diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 92af377f0..981991c01 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -6,8 +6,6 @@ tag_name = v{new_version} [bumpversion:file:CITATION.cff] -[bumpversion:file:BALSAMIC/containers/balsamic/Dockerfile] - [bumpversion:file:BALSAMIC/__version__.py] [bumpversion:file:BALSAMIC/__init__.py] diff --git a/.github/workflows/docker_build_push.yml b/.github/workflows/docker_build_push.yml index c94d28b2b..689da600c 100644 --- a/.github/workflows/docker_build_push.yml +++ b/.github/workflows/docker_build_push.yml @@ -11,7 +11,7 @@ jobs: strategy: fail-fast: true matrix: - container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs] + container-name: [align_qc, annotate, ascatNgs, cnvpytor, coverage_qc, delly, somalier, varcall_cnvkit, varcall_py3, varcall_py27, vcf2cytosure] steps: - name: Git checkout id: git_checkout diff --git a/.github/workflows/docker_build_push_release.yml b/.github/workflows/docker_build_push_release.yml index 59c9dc7af..040a4dae8 100644 --- a/.github/workflows/docker_build_push_release.yml +++ b/.github/workflows/docker_build_push_release.yml @@ -10,7 +10,7 @@ jobs: strategy: fail-fast: true matrix: - container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs] + container-name: [align_qc, annotate, ascatNgs, cnvpytor, coverage_qc, delly, somalier, varcall_cnvkit, varcall_py3, varcall_py27, vcf2cytosure] steps: - name: Git checkout id: git_checkout diff --git a/.github/workflows/docker_build_test_pull_request.yml b/.github/workflows/docker_build_test_pull_request.yml index d6fe68bf8..455a9c5c5 100644 --- a/.github/workflows/docker_build_test_pull_request.yml +++ b/.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_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs] + container-name: [align_qc, annotate, ascatNgs, cnvpytor, coverage_qc, delly, somalier, varcall_cnvkit, varcall_py3, varcall_py27, vcf2cytosure] steps: - name: Git checkout id: git_checkout diff --git a/BALSAMIC/constants/cache.py b/BALSAMIC/constants/cache.py index 420946ef6..27e32f03e 100644 --- a/BALSAMIC/constants/cache.py +++ b/BALSAMIC/constants/cache.py @@ -42,7 +42,6 @@ class DockerContainers(StrEnum): ALIGN_QC: str = "align_qc" ANNOTATE: str = "annotate" ASCAT: str = "ascatNgs" - BALSAMIC: str = "balsamic" CNVKIT: str = "varcall_cnvkit" CNVPYTOR: str = "cnvpytor" COVERAGE_QC: str = "coverage_qc" diff --git a/BALSAMIC/containers/balsamic/Dockerfile b/BALSAMIC/containers/balsamic/Dockerfile deleted file mode 100644 index 9a3f1bf76..000000000 --- a/BALSAMIC/containers/balsamic/Dockerfile +++ /dev/null @@ -1,34 +0,0 @@ -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="Hassan Foroughi hassan dot foroughi at scilifelab dot se" -LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer" -LABEL about.version="12.0.2" - -ENV PATH="/opt/conda/bin/:${PATH}" -ENV MUSL_LOCPATH="/usr/share/i18n/locales/musl" -ENV LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 - -RUN apk add --no-cache bash gcc git zlib-dev musl-dev libintl libffi-dev openssl-dev hdf5-dev jpeg-dev - -# Locale installation -RUN apk add --no-cache --virtual .locale_tmp cmake make gettext-dev && \ - git clone https://gitlab.com/rilian-la-te/musl-locales && \ - cd musl-locales && cmake -DLOCALE_PROFILE=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr . && make && make install && \ - cd .. && rm -r musl-locales && \ - apk del .locale_tmp - -ARG WORK_DIR=project -ARG CONTAINER_NAME - -# Copy all project files -COPY . /${WORK_DIR} - -RUN cd /${WORK_DIR}/BALSAMIC/containers/${CONTAINER_NAME}/ && /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME} -RUN cd /${WORK_DIR} && pip install --upgrade --no-cache-dir . - -# Clean work environment -RUN rm -rf /${WORK_DIR} && conda clean --all --yes diff --git a/BALSAMIC/containers/balsamic/__init__.py b/BALSAMIC/containers/balsamic/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/BALSAMIC/containers/balsamic/balsamic.sh b/BALSAMIC/containers/balsamic/balsamic.sh deleted file mode 100644 index 92f21aa23..000000000 --- a/BALSAMIC/containers/balsamic/balsamic.sh +++ /dev/null @@ -1 +0,0 @@ -conda env update -n base --file "${1}".yaml diff --git a/BALSAMIC/containers/balsamic/balsamic.yaml b/BALSAMIC/containers/balsamic/balsamic.yaml deleted file mode 100644 index 4b94d6092..000000000 --- a/BALSAMIC/containers/balsamic/balsamic.yaml +++ /dev/null @@ -1,9 +0,0 @@ -channels: - - conda-forge - - bioconda - - defaults - -dependencies: - - conda-forge::python=3.11 - - conda-forge::pip==23.2.1 - - conda-forge::pygraphviz==1.11 diff --git a/BALSAMIC/snakemake_rules/concatenation/concatenation.rule b/BALSAMIC/snakemake_rules/concatenation/concatenation.rule index 2c89f2382..270db4961 100644 --- a/BALSAMIC/snakemake_rules/concatenation/concatenation.rule +++ b/BALSAMIC/snakemake_rules/concatenation/concatenation.rule @@ -7,8 +7,6 @@ rule concatenate: fastq = concat_dir + "{sample}_R_{read}.fastq.gz" benchmark: Path(benchmark_dir, "{sample}_R_{read}.tsv").as_posix() - singularity: - Path(singularity_image, "balsamic.sif").as_posix() params: fastq_dir = fastq_dir, concat_dir = concat_dir, diff --git a/BALSAMIC/snakemake_rules/quality_control/qc_metrics.rule b/BALSAMIC/snakemake_rules/quality_control/qc_metrics.rule index c894f41e3..e8a76454a 100644 --- a/BALSAMIC/snakemake_rules/quality_control/qc_metrics.rule +++ b/BALSAMIC/snakemake_rules/quality_control/qc_metrics.rule @@ -24,8 +24,6 @@ rule collect_custom_qc_metrics: config_path = analysis_dir + config["analysis"]["case_id"] + ".json", collect_qc_metrics_script = get_script_path("collect_qc_metrics.py"), housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "qc-metrics"} - singularity: - Path(singularity_image, "balsamic.sif").as_posix() threads: get_threads(cluster_config, "collect_custom_qc_metrics") message: diff --git a/BALSAMIC/snakemake_rules/quality_control/report.rule b/BALSAMIC/snakemake_rules/quality_control/report.rule index 57067fc2d..ce93a440f 100644 --- a/BALSAMIC/snakemake_rules/quality_control/report.rule +++ b/BALSAMIC/snakemake_rules/quality_control/report.rule @@ -9,8 +9,6 @@ rule cnv_report: params: housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "clinical"}, cnv_report_script= get_script_path("generate_cnv_report.py"), - singularity: - Path(singularity_image, "balsamic.sif").as_posix() threads: get_threads(cluster_config, "cnv_report") message: diff --git a/CHANGELOG.rst b/CHANGELOG.rst index ae54d4665..a36ce6742 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,5 +1,6 @@ [X.X.X] ------- + Added: ^^^^^^ * Fastq concatenation https://github.com/Clinical-Genomics/BALSAMIC/pull/1069 @@ -35,6 +36,7 @@ Fixed: Removed: ^^^^^^^ * Config folder https://github.com/Clinical-Genomics/BALSAMIC/pull/1175 +* Balsamic container https://github.com/Clinical-Genomics/BALSAMIC/pull/1220 [12.0.2] -------- diff --git a/tests/conftest.py b/tests/conftest.py index 2cdd74bbf..5f18a88c8 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -936,7 +936,6 @@ def fixture_develop_containers() -> Dict[str, str]: DockerContainers.ASCAT.value: "docker://clinicalgenomics/balsamic:develop-ascatNgs", DockerContainers.VCF2CYTOSURE.value: "docker://clinicalgenomics/balsamic:develop-vcf2cytosure", DockerContainers.PYTHON_3.value: "docker://clinicalgenomics/balsamic:develop-varcall_py3", - DockerContainers.BALSAMIC.value: "docker://clinicalgenomics/balsamic:develop-balsamic", DockerContainers.SOMALIER.value: "docker://clinicalgenomics/balsamic:develop-somalier", DockerContainers.CNVPYTOR.value: "docker://clinicalgenomics/balsamic:develop-cnvpytor", DockerContainers.ALIGN_QC.value: "docker://clinicalgenomics/balsamic:develop-align_qc",