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[pkgsrc/trunk]: pkgsrc/biology/kallisto biology/kallisto: Upgrade to 0.46.1
details: https://anonhg.NetBSD.org/pkgsrc/rev/a344c1337c85
branches: trunk
changeset: 436030:a344c1337c85
user: bacon <bacon%pkgsrc.org@localhost>
date: Thu Jul 23 19:22:00 2020 +0000
description:
biology/kallisto: Upgrade to 0.46.1
Minor enhancements since 0.45
0.46.2 is available, but has serious regressions.
Reverted to bundled htslib 1.4.1, since kallisto source contains modified
htslib files that are incompatible with the current 1.10.2 package.
diffstat:
biology/kallisto/Makefile | 19 +++++++++----------
biology/kallisto/PLIST | 2 +-
biology/kallisto/distinfo | 12 +++++-------
3 files changed, 15 insertions(+), 18 deletions(-)
diffs (76 lines):
diff -r 6c9f0f19c3f2 -r a344c1337c85 biology/kallisto/Makefile
--- a/biology/kallisto/Makefile Thu Jul 23 19:17:03 2020 +0000
+++ b/biology/kallisto/Makefile Thu Jul 23 19:22:00 2020 +0000
@@ -1,29 +1,29 @@
-# $NetBSD: Makefile,v 1.2 2019/05/01 12:38:54 bacon Exp $
+# $NetBSD: Makefile,v 1.3 2020/07/23 19:22:00 bacon Exp $
-DISTNAME= kallisto-${PV}
-PKGREVISION= 1
+DISTNAME= kallisto-0.46.1
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=pachterlab/}
-GITHUB_TAG= v${PV}
+GITHUB_TAG= v${PKGVERSION_NOREV}
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://pachterlab.github.io/kallisto/
COMMENT= Quantify abundances of transcripts from RNA-Seq data
LICENSE= 2-clause-bsd
+USE_TOOLS+= autoconf gmake pax
USE_LANGUAGES= c c++
-USE_TOOLS+= pax
USE_CMAKE= yes
SUBST_CLASSES+= test
-SUBST_STAGE.test= post-build
+SUBST_STAGE.test= pre-configure
SUBST_FILES.test= kallisto-test
SUBST_SED.test= -e 's|/usr/local/share/kallisto|${DATADIR}|g'
-PV= 0.45.0
-DATADIR= ${PREFIX}/share/kallisto
+CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON
+MAKE_JOBS_SAFE= no # Doesn't finished bundled htslib first
+INSTALLATION_DIRS+= ${DATADIR}
-INSTALLATION_DIRS= bin ${DATADIR}
+DATADIR= ${PREFIX}/share/kallisto
post-extract:
${CP} ${FILESDIR}/kallisto-test ${WRKSRC}
@@ -32,7 +32,6 @@
${INSTALL_SCRIPT} ${WRKSRC}/kallisto-test ${DESTDIR}${PREFIX}/bin
cd ${WRKSRC} && pax -rw test ${DESTDIR}${DATADIR}
-.include "../../biology/htslib/buildlink3.mk"
.include "../../devel/hdf5/buildlink3.mk"
.include "../../archivers/libaec/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
diff -r 6c9f0f19c3f2 -r a344c1337c85 biology/kallisto/PLIST
--- a/biology/kallisto/PLIST Thu Jul 23 19:17:03 2020 +0000
+++ b/biology/kallisto/PLIST Thu Jul 23 19:22:00 2020 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2018/12/21 19:00:56 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2020/07/23 19:22:00 bacon Exp $
bin/kallisto
bin/kallisto-test
share/kallisto/test/README.md
diff -r 6c9f0f19c3f2 -r a344c1337c85 biology/kallisto/distinfo
--- a/biology/kallisto/distinfo Thu Jul 23 19:17:03 2020 +0000
+++ b/biology/kallisto/distinfo Thu Jul 23 19:22:00 2020 +0000
@@ -1,8 +1,6 @@
-$NetBSD: distinfo,v 1.1 2018/12/21 19:00:56 bacon Exp $
+$NetBSD: distinfo,v 1.2 2020/07/23 19:22:00 bacon Exp $
-SHA1 (kallisto-0.45.0.tar.gz) = ab0890c5d675d678dbcf415a86512b4694b3a4a6
-RMD160 (kallisto-0.45.0.tar.gz) = f482f7525dde0bfc2425cf803812c1c7748c882e
-SHA512 (kallisto-0.45.0.tar.gz) = b120c36ccb4725b19307c3e90c7f9b73b87efc53f08d3f2c12fc2e4b7afc3c03c52ba07dff623c9c8ad5a7e89c1eeb907389ccf3e4440236e81a0611500639e2
-Size (kallisto-0.45.0.tar.gz) = 2250430 bytes
-SHA1 (patch-CMakeLists.txt) = 2817091347e35898fec0bab77e8d9cc5ca5fff3f
-SHA1 (patch-src_CMakeLists.txt) = 2ef72024591c5216fbf44fb7cdfa4a8330b0c81a
+SHA1 (kallisto-0.46.1.tar.gz) = e39adb9801049836dcd7ac52e775f64af4d0a51b
+RMD160 (kallisto-0.46.1.tar.gz) = 8e42c5c52f19ec2e37f8591f7472a969b479bfd4
+SHA512 (kallisto-0.46.1.tar.gz) = 53a4db8fd5e0585693d8cd683651b4bdcc84c724a19e80a6162f1844fd491eb2d4e3180be2d9aabea7d49c9cbe0a05250f41da7d1de89d5d6cb6a8806f1afb7d
+Size (kallisto-0.46.1.tar.gz) = 2254560 bytes
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