[pkgsrc/trunk]: pkgsrc/biology/kallisto biology/kallisto: Upgrade to 0.46.1

[bacon <bacon%pkgsrc.org@localhost>]

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