From f84bc7bb68690c2b04acf8e7838c82bec23f024a Mon Sep 17 00:00:00 2001 From: mencian Date: Mon, 25 Nov 2024 10:25:13 -0600 Subject: [PATCH] Update ucsc-bedtobigbed to 473 --- recipes/ucsc-bedtobigbed/build.sh | 5 ++-- recipes/ucsc-bedtobigbed/build_osx.sh | 3 -- recipes/ucsc-bedtobigbed/htmshell.patch | 11 ------- recipes/ucsc-bedtobigbed/include.macos.patch | 27 ++++++++++++++++++ recipes/ucsc-bedtobigbed/include.patch | 30 +++++++++++++------- recipes/ucsc-bedtobigbed/meta.yaml | 20 +++++++------ 6 files changed, 59 insertions(+), 37 deletions(-) delete mode 100644 recipes/ucsc-bedtobigbed/build_osx.sh delete mode 100644 recipes/ucsc-bedtobigbed/htmshell.patch create mode 100644 recipes/ucsc-bedtobigbed/include.macos.patch diff --git a/recipes/ucsc-bedtobigbed/build.sh b/recipes/ucsc-bedtobigbed/build.sh index 2b2c5a16aad45..f9cb8a0ec3b07 100644 --- a/recipes/ucsc-bedtobigbed/build.sh +++ b/recipes/ucsc-bedtobigbed/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 +17,4 @@ 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 "${CPU_COUNT}") (cd kent/src/utils/bedToBigBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp bin/bedToBigBed "${PREFIX}/bin" -chmod 0755 "${PREFIX}/bin/bedToBigBed" +install -v -m 0755 bin/bedToBigBed "${PREFIX}/bin" diff --git a/recipes/ucsc-bedtobigbed/build_osx.sh b/recipes/ucsc-bedtobigbed/build_osx.sh deleted file mode 100644 index 9491724fd1121..0000000000000 --- a/recipes/ucsc-bedtobigbed/build_osx.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -mkdir -p $PREFIX/bin; cp bedToBigBed $PREFIX/bin -chmod +x $PREFIX/bin/bedToBigBed diff --git a/recipes/ucsc-bedtobigbed/htmshell.patch b/recipes/ucsc-bedtobigbed/htmshell.patch deleted file mode 100644 index 1e6f87375ed01..0000000000000 --- a/recipes/ucsc-bedtobigbed/htmshell.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 -+++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 -@@ -713,7 +713,7 @@ - puts("Status: 400\r"); - puts("Content-Type: text/plain; charset=UTF-8\r"); - puts("\r"); --if (format != NULL && args != NULL) -+if (format != NULL) - { - vfprintf(stdout, format, args); - fprintf(stdout, "\n"); diff --git a/recipes/ucsc-bedtobigbed/include.macos.patch b/recipes/ucsc-bedtobigbed/include.macos.patch new file mode 100644 index 0000000000000..979f87005a72e --- /dev/null +++ b/recipes/ucsc-bedtobigbed/include.macos.patch @@ -0,0 +1,27 @@ +--- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${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-bedtobigbed/include.patch b/recipes/ucsc-bedtobigbed/include.patch index edc04d0dc2f64..35fd16a3d9090 100644 --- a/recipes/ucsc-bedtobigbed/include.patch +++ b/recipes/ucsc-bedtobigbed/include.patch @@ -1,5 +1,5 @@ ---- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 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 @@ -9,16 +9,24 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- a/kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ b/kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${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 +--- 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 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict ---- 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 +-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 diff --git a/recipes/ucsc-bedtobigbed/meta.yaml b/recipes/ucsc-bedtobigbed/meta.yaml index 156f4100092c2..f2e33534cc625 100644 --- a/recipes/ucsc-bedtobigbed/meta.yaml +++ b/recipes/ucsc-bedtobigbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedtobigbed" %} {% set program = "bedToBigBed" %} -{% set version = "469" %} -{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} +{% set version = "473" %} +{% set sha256 = "ed929a7141440e0718ed453283e6e7dde103e8e2facf27d2367be7b34e53e597" %} 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) }} @@ -23,19 +23,21 @@ requirements: build: - make - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - libopenssl-static + - clangdev # [osx] + - ucsc-stringify - zlib - run: - libpng - libuuid - mysql-connector-c - libopenssl-static - - zlib + - ucsc-stringify test: commands: @@ -43,11 +45,11 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "https://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 https://genome.ucsc.edu/license" summary: "Convert bed file to bigBed. (BigBed version: 4)" 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: