From fb974ccb1a2a0ce0ff31e56b9a77b529b615f57f Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 28 Oct 2024 15:48:17 -0500 Subject: [PATCH] Update ucsc-wigtobigwig to 472 (#51702) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/ucsc-wigtobigwig/build.sh | 6 ++--- recipes/ucsc-wigtobigwig/htmshell.patch | 11 -------- recipes/ucsc-wigtobigwig/include.macos.patch | 27 ++++++++++++++++++++ recipes/ucsc-wigtobigwig/meta.yaml | 19 +++++++------- 4 files changed, 39 insertions(+), 24 deletions(-) delete mode 100644 recipes/ucsc-wigtobigwig/htmshell.patch create mode 100644 recipes/ucsc-wigtobigwig/include.macos.patch diff --git a/recipes/ucsc-wigtobigwig/build.sh b/recipes/ucsc-wigtobigwig/build.sh index 113f9a2031ecb..2d32f36cdfac3 100644 --- a/recipes/ucsc-wigtobigwig/build.sh +++ b/recipes/ucsc-wigtobigwig/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 "${CPU_COUNT}") (cd kent/src/utils/wigToBigWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp bin/wigToBigWig "${PREFIX}/bin" -chmod 0755 "${PREFIX}/bin/wigToBigWig" +chmod 0755 bin/wigToBigWig +mv bin/wigToBigWig "${PREFIX}/bin" diff --git a/recipes/ucsc-wigtobigwig/htmshell.patch b/recipes/ucsc-wigtobigwig/htmshell.patch deleted file mode 100644 index 1e6f87375ed01..0000000000000 --- a/recipes/ucsc-wigtobigwig/htmshell.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 -+++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 -@@ -713,7 +713,7 @@ - puts("Status: 400\r"); - puts("Content-Type: text/plain; charset=UTF-8\r"); - puts("\r"); --if (format != NULL && args != NULL) -+if (format != NULL) - { - vfprintf(stdout, format, args); - fprintf(stdout, "\n"); diff --git a/recipes/ucsc-wigtobigwig/include.macos.patch b/recipes/ucsc-wigtobigwig/include.macos.patch new file mode 100644 index 0000000000000..979f87005a72e --- /dev/null +++ b/recipes/ucsc-wigtobigwig/include.macos.patch @@ -0,0 +1,27 @@ +--- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${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-wigtobigwig/meta.yaml b/recipes/ucsc-wigtobigwig/meta.yaml index ac2226d78ed5d..33106d75a2610 100644 --- a/recipes/ucsc-wigtobigwig/meta.yaml +++ b/recipes/ucsc-wigtobigwig/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-wigtobigwig" %} {% set program = "wigToBigWig" %} -{% 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) }} @@ -28,14 +28,13 @@ requirements: - libuuid - mysql-connector-c - libopenssl-static + - clangdev # [osx] - 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/" - license: "Varies; see http://genome.ucsc.edu/license" - summary: "Convert ascii format wig file (in fixedStep, variableStep" + home: "https://hgdownload.cse.ucsc.edu/admin/exe" + license: "Varies; see https://genome.ucsc.edu/license" + summary: "Convert ascii format wig file (in fixedStep, variableStep)." 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: