From 530bcc9945cff18376dcda7d4d610c23cfb403a7 Mon Sep 17 00:00:00 2001 From: maxibor Date: Thu, 3 Nov 2022 14:32:51 +0100 Subject: [PATCH] fix: update versions to fix #37 fix: remove platform specific dependancies fix: fix container update: version update --- .github/workflows/ci.yml | 2 +- .github/workflows/linting.yml | 2 +- CHANGELOG.md | 6 +++ Dockerfile | 11 ++--- environment.yml | 92 +++++++++++++++++++++++++---------- nextflow.config | 2 +- 6 files changed, 78 insertions(+), 37 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 356b5bc..1b148b5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -22,7 +22,7 @@ jobs: - name: Pull docker image run: | docker pull nfcore/coproid:dev - docker tag nfcore/coproid:dev nfcore/coproid:1.1 + docker tag nfcore/coproid:dev nfcore/coproid:1.1.1 - name: Run pipeline with test data run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1e0827a..3af93a7 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -45,6 +45,6 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==1.9 - name: Run nf-core lint run: nf-core lint ${GITHUB_WORKSPACE} diff --git a/CHANGELOG.md b/CHANGELOG.md index 54bc43c..1711aa1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # nf-core/coproid: Changelog +## v.1.1.1 + +### Fixed + +- Fix [#37](https://github.com/nf-core/coproid/issues/37) with conda environment and docker container update + ## v1.1 - Update mapped basepair count to be quicker and include it in report [#14](https://github.com/nf-core/coproid/pull/14) diff --git a/Dockerfile b/Dockerfile index 5faa963..0db7838 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,15 +1,12 @@ -FROM nfcore/base:1.9 +FROM condaforge/mambaforge LABEL authors="Maxime Borry" \ description="Docker image containing all software requirements for the nf-core/coproid pipeline" # Install the conda environment COPY environment.yml / -RUN conda env create -f /environment.yml && conda clean -a -RUN conda env export --name nf-core-coproid-1.1 > nf-core-coproid-1.1.yml -ENV PATH /opt/conda/envs/nf-core-coproid-1.1/bin:$PATH - -# Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-coproid-1.1 > nf-core-coproid-1.1.yml +RUN mamba env create -f /environment.yml && mamba clean -a +RUN mamba env export --name nf-core-coproid-1.1.1 > nf-core-coproid-1.1.1.yml +ENV PATH /opt/conda/envs/nf-core-coproid-1.1.1/bin:$PATH # Numba cache dir patch ENV NUMBA_CACHE_DIR /tmp diff --git a/environment.yml b/environment.yml index cb67af9..e02a26c 100644 --- a/environment.yml +++ b/environment.yml @@ -1,32 +1,70 @@ -# You can use this file to create a conda environment for this pipeline: -# conda env create -f environment.yml -name: nf-core-coproid-1.1 +name: nf-core-coproid-1.1.1 channels: - conda-forge - - maxibor - bioconda - defaults dependencies: - - conda-forge::openblas=0.3.7 - - bioconda::adapterremoval=2.3.1 - - conda-forge::bokeh=2.0.1 - - bioconda::bowtie2=2.3.5.1 - - bioconda::damageprofiler=0.4.9 - - bioconda::fastqc=0.11.9 - - conda-forge::jupyter=1.0.0 - - bioconda::kraken2=2.0.8_beta - - conda-forge::notebook=6.0.3 - - conda-forge::nbconvert=5.6.1 - - bioconda::pmdtools=0.60 - - bioconda::pysam=0.15.3 - - bioconda::samtools=1.10 - - maxibor::sourcepredict=0.5 - - conda-forge::scipy=1.4.1 - - conda-forge::matplotlib=3.2.1 - - bioconda::multiqc=1.7 - - conda-forge::jupyter_contrib_nbextensions=0.5.1 - - conda-forge::plotnine=0.6.0 - - conda-forge::markdown=3.2.1 - - conda-forge::pymdown-extensions=7.0 - - conda-forge::pygments=2.6.1 - - conda-forge::tbb=2020.1 + - adapterremoval=2.3.1 + - blast=2.11.0 + - bokeh=2.4.3 + - bottleneck=1.3.5 + - bowtie2=2.5.0 + - damageprofiler=0.4.9 + - fastqc=0.11.9 + - htslib=1.12 + - ipykernel=6.16.2 + - ipython=8.6.0 + - ipython_genutils=0.2.0 + - ipywidgets=8.0.2 + - jupyter=1.0.0 + - jupyter_contrib_core=0.4.0 + - jupyter_contrib_nbextensions=0.5.1 + - jupyter_core=4.11.2 + - jupyter_highlight_selected_word=0.2.0 + - jupyter_latex_envs=1.4.6 + - jupyter_nbextensions_configurator=0.4.1 + - jupyterlab_widgets=3.0.3 + - kraken2=2.1.2 + - make=4.3 + - markdown=3.2.1 + - multiqc=1.7 + - nbconvert=5.6.1 + - networkx=2.5.1 + - numpy=1.22.4 + - openjdk=11.0.8 + - pandas=1.5.1 + - pandocfilters=1.5.0 + - pip=22.3 + - plotnine=0.6.0 + - pmdtools=0.60 + - pysam=0.16.0.1 + - python=3.9.9 + - samtools=1.12 + - sed=4.8 + - sqlite=3.37.0 + - yaml=0.2.5 + - pip: + - cachecontrol==0.12.11 + - cython==0.29.32 + - ete3==3.1.2 + - h5py==3.7.0 + - hdmedians==0.14.2 + - joblib==1.2.0 + - jupyter-client==6.1.12 + - jupyter-console==6.4.0 + - llvmlite==0.39.1 + - lockfile==0.12.2 + - matplotlib==3.5.3 + - msgpack==1.0.4 + - natsort==8.2.0 + - numba==0.56.3 + - pynndescent==0.5.8 + - pyyaml==5.4.1 + - scikit-bio==0.5.7 + - scikit-learn==1.1.3 + - scipy==1.8.1 + - sourcepredict==0.5 + - threadpoolctl==3.1.0 + - tqdm==4.64.1 + - umap-learn==0.5.3 + - pymdown-extensions \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 376d4b7..719e6c6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -133,7 +133,7 @@ manifest { description = 'Coprolite Identification' mainScript = 'main.nf' nextflowVersion = '>=19.10.0' - version = '1.1' + version = '1.1.1' } // Function to ensure that resource requirements don't go beyond