diff --git a/recipes/ucsc-twobitinfo/build.sh b/recipes/ucsc-twobitinfo/build.sh index 510984dbad870..2fde6d85012b6 100644 --- a/recipes/ucsc-twobitinfo/build.sh +++ b/recipes/ucsc-twobitinfo/build.sh @@ -9,7 +9,7 @@ export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" -export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") @@ -17,5 +17,5 @@ mkdir -p "${BINDIR}" (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/twoBitInfo && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp bin/twoBitInfo "${PREFIX}/bin" +cp -f bin/twoBitInfo "${PREFIX}/bin" chmod 0755 "${PREFIX}/bin/twoBitInfo" diff --git a/recipes/ucsc-twobitinfo/include.macos.patch b/recipes/ucsc-twobitinfo/include.macos.patch new file mode 100644 index 0000000000000..979f87005a72e --- /dev/null +++ b/recipes/ucsc-twobitinfo/include.macos.patch @@ -0,0 +1,27 @@ +--- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${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. diff --git a/recipes/ucsc-twobitinfo/meta.yaml b/recipes/ucsc-twobitinfo/meta.yaml index f02d59ed3bbbe..efd408cb42f7b 100644 --- a/recipes/ucsc-twobitinfo/meta.yaml +++ b/recipes/ucsc-twobitinfo/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobitinfo" %} {% set program = "twoBitInfo" %} -{% set version = "469" %} -{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} +{% set version = "472" %} +{% set sha256 = "26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2" %} package: name: "{{ package }}" @@ -11,10 +11,10 @@ source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" sha256: "{{ sha256 }}" patches: - - "include.patch" + - include.patch # [linux] + - include.macos.patch # [osx] build: - skip: True # [osx] number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -24,18 +24,17 @@ requirements: - make - {{ compiler('c') }} host: + - clangdev # [osx] - libpng - libuuid - mysql-connector-c - libopenssl-static - zlib - run: - libpng - libuuid - mysql-connector-c - libopenssl-static - - zlib test: commands: @@ -43,11 +42,11 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + home: "https://hgdownload.cse.ucsc.edu/admin/exe" license: "Varies; see http://genome.ucsc.edu/license" - summary: "get information about sequences in a .2bit file" + summary: "Get information about sequences in a .2bit file." dev_url: "https://github.com/ucscGenomeBrowser/kent" - doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README" extra: identifiers: