gffread: add arm64 build (#53205)

bioconda · Jan 13, 2025 · ef99432 · ef99432
1 parent 6c72079
commit ef99432
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Showing 3 changed files with 29 additions and 17 deletions.
diff --git a/recipes/gffread/Makefile.patch b/recipes/gffread/Makefile.patch
@@ -1,7 +1,8 @@
-diff -ruN gffread-0.12.7/Makefile gffread-0.12.7/Makefile
---- gffread-0.12.7/Makefile	2021-07-23 16:31:39.000000000 +0200
-+++ gffread-0.12.7/Makefile	2021-09-24 14:24:52.376666651 +0200
-@@ -5,7 +5,7 @@
+diff --git a/Makefile b/Makefile
+index e2ed080..c1fdd13 100644
+--- a/Makefile
++++ b/Makefile
+@@ -5,11 +5,11 @@ SEARCHDIRS := -I. -I${GCLDIR}
  SYSTYPE :=     $(shell uname)
 
  CXX   := $(if $(CXX),$(CXX),g++)
@@ -10,3 +11,8 @@ diff -ruN gffread-0.12.7/Makefile gffread-0.12.7/Makefile
 
  LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
 
+-BASEFLAGS  := -Wall -Wextra -std=c++11 ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 \
++BASEFLAGS  := -Wall -Wextra -std=c++14 ${SEARCHDIRS} -D_FILE_OFFSET_BITS=64 \
+  -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing \
+  -fno-exceptions -fno-rtti
+
diff --git a/recipes/gffread/build.sh b/recipes/gffread/build.sh
@@ -1,4 +1,8 @@
 #!/bin/bash
+
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
 mkdir -p "$PREFIX"/bin
-make release
-mv gffread "$PREFIX"/bin 
+
+make release -j"${CPU_COUNT}" CXX="${CXX}" LINKER="${CXX}"
+install -v -m 0755 gffread "${PREFIX}/bin"
diff --git a/recipes/gffread/meta.yaml b/recipes/gffread/meta.yaml
@@ -6,13 +6,13 @@ package:
   version: {{ version }}
 
 source:
-  - url: /~https://github.com/gpertea/gffread/releases/download/v{{ version }}/gffread-{{ version }}.tar.gz
-    sha256: bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5
-    patches:
-      - Makefile.patch
+  url: /~https://github.com/gpertea/gffread/releases/download/v{{ version }}/gffread-{{ version }}.tar.gz
+  sha256: bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5
+  patches:
+    - Makefile.patch
 
 build:
-  number: 5
+  number: 6
   run_exports:
     - {{ pin_subpackage("gffread", max_pin="x.x") }}
 
@@ -22,23 +22,25 @@ requirements:
     - make
   host:
     - zlib
-  run:
-    - zlib
-
+
 test:
   commands:
     - gffread --version
 
 about:
-  home: http://ccb.jhu.edu/software/stringtie/gff.shtml
+  home: "https://ccb.jhu.edu/software/stringtie/gff.shtml"
   license: 'MIT'
+  license_family: MIT
+  license_file: LICENSE
   summary: 'GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.'
   dev_url: "/~https://github.com/gpertea/gffread"
+  doc_url: "https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread"
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - biotools:gffread
-  skip-lints:
-    - should_not_be_noarch_source
+    - usegalaxy-eu:gffread
+    - doi:10.12688/f1000research.23297.2