Update bam-readcount to v1.0.1 (bioconda#47911)

* feat: updates bam-readcount to version v1.0.1

* fix: removed -j2 flag from make as it caused errors in the build

* feat: adds sha256 of the tar.gz

* fix: removes from blacklist

* clean up recipe

* edit build.sh

* clean up recipe

* edit patch

* edit patch

* edit patch

* edit build.sh

* clean up recipe

* add macos target

* edit build.sh

* edit build.sh

* unfortunately have to skip OSX build

---------

Co-authored-by: Joshua Zhuang <[email protected]>
Co-authored-by: mencian <[email protected]>

build-fail-blacklist

@@ -309,7 +309,6 @@ recipes/biolite
 recipes/pauda
 recipes/hicbrowser
 recipes/vqsr_cnn
-recipes/bam-readcount
 recipes/mqc
 recipes/roprofile
 recipes/chanjo

recipes/bam-readcount/build.sh

@@ -1,5 +1,36 @@
-#!/bin/bash
+#!/bin/bash -euo
 
-cd $PREFIX
-cmake $SRC_DIR
-make -j 2
+wget https://github.com/boostorg/boost/releases/download/boost-1.85.0/boost-1.85.0-cmake.tar.gz
+
+mv boost-1.85.0-cmake.tar.gz vendor/boost-1.55-bamrc.tar.gz
+
+mkdir -p "${PREFIX}/bin"
+
+# Needed for building utils dependency
+export INCLUDES="-I{PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -pthread -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [ `uname` == Darwin ]; then
+    export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib -lz -lbz2"
+    export MACOSX_DEPLOYMENT_TARGET=10.13
+    # See https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk for -D_LIBCPP_DISABLE_AVAILABILITY
+    # export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+fi
+
+mkdir -p build
+pushd build
+cmake -S .. -B . -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_C_COMPILER="${CC}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	-Wno-dev -Wno-deprecated --no-warn-unused-cli
+
+make clean
+make CXX="${CXX} ${LDFLAGS}" CC="${CC}" CXXFLAGS="${CXXFLAGS}"
+
+chmod 755 bin/bam-readcount
+cp -f bin/bam-readcount "${PREFIX}/bin"
+popd

recipes/bam-readcount/meta.yaml

@@ -1,36 +1,49 @@
+{% set name = "bam-readcount" %}
+{% set version = "1.0.1" %}
+
 package:
-  name: bam-readcount
-  version: "0.8"
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://github.com/genome/bam-readcount/archive/v0.8.0.tar.gz
-  md5: 58d72588866f16f658ce4f40a3809af9
+  url: https://github.com/genome/{{ name }}/archive/v{{ version }}.tar.gz
+  sha256: 8ebf84d9efee0f2d3b43f0452dbf16b27337c960e25128f6a7173119e62588b8
 
 build:
-  number: 5
+  number: 0
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('bam-readcount', max_pin="x") }}
 
 requirements:
   build:
     - make
-    - cmake >=2.8.3
-    - {{ compiler('c') }}
+    - cmake
     - {{ compiler('cxx') }}
+    - {{ compiler('c') }}
   host:
     - zlib
-    - ncurses
-    - perl
-    - python
+    - pthread-stubs
+    - wget
+    - clangdev
   run:
     - python
-    - zlib
-    - ncurses
-    - perl
+    - pthread-stubs
 
 test:
   commands:
-    - bam-readcount 2>&1 | grep bam-readcount > /dev/null
+    - "bam-readcount 2>&1 | grep bam-readcount > /dev/null"
 
 about:
-  home: https://github.com/genome/bam-readcount
+  home: "https://github.com/genome/bam-readcount"
   license: MIT
-  summary: bam-readcount generates metrics at single nucleotide positions.
+  license_family: MIT
+  license_file: LICENSE
+  summary: "bam-readcount generates metrics at single nucleotide positions."
+  dev_url: "https://github.com/genome/bam-readcount"
+  doc_url: "https://github.com/genome/bam-readcount/blob/master/README.md"
+
+extra:
+  identifiers:
+    - doi:10.21105/joss.03722
+    - biotools:bam-readcount