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Update ucsc-wigtobigwig to 472 #51702

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merged 2 commits into from
Oct 28, 2024
Merged

Update ucsc-wigtobigwig to 472 #51702

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6f5d486
Update ucsc-wigtobigwig to 472
mencian Oct 28, 2024
226ec0a
Merge branch 'master' into wigtobigwig
bgruening Oct 28, 2024
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6 changes: 3 additions & 3 deletions recipes/ucsc-wigtobigwig/build.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,13 @@ 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 "${CPU_COUNT}")
(cd kent/src/utils/wigToBigWig && make CC="${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"
11 changes: 0 additions & 11 deletions recipes/ucsc-wigtobigwig/htmshell.patch
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This file was deleted.

27 changes: 27 additions & 0 deletions recipes/ucsc-wigtobigwig/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.
Comment on lines +23 to +27
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🛠️ Refactor suggestion

Consider adding explicit Python version compatibility handling.

Since this script is part of a bioinformatics tool, it's recommended to:

  1. Add explicit version checking at runtime
  2. Include compatibility imports if needed
  3. Document supported Python versions in the script's docstring

Example addition:

#!/usr/bin/env python
import sys

if sys.version_info[0] < 3:
    from __future__ import print_function, division

# Version check
min_python = (2, 7)
if sys.version_info[:2] < min_python:
    sys.exit("Python %s.%s or later is required." % min_python)

# expMatrixToBarchartBed
"""
Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
Supported Python versions: 2.7+, 3.x
"""

19 changes: 9 additions & 10 deletions recipes/ucsc-wigtobigwig/meta.yaml
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Original file line number Diff line number Diff line change
@@ -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 }}"
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 @@ -28,26 +28,25 @@ requirements:
- libuuid
- mysql-connector-c
- libopenssl-static
- clangdev # [osx]
- zlib

run:
- libpng
- libuuid
- mysql-connector-c
- libopenssl-static
- zlib

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"
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:
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