Merge pull request #404 from apriltuesday/conda

Conda recipe
EBIvariation · Dec 7, 2023 · 4d367cd · 4d367cd
2 parents d55aced + 1f3a405
commit 4d367cd
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Showing 6 changed files with 118 additions and 2 deletions.
diff --git a/bin/cmat/VERSION b/bin/cmat/VERSION
@@ -0,0 +1 @@
+3.0.6.dev4
diff --git a/bin/cmat/cmat b/bin/cmat/cmat
@@ -0,0 +1,41 @@
+#!/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).
+
+CONDA_ENV=$(which cmat | sed 's=bin/cmat==')
+VERSION=$(cat "${CONDA_ENV}/bin/VERSION")
+CMAT_NF="${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
diff --git a/cmat/consequence_prediction/common/biomart.py b/cmat/consequence_prediction/common/biomart.py
@@ -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
 

diff --git a/conda/build.sh b/conda/build.sh
@@ -0,0 +1,11 @@
+#!/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}
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -0,0 +1,61 @@
+{% set version = "3.0.6.dev4" %}
+
+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
+
+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
diff --git a/setup.py b/setup.py
@@ -6,6 +6,8 @@
 # allow setup.py to be run from any path
 os.chdir(os.path.normpath(os.path.join(os.path.abspath(__file__), os.pardir)))
 
+version = open(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'bin', 'cmat', 'VERSION')).read().strip()
+
 
 def get_requires():
     requires = []
@@ -27,7 +29,7 @@ def get_requires():
     long_description = fh.read()
 
 setup(name='cmat',
-      version='3.0.5',
+      version=version,
       author_email='[email protected]',
       url='https://github.com/EBIvariation/CMAT',
       packages=find_packages(),