diff options
| author | bacon <bacon@pkgsrc.org> | 2020-07-23 19:22:00 +0000 |
|---|---|---|
| committer | bacon <bacon@pkgsrc.org> | 2020-07-23 19:22:00 +0000 |
| commit | 2f2f91b083385f5da724bea5f01b11458f6d36b0 (patch) | |
| tree | 7f62a29cfdbc143626849f879c4fc20c7429eb64 /biology | |
| parent | 8d99d6063d15fa74945c0bb230bee35d6ef88c14 (diff) | |
| download | pkgsrc-2f2f91b083385f5da724bea5f01b11458f6d36b0.tar.gz | |
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 (limited to 'biology')
| -rw-r--r-- | biology/kallisto/Makefile | 19 | ||||
| -rw-r--r-- | biology/kallisto/PLIST | 2 | ||||
| -rw-r--r-- | biology/kallisto/distinfo | 12 |
3 files changed, 15 insertions, 18 deletions
diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 81fc9235dca..730338ac22d 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -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${PKGVERSION_NOREV} MAINTAINER= bacon@NetBSD.org HOMEPAGE= https://pachterlab.github.io/kallisto/ COMMENT= Quantify abundances of transcripts from RNA-Seq data LICENSE= 2-clause-bsd +USE_TOOLS+= autoconf gmake pax USE_LANGUAGES= c c++ -USE_TOOLS+= pax USE_CMAKE= yes SUBST_CLASSES+= test -SUBST_STAGE.test= post-build +SUBST_STAGE.test= pre-configure SUBST_FILES.test= kallisto-test SUBST_SED.test= -e 's|/usr/local/share/kallisto|${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 @@ post-install: ${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 --git a/biology/kallisto/PLIST b/biology/kallisto/PLIST index 7835b3fd81a..870b133476a 100644 --- a/biology/kallisto/PLIST +++ b/biology/kallisto/PLIST @@ -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 --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo index 00932381cce..ca510f2b118 100644 --- a/biology/kallisto/distinfo +++ b/biology/kallisto/distinfo @@ -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 |