From dc39b5cf5401e94e8e4929b8cf61140280728eda Mon Sep 17 00:00:00 2001
From: Brad Chapman <chapmanb@fastmail.com>
Date: Mon, 26 Jun 2017 13:46:01 -0400
Subject: [PATCH] Update htslib to latest 1.5 release (#5052)

Bumps CONDA_HTSLIB and re-builds packages that reference it.
Pin pysam to CONDA_HTSLIB. Fixes chapmanb/bcbio-nextgen#1987
---
 recipes/libsequence/meta.yaml     |  1 +
 recipes/perl-bio-db-hts/meta.yaml |  8 +++++---
 recipes/pindel/meta.yaml          |  4 ++--
 recipes/pysam/meta.yaml           | 15 ++++++++-------
 scripts/env_matrix.yml            |  2 +-
 5 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/recipes/libsequence/meta.yaml b/recipes/libsequence/meta.yaml
index 71e9a0b903..198c1fe85a 100644
--- a/recipes/libsequence/meta.yaml
+++ b/recipes/libsequence/meta.yaml
@@ -15,6 +15,7 @@ requirements:
     - htslib {{CONDA_HTSLIB}}*
 build:
   number: 1
+  string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}"
 package:
   name: libsequence
   version: '1.9.1'
diff --git a/recipes/perl-bio-db-hts/meta.yaml b/recipes/perl-bio-db-hts/meta.yaml
index 93228b1704..18bbff80e4 100644
--- a/recipes/perl-bio-db-hts/meta.yaml
+++ b/recipes/perl-bio-db-hts/meta.yaml
@@ -28,9 +28,11 @@ requirements:
     - htslib {{CONDA_HTSLIB}}*
 
 test:
-  imports:
-    - Bio::DB::HTS
-    - Bio::DB::HTS::Faidx
+  # disable temporarily because of bug in conda-build
+  # https://github.com/conda/conda-build/issues/1967
+  #imports:
+  #  - Bio::DB::HTS
+  #  - Bio::DB::HTS::Faidx
 
 about:
   home: https://metacpan.org/pod/Bio::DB::HTS
diff --git a/recipes/pindel/meta.yaml b/recipes/pindel/meta.yaml
index 11f669079d..9209260fd6 100644
--- a/recipes/pindel/meta.yaml
+++ b/recipes/pindel/meta.yaml
@@ -24,8 +24,8 @@ requirements:
 
 test:
   commands:
-    - "pindel -h 2>&1 | grep 'Pindel version'"
-    - "pindel2vcf  --help | grep Example:"
+    - 'pindel -h 2>&1 | grep "Pindel version"'
+    - 'pindel2vcf  --help | grep Example:'
 
 about:
   home: http://gmt.genome.wustl.edu/packages/pindel/index.html
diff --git a/recipes/pysam/meta.yaml b/recipes/pysam/meta.yaml
index 68c9f2ed38..a741e57f97 100644
--- a/recipes/pysam/meta.yaml
+++ b/recipes/pysam/meta.yaml
@@ -10,17 +10,18 @@ source:
       - osx_rpath.patch [osx]
 
 build:
-    number: 1
+    number: 2
     skip: False
     binary_relocation: False # [linux]
+    string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}"
 
 requirements:
     build:
         - gcc  # [linux]
         - llvm # [osx]
-        - htslib >=1.4.1
-        - samtools >=1.4.1
-        - bcftools >=1.4.1
+        - htslib {{CONDA_HTSLIB}}*
+        - samtools {{CONDA_HTSLIB}}*
+        - bcftools {{CONDA_HTSLIB}}*
         - cython
         - python
         - setuptools
@@ -29,9 +30,9 @@ requirements:
 
     run:
         - libgcc # [linux]
-        - htslib >=1.4.1
-        - samtools >=1.4.1
-        - bcftools >=1.4.1
+        - htslib {{CONDA_HTSLIB}}*
+        - samtools {{CONDA_HTSLIB}}*
+        - bcftools {{CONDA_HTSLIB}}*
         - python
         - zlib
         - curl
diff --git a/scripts/env_matrix.yml b/scripts/env_matrix.yml
index c18e8496d9..24bb95a5fd 100644
--- a/scripts/env_matrix.yml
+++ b/scripts/env_matrix.yml
@@ -2,7 +2,7 @@ CONDA_PY:
   - 27
   - 35
   - 36
-CONDA_HTSLIB: "1.4"
+CONDA_HTSLIB: "1.5"
 CONDA_BOOST: "1.61"
 CONDA_R: "3.3.2"
 CONDA_PERL: "5.22.0"