From 0ace3190f3b6d034ea94c9e9d8ec9c718bc91003 Mon Sep 17 00:00:00 2001 From: April Shen Date: Tue, 2 Jan 2024 10:33:34 +0000 Subject: [PATCH 1/3] tweaks to meta for bioconda --- conda/meta.yaml | 55 ++++++++++++++++++++++++++----------------------- 1 file changed, 29 insertions(+), 26 deletions(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 0721b906..69e11aa4 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -1,54 +1,57 @@ +{% set name = "cmat" %} {% set version = "3.1.0" %} package: - name: cmat + name: {{ name }} version: {{ version }} source: url: https://github.com/EBIvariation/CMAT/archive/v{{version}}.tar.gz - sha256: 29bdeb28674486785c5f5825afa7d1237bd5dd2c76923145d68543f3a6bb5594 + sha256: 1e46a83d3d7e46a41f9f62ff4af0c151851fbbebc1c6b129255f987d75b64079 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: - nextflow >=21.10 - python >=3.8,<3.10 # restriction from biopython - # From requirements.txt - - biopython==1.77 - - coverage==6.5.0 - - coveralls==3.3.1 - - jsonschema==3.2.0 - - numpy==1.24.3 - - pandas==1.5.3 - - pytest==7.2.2 - - pytest-cov==2.10.0 - - requests==2.31.0 - - requests-mock==1.8.0 - - retry==0.9.2 + - biopython ==1.77 + - coverage ==6.5.0 + - coveralls ==3.3.1 + - jsonschema ==3.2.0 + - numpy ==1.24.3 + - pandas ==1.5.3 + - pytest ==7.2.2 + - pytest-cov ==2.10.0 + - requests ==2.31.0 + - requests-mock ==1.8.0 + - retry ==0.9.2 run: - nextflow >=21.10.0 - python >=3.8,<3.10 - - biopython==1.77 - - coverage==6.5.0 - - coveralls==3.3.1 - - jsonschema==3.2.0 - - numpy==1.24.3 - - pandas==1.5.3 - - pytest==7.2.2 - - pytest-cov==2.10.0 - - requests==2.31.0 - - requests-mock==1.8.0 - - retry==0.9.2 + - biopython ==1.77 + - coverage ==6.5.0 + - coveralls ==3.3.1 + - jsonschema ==3.2.0 + - numpy ==1.24.3 + - pandas ==1.5.3 + - pytest ==7.2.2 + - pytest-cov ==2.10.0 + - requests ==2.31.0 + - requests-mock ==1.8.0 + - retry ==0.9.2 test: imports: - cmat commands: - cmat - - cmat annotate --help + # rm to avoid this: https://github.com/bioconda/bioconda-utils/issues/172 + - cmat annotate --help && rm -rf .nextflow about: home: https://github.com/EBIvariation/CMAT From 63da22abe9269de5cc87f581ad9aeeee6e175715 Mon Sep 17 00:00:00 2001 From: April Shen Date: Tue, 2 Jan 2024 10:50:21 +0000 Subject: [PATCH 2/3] add conda installation to readme --- README.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/README.md b/README.md index c785927c..46f97b4a 100644 --- a/README.md +++ b/README.md @@ -52,6 +52,19 @@ nextflow run ${CODE_ROOT}/pipelines/annotation_pipeline.nf \ --mappings ${LATEST_MAPPINGS} ``` +### Conda + +You can also install CMAT using Conda. +For example the following installs CMAT in a new environment called `cmat`, activates the environment, and prints usage: +```bash +conda create -n cmat -c conda-forge -c bioconda cmat +conda activate cmat +cmat +``` + +Note that with conda installation you can't invoke the pipelines directly via Nextflow, so you will need to use the corresponding `cmat` commands - e.g. `cmat annotate` instead of `nextflow run annotation_pipeline.nf`. +All the same command line options apply. + ## Run CMAT includes a main annotation pipeline (which also performs consequence and gene mapping), as well as two pipelines to help manage trait mapping curation. From 57d514a4319bf70cc70940781d84986fd6c3bde7 Mon Sep 17 00:00:00 2001 From: April Shen Date: Tue, 9 Jan 2024 14:47:06 +0000 Subject: [PATCH 3/3] update readme --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 46f97b4a..1c673fd0 100644 --- a/README.md +++ b/README.md @@ -85,6 +85,7 @@ cd ${ANNOTATION_ROOT} mkdir -p gene_mapping logs # Run the nextflow pipeline, resuming execution of previous attempt if possible. +# For conda, use instead: cmat annotate nextflow run ${CODE_ROOT}/pipelines/annotation_pipeline.nf \ --output_dir ${ANNOTATION_ROOT} \ --mappings ${LATEST_MAPPINGS} \ @@ -116,6 +117,7 @@ mkdir -p ${CURATION_ROOT} cd ${CURATION_ROOT} # Run the nextflow pipeline, resuming execution of previous attempt if possible. +# For conda, use instead: cmat generate-curation nextflow run ${CODE_ROOT}/pipelines/generate_curation_spreadsheet.nf \ --curation_root ${CURATION_ROOT} \ --mappings ${LATEST_MAPPINGS} \ @@ -143,6 +145,7 @@ Download the spreadsheet as a CSV file, making sure that all the data is visible cd ${CURATION_ROOT} # Run the nextflow pipeline, resuming execution of previous attempt if possible. +# For conda, use instead: cmat export-curation nextflow run ${CODE_ROOT}/pipelines/export_curation_spreadsheet.nf \ --input_csv ${CURATION_ROOT}/finished_curation_spreadsheet.csv \ --curation_root ${CURATION_ROOT} \