ucsc-fatotwobit: update macOS build (bioconda#50369)

* ucsc-fatotwobit: update macOS build

* try without mariadb

recipes/ucsc-fatotwobit/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 "$BINDIR"
-(cd kent/src/lib && make)
-(cd kent/src/htslib && make)
-(cd kent/src/jkOwnLib && make)
-(cd kent/src/hg/lib && make)
-(cd kent/src/utils/faToTwoBit && make)
-cp bin/faToTwoBit "$PREFIX/bin"
-chmod +x "$PREFIX/bin/faToTwoBit"
+
+if [[ "$(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 ${CPU_COUNT})
+(cd kent/src/utils/faToTwoBit && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+cp -rf bin/faToTwoBit "$PREFIX/bin"
+chmod 0755 "$PREFIX/bin/faToTwoBit"

recipes/ucsc-fatotwobit/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-fatotwobit/include.patch

@@ -1,5 +1,5 @@
---- kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
-+++ kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+--- 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
 
@@ -9,24 +9,24 @@
 
  # to check for Mac OSX Darwin specifics:
  UNAME_S := $(shell uname -s)
---- kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
-+++ kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
+--- a/kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
++++ b/kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
 @@ -147,4 +147,4 @@
 -       L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl
 +       L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl
     else
       ifneq ($(wildcard /opt/local/lib/libssl.a),)
           L+=/opt/local/lib/libssl.a
---- kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
-+++ kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+--- 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
---- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
-+++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+--- 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

recipes/ucsc-fatotwobit/meta.yaml

@@ -1,7 +1,7 @@
 {% set package = "ucsc-fatotwobit" %}
 {% set program = "faToTwoBit" %}
-{% set version = "455" %}
-{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %}
+{% set version = "469" %}
+{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
 
 package:
   name: "{{ package }}"
@@ -11,15 +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:
-  skip: True # [osx]
-  number: 2
-  ignore_run_exports:
-    - libpng
-    - libuuid
+  number: 1
   run_exports:
     - {{ pin_subpackage("ucsc-fatotwobit", max_pin=None) }}
 
@@ -28,29 +24,31 @@ requirements:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - binutils # [linux]
+    - binutils  # [linux]
   host:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
     - libopenssl-static
-    - zlib >=1.3.1,<2.0a0
+    - clangdev  # [osx]
+    - zlib
   run:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
+    - 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"
-  summary: "Convert DNA from fasta to 2bit format"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see http://genome.ucsc.edu/license"
+  summary: "Convert DNA from fasta to 2bit format."
+  dev_url: "https://github.com/ucscGenomeBrowser/kent"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   additional-platforms: