Add ampliconsuite recipe (#41396)

* Add ampliconsuite * Fix ampliconsuite meta.yaml Fix ampliconsuite meta.yaml Fix ampliconsuite meta.yaml add "noarch: python" * Fix ampliconsuite meta.yaml * adjust recipe based on reviewer feedback * bugfix for ampliconarchitectlib src pathing * bump ampsuite version
bioconda · Jun 19, 2023 · bff136c · bff136c
1 parent 098bc7d
commit bff136c
Show file tree

Hide file tree

Showing 2 changed files with 78 additions and 0 deletions.
diff --git a/recipes/ampliconsuite/build.sh 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
@@ -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.