC"
+LABEL about.documentation="https://balsamic.readthedocs.io/"
+LABEL about.license="MIT License (MIT)"
+LABEL about.maintainer="Ashwini Jeggari ashwini dot jeggari at scilifelab dot se"
+LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"
+
+ARG CONTAINER_NAME
+ENV PATH="/opt/${CONTAINER_NAME}/bin:${PATH}"
+ENV PYTHONPATH="/opt/${CONTAINER_NAME}"
+
+
+RUN apk add --no-cache bash gcc git python3
+
+RUN cd /opt \
+    && git clone https://github.com/NBISweden/vcf2cytosure.git \
+    && cd /opt/${CONTAINER_NAME}/  \
+    && pip install --no-cache-dir .

BALSAMIC/containers/vcf2cytosure/vcf2cytosure.yaml

@@ -0,0 +1 @@
+- vcf2cytosure=0.7.1

CHANGELOG.rst

@@ -8,11 +8,14 @@ Added:
 * Call umi variants using TNscope in bed defined regions #821
 * UMI duplication metrics to report in multiqc_picard_dups.json #844
 * QC default validation conditions (for not defined capture kits) #855
+* Docker container for vcf2cytosure #858
 * SVDB to the varcall_py36 container
+
 Changed:
 ^^^^^^^^
 
 * Merge QC metric extraction workflows #833
+* Changed the base-image for balsamic container to 4.10.3-alpine #869
 
 Fixed:
 ^^^^^^

container_tests/annotate/annotate.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 # Test if commands exist
 
-valid_commands=( "bcftools" "vcfanno" "vcf2cytosure" "genmod" "vep" "vep_install" )
+valid_commands=( "bcftools" "vcfanno" "genmod" "vep" "vep_install" )
 
 for valid_command in "${valid_commands[@]}"
 do

container_tests/vcf2cytosure/vcf2cytosure.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+# Test if commands exist
+
+valid_commands=( "pip" "vcf2cytosure" )
+
+for valid_command in "${valid_commands[@]}"
+do
+  if ! command -v "${valid_command}" &> /dev/null
+  then
+    echo "${valid_command} could not be found"
+    exit 1
+  else
+    echo "${valid_command} command is found and valid"
+  fi
+done