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py-macs3: Fix build
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Thu Dec 21 16:25:47 2023 -0600
Changeset: 1beb3edd247f33cabdc67eeb769107c6046127f3
Modified Files:
py-macs3/Makefile
py-macs3/PLIST
py-macs3/distinfo
Added Files:
py-macs3/patches/patch-MACS3_fermi-lite_ksw.c
Log Message:
py-macs3: Fix build
Fix path to SIMDE header
Generate PLIST
Silence pkglint
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1beb3edd247f33cabdc67eeb769107c6046127f3
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
py-macs3/Makefile | 7 +-
py-macs3/PLIST | 104 ++++++++++++++++++++++++++
py-macs3/distinfo | 1 +
py-macs3/patches/patch-MACS3_fermi-lite_ksw.c | 15 ++++
4 files changed, 121 insertions(+), 6 deletions(-)
diffs:
diff --git a/py-macs3/Makefile b/py-macs3/Makefile
index c3b67c83ae..d6375a8a62 100644
--- a/py-macs3/Makefile
+++ b/py-macs3/Makefile
@@ -5,7 +5,7 @@ PKGNAME= ${PYPKGPREFIX}-macs-3.0.0
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=macs3-project/}
GITHUB_PROJECT= MACS
-GITHUB_TAG= v${PKGVERSION_NOREV}
+GITHUB_TAG= v${PKGVERSION_NOREV}
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://pypi.python.org/pypi/macs2
@@ -14,11 +14,6 @@ LICENSE= modified-bsd
DEPENDS+= ${PYPKGPREFIX}-hmmlearn>=0:../../wip/py-hmmlearn
-post-install:
- ${STRIP} \
- ${DESTDIR}${PYTHON_SITELIBDIR}/MACS2/*.so \
- ${DESTDIR}${PYTHON_SITELIBDIR}/MACS2/*/*.so
-
.include "../../lang/python/wheel.mk"
.include "../../math/py-numpy/buildlink3.mk"
.include "../../devel/py-cython/buildlink3.mk"
diff --git a/py-macs3/PLIST b/py-macs3/PLIST
index e69de29bb2..eb152751d1 100644
--- a/py-macs3/PLIST
+++ b/py-macs3/PLIST
@@ -0,0 +1,104 @@
+@comment $NetBSD$
+bin/macs3
+${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/LICENSE
+${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/METADATA
+${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/RECORD
+${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/WHEEL
+${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/top_level.txt
+${PYSITELIB}/MACS3/Commands/__init__.py
+${PYSITELIB}/MACS3/Commands/__init__.pyc
+${PYSITELIB}/MACS3/Commands/__init__.pyo
+${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.py
+${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyc
+${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyo
+${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.py
+${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.pyc
+${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.pyo
+${PYSITELIB}/MACS3/Commands/bdgdiff_cmd.py
+${PYSITELIB}/MACS3/Commands/bdgdiff_cmd.pyc
+${PYSITELIB}/MACS3/Commands/bdgdiff_cmd.pyo
+${PYSITELIB}/MACS3/Commands/bdgopt_cmd.py
+${PYSITELIB}/MACS3/Commands/bdgopt_cmd.pyc
+${PYSITELIB}/MACS3/Commands/bdgopt_cmd.pyo
+${PYSITELIB}/MACS3/Commands/bdgpeakcall_cmd.py
+${PYSITELIB}/MACS3/Commands/bdgpeakcall_cmd.pyc
+${PYSITELIB}/MACS3/Commands/bdgpeakcall_cmd.pyo
+${PYSITELIB}/MACS3/Commands/callpeak_cmd.py
+${PYSITELIB}/MACS3/Commands/callpeak_cmd.pyc
+${PYSITELIB}/MACS3/Commands/callpeak_cmd.pyo
+${PYSITELIB}/MACS3/Commands/callvar_cmd.py
+${PYSITELIB}/MACS3/Commands/callvar_cmd.pyc
+${PYSITELIB}/MACS3/Commands/callvar_cmd.pyo
+${PYSITELIB}/MACS3/Commands/cmbreps_cmd.py
+${PYSITELIB}/MACS3/Commands/cmbreps_cmd.pyc
+${PYSITELIB}/MACS3/Commands/cmbreps_cmd.pyo
+${PYSITELIB}/MACS3/Commands/diffpeak_cmd.py
+${PYSITELIB}/MACS3/Commands/diffpeak_cmd.pyc
+${PYSITELIB}/MACS3/Commands/diffpeak_cmd.pyo
+${PYSITELIB}/MACS3/Commands/filterdup_cmd.py
+${PYSITELIB}/MACS3/Commands/filterdup_cmd.pyc
+${PYSITELIB}/MACS3/Commands/filterdup_cmd.pyo
+${PYSITELIB}/MACS3/Commands/hmmratac_cmd.py
+${PYSITELIB}/MACS3/Commands/hmmratac_cmd.pyc
+${PYSITELIB}/MACS3/Commands/hmmratac_cmd.pyo
+${PYSITELIB}/MACS3/Commands/pileup_cmd.py
+${PYSITELIB}/MACS3/Commands/pileup_cmd.pyc
+${PYSITELIB}/MACS3/Commands/pileup_cmd.pyo
+${PYSITELIB}/MACS3/Commands/predictd_cmd.py
+${PYSITELIB}/MACS3/Commands/predictd_cmd.pyc
+${PYSITELIB}/MACS3/Commands/predictd_cmd.pyo
+${PYSITELIB}/MACS3/Commands/randsample_cmd.py
+${PYSITELIB}/MACS3/Commands/randsample_cmd.pyc
+${PYSITELIB}/MACS3/Commands/randsample_cmd.pyo
+${PYSITELIB}/MACS3/Commands/refinepeak_cmd.py
+${PYSITELIB}/MACS3/Commands/refinepeak_cmd.pyc
+${PYSITELIB}/MACS3/Commands/refinepeak_cmd.pyo
+${PYSITELIB}/MACS3/IO/BAM.so
+${PYSITELIB}/MACS3/IO/BedGraphIO.so
+${PYSITELIB}/MACS3/IO/OutputWriter.py
+${PYSITELIB}/MACS3/IO/OutputWriter.pyc
+${PYSITELIB}/MACS3/IO/OutputWriter.pyo
+${PYSITELIB}/MACS3/IO/Parser.so
+${PYSITELIB}/MACS3/IO/PeakIO.so
+${PYSITELIB}/MACS3/IO/__init__.py
+${PYSITELIB}/MACS3/IO/__init__.pyc
+${PYSITELIB}/MACS3/IO/__init__.pyo
+${PYSITELIB}/MACS3/Signal/BedGraph.so
+${PYSITELIB}/MACS3/Signal/CallPeakUnit.so
+${PYSITELIB}/MACS3/Signal/FixWidthTrack.so
+${PYSITELIB}/MACS3/Signal/HMMR_EM.so
+${PYSITELIB}/MACS3/Signal/HMMR_HMM.so
+${PYSITELIB}/MACS3/Signal/HMMR_Signal_Processing.so
+${PYSITELIB}/MACS3/Signal/PairedEndTrack.so
+${PYSITELIB}/MACS3/Signal/PeakDetect.so
+${PYSITELIB}/MACS3/Signal/PeakModel.so
+${PYSITELIB}/MACS3/Signal/PeakVariants.so
+${PYSITELIB}/MACS3/Signal/Pileup.so
+${PYSITELIB}/MACS3/Signal/PileupV2.so
+${PYSITELIB}/MACS3/Signal/PosReadsInfo.so
+${PYSITELIB}/MACS3/Signal/Prob.so
+${PYSITELIB}/MACS3/Signal/RACollection.so
+${PYSITELIB}/MACS3/Signal/ReadAlignment.so
+${PYSITELIB}/MACS3/Signal/Region.so
+${PYSITELIB}/MACS3/Signal/ScoreTrack.so
+${PYSITELIB}/MACS3/Signal/SignalProcessing.so
+${PYSITELIB}/MACS3/Signal/UnitigRACollection.so
+${PYSITELIB}/MACS3/Signal/VariantStat.so
+${PYSITELIB}/MACS3/Signal/__init__.py
+${PYSITELIB}/MACS3/Signal/__init__.pyc
+${PYSITELIB}/MACS3/Signal/__init__.pyo
+${PYSITELIB}/MACS3/Utilities/Constants.py
+${PYSITELIB}/MACS3/Utilities/Constants.pyc
+${PYSITELIB}/MACS3/Utilities/Constants.pyo
+${PYSITELIB}/MACS3/Utilities/Logger.py
+${PYSITELIB}/MACS3/Utilities/Logger.pyc
+${PYSITELIB}/MACS3/Utilities/Logger.pyo
+${PYSITELIB}/MACS3/Utilities/OptValidator.py
+${PYSITELIB}/MACS3/Utilities/OptValidator.pyc
+${PYSITELIB}/MACS3/Utilities/OptValidator.pyo
+${PYSITELIB}/MACS3/Utilities/__init__.py
+${PYSITELIB}/MACS3/Utilities/__init__.pyc
+${PYSITELIB}/MACS3/Utilities/__init__.pyo
+${PYSITELIB}/MACS3/__init__.py
+${PYSITELIB}/MACS3/__init__.pyc
+${PYSITELIB}/MACS3/__init__.pyo
diff --git a/py-macs3/distinfo b/py-macs3/distinfo
index 706bd1991e..d247a1d51f 100644
--- a/py-macs3/distinfo
+++ b/py-macs3/distinfo
@@ -3,3 +3,4 @@ $NetBSD$
BLAKE2s (macs-3.0.0.tar.gz) = 6a28a732c0cef04e57c27f1679f372b40a48dc1aba23d8daa0555c63e02aa1bd
SHA512 (macs-3.0.0.tar.gz) = 44daa10901cea110ae6d0a5749e9696fa64883151b11af6b13c8d4ae589bc3207048d0de4420308a922a96b5dd542b694897ceabaac32becc07aef0061ee2257
Size (macs-3.0.0.tar.gz) = 197389439 bytes
+SHA1 (patch-MACS3_fermi-lite_ksw.c) = 7df96d1d970a3e70c4611bd618d1aa539297dbcc
diff --git a/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c b/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c
new file mode 100644
index 0000000000..6b6dd6540b
--- /dev/null
+++ b/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Use SIMDE sse2.h
+
+--- MACS3/fermi-lite/ksw.c.orig 2023-12-21 22:20:16.716124047 +0000
++++ MACS3/fermi-lite/ksw.c
+@@ -28,7 +28,7 @@
+
+ /* I modified this according to https://github.com/lh3/bwa/pull/283/*/
+ #ifdef USE_SIMDE
+-#include "lib/x86/sse2.h"
++#include <simde/x86/sse2.h>
+ #else
+ #include <emmintrin.h>
+ #endif
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