From d9c481d8fd104808e8a3ea8c4fd4a9bd871d7b05 Mon Sep 17 00:00:00 2001 From: mencian Date: Mon, 28 Oct 2024 02:05:23 -0500 Subject: [PATCH 1/4] Update ucsc-pslcdnafilter to 472 --- recipes/ucsc-pslcdnafilter/build.sh | 6 ++--- .../ucsc-pslcdnafilter/include.macos.patch | 27 +++++++++++++++++++ recipes/ucsc-pslcdnafilter/meta.yaml | 18 ++++++------- 3 files changed, 38 insertions(+), 13 deletions(-) create mode 100644 recipes/ucsc-pslcdnafilter/include.macos.patch diff --git a/recipes/ucsc-pslcdnafilter/build.sh b/recipes/ucsc-pslcdnafilter/build.sh index 6f9c17e7cba0b..0d01ae296724e 100644 --- a/recipes/ucsc-pslcdnafilter/build.sh +++ b/recipes/ucsc-pslcdnafilter/build.sh @@ -8,7 +8,7 @@ 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 ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" mkdir -p "${BINDIR}" @@ -18,5 +18,5 @@ mkdir -p "${BINDIR}" (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslCDnaFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp bin/pslCDnaFilter "${PREFIX}/bin" -chmod 0755 "${PREFIX}/bin/pslCDnaFilter" +chmod 0755 bin/pslCDnaFilter +mv bin/pslCDnaFilter "${PREFIX}/bin" diff --git a/recipes/ucsc-pslcdnafilter/include.macos.patch b/recipes/ucsc-pslcdnafilter/include.macos.patch new file mode 100644 index 0000000000000..979f87005a72e --- /dev/null +++ b/recipes/ucsc-pslcdnafilter/include.macos.patch @@ -0,0 +1,27 @@ +--- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${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-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml index 58d533a67e4ff..eedf9b4fd8df9 100644 --- a/recipes/ucsc-pslcdnafilter/meta.yaml +++ b/recipes/ucsc-pslcdnafilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslcdnafilter" %} {% set program = "pslCDnaFilter" %} -{% 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: @@ -43,8 +42,8 @@ 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: " Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given @@ -52,10 +51,9 @@ cDNA and non-comparative, based only on the quality of an individual alignment. " 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: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file From a842acfb4e06f84f5d7447923db8e8030955131f Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 28 Oct 2024 02:28:45 -0500 Subject: [PATCH 2/4] add linux-aarch64 build --- recipes/ucsc-pslcdnafilter/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/ucsc-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml index eedf9b4fd8df9..cdd5ee593d669 100644 --- a/recipes/ucsc-pslcdnafilter/meta.yaml +++ b/recipes/ucsc-pslcdnafilter/meta.yaml @@ -57,3 +57,5 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 From dcae61de12701a9ee36fd30a5e40e1de2cc72f35 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 28 Oct 2024 02:36:16 -0500 Subject: [PATCH 3/4] revert linux-aarch64 --- recipes/ucsc-pslcdnafilter/meta.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/recipes/ucsc-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml index cdd5ee593d669..eedf9b4fd8df9 100644 --- a/recipes/ucsc-pslcdnafilter/meta.yaml +++ b/recipes/ucsc-pslcdnafilter/meta.yaml @@ -57,5 +57,3 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - additional-platforms: - - linux-aarch64 From b23ff546a6915e6b02b1fbceaa50e6f3bee3f241 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 28 Oct 2024 16:06:14 -0500 Subject: [PATCH 4/4] revert osx --- recipes/ucsc-pslcdnafilter/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/ucsc-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml index eedf9b4fd8df9..bb1f6757f31f7 100644 --- a/recipes/ucsc-pslcdnafilter/meta.yaml +++ b/recipes/ucsc-pslcdnafilter/meta.yaml @@ -16,6 +16,7 @@ source: build: number: 0 + skip: True # [osx] run_exports: - {{ pin_subpackage(package, max_pin=None) }}