From bd716f6a1bba642617d2530f16f9fa0d72d2113e Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@users.noreply.github.com>
Date: Fri, 13 Dec 2019 14:10:06 +0100
Subject: [PATCH] [ci skip] Merge PR 19262

Merge PR #19262, commits were:
 * add gitter token
 * Maintain pysam 0.15.2 for medaka
---
 .github/workflows/CommentResponder.yml |  1 +
 recipes/pysam/0.15.2/build.sh          | 12 ++++++
 recipes/pysam/0.15.2/meta.yaml         | 51 ++++++++++++++++++++++++++
 3 files changed, 64 insertions(+)
 create mode 100644 recipes/pysam/0.15.2/build.sh
 create mode 100644 recipes/pysam/0.15.2/meta.yaml

diff --git a/.github/workflows/CommentResponder.yml b/.github/workflows/CommentResponder.yml
index 746fa5f90462e..60601261cd73b 100644
--- a/.github/workflows/CommentResponder.yml
+++ b/.github/workflows/CommentResponder.yml
@@ -18,6 +18,7 @@ jobs:
         ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
         QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
+        GITTER_TOKEN: ${{ secrets.GITTER_TOKEN }}
         CODE_SIGNING_KEY: ${{ secrets.CODE_SIGNING_KEY }}
         JOB_CONTEXT: ${{ toJson(github) }}
       uses: bioconda/bioconda-actions/bioconda_recipes_issue_responder/@issue_responder
diff --git a/recipes/pysam/0.15.2/build.sh b/recipes/pysam/0.15.2/build.sh
new file mode 100644
index 0000000000000..b69d0ef547fbd
--- /dev/null
+++ b/recipes/pysam/0.15.2/build.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+# linking htslib, see:
+# http://pysam.readthedocs.org/en/latest/installation.html#external
+# https://github.com/pysam-developers/pysam/blob/v0.9.0/setup.py#L79
+export CFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
+export CPPFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
+export LDFLAGS="-L$PREFIX/lib"
+
+export HTSLIB_LIBRARY_DIR=$PREFIX/lib
+export HTSLIB_INCLUDE_DIR=$PREFIX/include
+$PYTHON -m pip install . --ignore-installed --no-deps -vv
diff --git a/recipes/pysam/0.15.2/meta.yaml b/recipes/pysam/0.15.2/meta.yaml
new file mode 100644
index 0000000000000..585c477e8e95a
--- /dev/null
+++ b/recipes/pysam/0.15.2/meta.yaml
@@ -0,0 +1,51 @@
+{% set version = "0.15.2" %}
+{% set htslib_version = "1.9" %}
+{% set samtools_version = "1.9" %}
+{% set bcftools_version = "1.9" %}
+
+package:
+  name: pysam
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/pysam-developers/pysam/archive/v{{ version }}.tar.gz
+  sha256: 8cb3dd70f0d825086ac059ec2445ebd2ec5f14af73e7f1f4bd358966aaee5ed3
+
+build:
+  number: 4
+  binary_relocation: False # [linux]
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+  host:
+    - htslib {{ htslib_version }}
+    - samtools {{ samtools_version }}
+    - bcftools {{ bcftools_version }}
+    - cython
+    - python
+    - setuptools
+    - zlib
+    - curl
+    - libdeflate
+  run:
+    - samtools {{ samtools_version }}
+    - bcftools {{ bcftools_version }}
+    - python
+    - curl
+    - libdeflate
+
+test:
+  imports:
+    - pysam
+
+about:
+  home: https://github.com/pysam-developers/pysam
+  license: MIT
+  license_file: COPYING
+  summary: "Pysam is a python module for reading and manipulating Samfiles. It is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix."
+
+extra:
+  identifiers:
+    - biotools:pysam
+    - doi:10.1093/bioinformatics/btp352