diff --git a/recipes/ampliconsuite/build.sh b/recipes/ampliconsuite/build.sh new file mode 100644 index 0000000000000..2e0bd4e37c1ec --- /dev/null +++ b/recipes/ampliconsuite/build.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +set -ex + +# we have to slightly reorganize the AA src files to make everything work +mv ampliconarchitectlib/src/*.py ampliconarchitectlib/ + +# add init for ampliconarchitect and ampliconclassifier tools, so they can be imported by AmpliconSuite-pipeline +touch ampliconarchitectlib/__init__.py +touch ampliconclassifierlib/__init__.py + +# make the bin dir if it doesn't exist +mkdir -p $PREFIX/bin + +# copy driver scripts +# setup.py will handle this in the next release +cp AmpliconSuite-pipeline.py ${PREFIX}/bin/AmpliconSuite-pipeline.py +cp GroupedAnalysisAmpSuite.py ${PREFIX}/bin/GroupedAnalysisAmpSuite.py + +# Python command to install the package. +$PYTHON setup.py install --install-data aa_data_repo/ --single-version-externally-managed --record=record.txt diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml new file mode 100644 index 0000000000000..1b28858e896d9 --- /dev/null +++ b/recipes/ampliconsuite/meta.yaml @@ -0,0 +1,57 @@ +{% set AS_version="0.1555.2" %} +{% set AA_version="1.3.r5" %} +{% set AC_version="0.5.3" %} + +package: + name: ampliconsuite + version: {{ AS_version }} + +source: + # the sha256 sum is generate by doing + # $ wget -O- [URL] | shasum -a 256 + - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz + sha256: 1245d036c691821fcc2807e923010e29e3588796a72e63c36d2f630dae333ab9 + - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz + sha256: f103223da49901ef0d04d0886ed8ea86f23067df93b15424c5af6a95850f3777 + folder: ampliconarchitectlib + - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz + sha256: 222405cc78f12b6089e03831592161c207f1440f6a9b96ed8ace74c721d5df02 + folder: ampliconclassifierlib + +build: + noarch: python + number: 0 + +requirements: + build: + - python >=3 + - setuptools + - unzip + - wget + + run: + - python >=3 + - bwa + - cnvkit + - Flask + - future >=0.18.3 + - intervaltree + - matplotlib-base >=3.5.1 + - mscorefonts + - numpy >=1.22.4 + - pysam + - samtools + - scipy >=1.7.3 + +test: + commands: + - AmpliconSuite-pipeline.py -v + imports: + - paalib + - ampliconarchitectlib + - ampliconclassifierlib + +about: + home: https://github.com/AmpliconSuite + license: BSD 2-Clause License + summary: An end-to-end wrapper for focal amplification analysis from whole-genome sequencing using AmpliconArchitect and associated tools.