ucsc-bigwigsummary: update macOS build (#50368)

* ucsc-bigwigsummary: update macOS build

* edit build.sh

* edit meta.yaml

recipes/ucsc-bigwigsummary/build.sh

@@ -1,13 +1,26 @@
 #!/bin/bash
+
 mkdir -p "$PREFIX/bin"
+
 export MACHTYPE=$(uname -m)
-export BINDIR=$(pwd)/bin
+export BINDIR="$(pwd)/bin"
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
 export L="${LDFLAGS}"
+
 mkdir -p "$BINDIR"
-(cd kent/src/lib && make -j ${CPU_COUNT})
-(cd kent/src/htslib && make -j ${CPU_COUNT})
-(cd kent/src/jkOwnLib && make -j ${CPU_COUNT})
-(cd kent/src/hg/lib && make -j ${CPU_COUNT})
-(cd kent/src/utils/bigWigSummary && make -j ${CPU_COUNT})
-cp bin/bigWigSummary "$PREFIX/bin"
-chmod +x "$PREFIX/bin/bigWigSummary"
+
+if [[ "$(uname)" == Darwin ]]; then
+	export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib"
+	export CFLAGS="${CFLAGS} -Wno-unused-command-line-argument"
+fi
+
+(cd kent/src/lib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/htslib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/jkOwnLib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/hg/lib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/utils/bigWigSummary && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+cp -rf bin/bigWigSummary "$PREFIX/bin"
+chmod 0755 "$PREFIX/bin/bigWigSummary"

recipes/ucsc-bigwigsummary/include.macos.patch

@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.

recipes/ucsc-bigwigsummary/meta.yaml

@@ -1,7 +1,7 @@
 {% set package = "ucsc-bigwigsummary" %}
 {% set program = "bigWigSummary" %}
-{% set version = "448" %}
-{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %}
+{% set version = "469" %}
+{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
 
 package:
   name: {{ package }}
@@ -11,12 +11,11 @@ source:
   url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz
   sha256: {{ sha256 }}
   patches:
-    - include.patch
-    - htmshell.patch
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
   number: 1
-  skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(package|lower, max_pin=None) }}
 
@@ -25,29 +24,33 @@ requirements:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - binutils # [linux]
+    - binutils  # [linux]
   host:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
+    - mariadb-connector-c
     - libopenssl-static
+    - clangdev  # [osx]
     - zlib
   run:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
+    - mariadb-connector-c
+    - libopenssl-static
 
 test:
   commands:
-    # just check for existence, because the individual packages have no unified behavior
-    - which {{ program }}
+    # just check for existence and exec bit, because the individual packages have no unified behavior
+    - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
-  license: "varies; see http://genome.ucsc.edu/license"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see http://genome.ucsc.edu/license"
   summary: "Extract summary information from a bigWig file."
+  dev_url: "https://github.com/ucscGenomeBrowser/kent"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   additional-platforms: