[ci skip] Merge PR 30300

Merge PR bioconda#30300, commits were: * Skip OSX for now - throws 'dyld: Symbol not found:_dyld_enumerate_tlv_storage'. Seemingly related issues: d-language-server/dls#60 https://forum.dlang.org/thread/[email protected]?page=1 The CF ldc package likely needs updated and rebuilt on OS X. * Remove from blacklist. * Update sambamba to 0.8.1.
salvoc81 · Aug 28, 2021 · 00e9a44 · 00e9a44
1 parent 8583492
commit 00e9a44
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Showing 4 changed files with 37 additions and 19 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -168,7 +168,6 @@ recipes/megahit
 recipes/atac
 
 # ldc requires a rebuild
-recipes/sambamba
 recipes/sambamba/0.5.9
 
 # incompatible with htslib >1.10

diff --git a/recipes/sambamba/build.sh b/recipes/sambamba/build.sh
@@ -5,11 +5,9 @@ export C_INCLUDE_PATH=${PREFIX}/include
 export LIBRARY_PATH=${PREFIX}/lib
 
 if [ $(uname) == "Darwin" ]; then
- export LDFLAGS="-headerpad_max_install_names $LDFLAGS"
+ export LDFLAGS="-headerpad_max_install_names ${LDFLAGS}"
 fi
-sed -i.bak 's/ gcc / $(CC) /g' Makefile
-make CC=$CC LIBRARY_PATH=$PREFIX/lib
+
+make CC=${CC} LIBRARY_PATH=${PREFIX}/lib prefix=${PREFIX}
 make test
-mkdir -p ${PREFIX}/bin
-ls -l bin
-cp bin/sambamba-${PKG_VERSION} ${PREFIX}/bin/sambamba
+make install prefix=${PREFIX}
diff --git a/recipes/sambamba/makefile.patch b/recipes/sambamba/makefile.patch
@@ -0,0 +1,11 @@
+--- Makefile.org 2021-08-27 21:10:36.161486256 -0500
++++ Makefile 2021-08-27 21:12:13.995234557 -0500
+@@ -109,7 +109,7 @@
+ pgo-static: static debug-strip
+
+ install:
+- install -m 0755 bin/sambamba $(prefix)/bin
++ install -m 0755 $(OUT) $(prefix)/bin/sambamba
+
+ clean: clean-d
+ rm lz4/lib/*.[oa]
diff --git a/recipes/sambamba/meta.yaml b/recipes/sambamba/meta.yaml
@@ -1,21 +1,28 @@
-{% set version='0.8.0' %}
-
+{% set name = "sambamba" %}
+{% set version = "0.8.1" %}
+{% set sha256 = "f432fdce3c51d333f2472c5fb1f84c87822a32639afe2b96434a13e7e7b7f7ef" %}
 package:
- name: sambamba
+ name: {{ name }}
  version: {{ version }}
 
 source:
- git_url: https://github.com/biod/sambamba
- git_revision: {{version}}
- sha256: b3d9df34208c0b2d17153de0839116d8794c2d0c4bd846d806eafaf398e66663
+ - url: https://github.com/biod/sambamba/archive/refs/tags/v{{ version }}.tar.gz
+ sha256: {{ sha256 }}
+ patches:
+ - makefile.patch
+ - url: https://github.com/lz4/lz4/archive/b3692db46d2b23a7c0af2d5e69988c94f126e10a.zip
+ sha256: 341fc478ccaf5f3ec1b620607d68541dfca3324dd2dbd386e9d45e85d2d26603
+ folder: lz4
 
 build:
- number: 1
+ number: 0
+ skip: True # [osx]
 
 requirements:
  build:
  - make
  - {{ compiler('c') }}
+ - python >=3
  host:
  - ldc >=1.17.0
  - bzip2
@@ -30,11 +37,14 @@ test:
  - sambamba view --help
 
 about:
- home: https://github.com/biod/sambamba
- license: GPLv2
+ home: "https://github.com/biod/sambamba"
+ doc_url: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html"
+ dev_url: "https://github.com/biod/sambamba"
+ license: GPL2
+ license_family: GPL2
  license_file: LICENSE
- summary: Tools for working with SAM/BAM data
+ summary: "Tools for working with SAM/BAM data"
 
 extra:
- skip-lints:
- - uses_vcs_url
+ identifiers:
+ - doi:10.1093/bioinformatics/btv098