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Update ucsc-bedtobigbed to 473 #52365

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Nov 25, 2024
Merged

Update ucsc-bedtobigbed to 473 #52365

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5 changes: 2 additions & 3 deletions recipes/ucsc-bedtobigbed/build.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,12 @@ 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}")
(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
(cd kent/src/jkOwnLib && make CC="${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"
3 changes: 0 additions & 3 deletions recipes/ucsc-bedtobigbed/build_osx.sh
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This file was deleted.

11 changes: 0 additions & 11 deletions recipes/ucsc-bedtobigbed/htmshell.patch
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27 changes: 27 additions & 0 deletions recipes/ucsc-bedtobigbed/include.macos.patch
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Original file line number Diff line number Diff line change
@@ -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.
30 changes: 19 additions & 11 deletions recipes/ucsc-bedtobigbed/include.patch
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Original file line number Diff line number Diff line change
@@ -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

Expand All @@ -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
Expand Down
20 changes: 11 additions & 9 deletions recipes/ucsc-bedtobigbed/meta.yaml
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Original file line number Diff line number Diff line change
@@ -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 }}"
Expand All @@ -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) }}
Expand All @@ -23,31 +23,33 @@ 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:
# just check for existence and exec bit, because the individual packages have no unified behavior
- 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:
Expand Down