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Conda recipe #404

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merged 4 commits into from
Dec 7, 2023
Merged

Conda recipe #404

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c83ad7a
add conda recipe and wrapper script
apriltuesday Nov 28, 2023
c20af12
fix biomart query and conda dependencies
apriltuesday Nov 28, 2023
5066e4a
clean up build.sh
apriltuesday Nov 28, 2023
1f3a405
single source of version for wrapper and setup
apriltuesday Dec 6, 2023
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41 changes: 41 additions & 0 deletions bin/cmat/cmat
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#!/usr/bin/env bash

# This is a wrapper around CMAT for packaging the Conda recipe, based largely on the
# ones in Andries Feder's Cladebreaker (https://github.com/andriesfeder/cladebreaker)
# and Robert A. Petit III's Bactopia (https://bactopia.github.io).

VERSION=3.0.6.dev3
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Is it worth moving the version to a text file and read that from both the setup.py and this wrapper script?

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I think there's a chicken and egg problem, because this wrapper script uses the version to figure out where the shared files are, which presumably would include the separate text file...

Perhaps the conda build script could modify this wrapper to include the correct version number, but I'd have to think it through.

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Is there not a better way to store the version, especially when there's also the {% set version = "3.0.6.dev3" %} at the meta.yaml file?
We end up having the same information in different places, no?

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Yes, right now the version is in 3 places, which is not great...

I think the version has to be in at least 2 places though, i.e. somewhere in this repo and in bioconda-recipes (which is what everything in the conda directory is reflecting).

I will try to get the setup.py and the wrapper script to use a single source though.

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I managed to get this working with 2 sources of version without too much difficulty. I also created #406 for automating the conda release which I believe should let us have just 1 source of version, as the automated release would generate the meta.yaml file using the same VERSION file.

CONDA_ENV=$(which cmat | sed 's=bin/cmat==')
CMAT_NF="${CONDA_ENV}/share/cmat-${VERSION}/pipelines"
MAPPINGS_FILE="${CONDA_ENV}/share/cmat-${VERSION}/mappings/latest_mappings.tsv"

if [[ $# == 0 ]]; then
echo "ClinVar Mapping and Annotation Toolkit (cmat) - v${VERSION}"
echo ""
echo "Available commands (use --help to print usage):"
echo " * cmat annotate - Annotate ClinVar XML file"
echo " * cmat generate-curation - Generate term curation spreadsheet"
echo " * cmat export-curation - Export term curation spreadsheet"
echo ""
exit
fi

if [[ "$1" == "version" ]] || [[ "$1" == "--version" ]]; then
echo "cmat ${VERSION}"
exit
fi

# All other commands take an optional --mappings arg
# If not present, use the latest mappings file included with CMAT
MAPPINGS_ARG="--mappings ${MAPPINGS_FILE}"
if [[ "$*" == *"--mappings"* ]]; then
MAPPINGS_ARG=""
fi

if [[ "$1" == "annotate" ]]; then
nextflow run "${CMAT_NF}/annotation_pipeline.nf" "${@:1}" ${MAPPINGS_ARG}
elif [[ "$1" == "generate-curation" ]]; then
nextflow run "${CMAT_NF}/generate_curation_spreadsheet.nf" "${@:1}" ${MAPPINGS_ARG}
elif [[ "$1" == "export-curation" ]]; then
nextflow run "${CMAT_NF}/export_curation_spreadsheet.nf" "${@:1}" ${MAPPINGS_ARG}
fi
2 changes: 1 addition & 1 deletion cmat/consequence_prediction/common/biomart.py
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Expand Up @@ -41,7 +41,7 @@ def process_biomart_request(query):
# If there was an HTTP error, raise an exception. This will be caught by @retry.
result.raise_for_status()
# Some errors from BioMart come back as 200 but with an error message in the content.
if result.text.lower().startswith('query error'):
if result.text.lower().startswith('query error') or result.text.lower().startswith('<html>'):
raise requests.exceptions.HTTPError(result.text)
return result.text

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11 changes: 11 additions & 0 deletions conda/build.sh
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#!/bin/bash

$PYTHON -m pip install .

CMAT="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}"
mkdir -p ${PREFIX}/bin ${CMAT}

chmod 775 bin/cmat/*
cp bin/cmat/* ${PREFIX}/bin

mv bin/ mappings/ pipelines/ ${CMAT}
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61 changes: 61 additions & 0 deletions conda/meta.yaml
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{% set version = "3.0.6.dev3" %}

package:
name: cmat
version: {{ version }}

source:
url: https://github.com/EBIvariation/CMAT/archive/v{{version}}.tar.gz
sha256: 29bdeb28674486785c5f5825afa7d1237bd5dd2c76923145d68543f3a6bb5594

build:
number: 0
noarch: generic

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
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
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Not sure why these requirements have to be present in both host and run sections, but it's the only way I could get it to work...


test:
imports:
- cmat
commands:
- cmat
- cmat annotate --help

about:
home: https://github.com/EBIvariation/CMAT
summary: ClinVar Mapping and Annotation Toolkit
license: Apache-2.0
license_file: LICENSE

extra:
recipe-maintainers:
- apriltuesday
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -27,7 +27,7 @@ def get_requires():
long_description = fh.read()

setup(name='cmat',
version='3.0.5',
version='3.0.6.dev3',
author_email='[email protected]',
url='https://github.com/EBIvariation/CMAT',
packages=find_packages(),
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