kallisto: Work on 0.46.1 upgrade

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Jul 22 11:59:28 2020 -0500
Changeset:	f7d50308efe361b44b8d782f2c30e728d01b7e02

Modified Files:
	kallisto/Makefile
	kallisto/distinfo

Log Message:
kallisto: Work on 0.46.1 upgrade

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f7d50308efe361b44b8d782f2c30e728d01b7e02

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 kallisto/Makefile | 10 +++++-----
 kallisto/distinfo |  9 +++++----
 2 files changed, 10 insertions(+), 9 deletions(-)

diffs:
diff --git a/kallisto/Makefile b/kallisto/Makefile
index 64b3a17879..b8e6e3b03d 100644
--- a/kallisto/Makefile
+++ b/kallisto/Makefile
@@ -1,9 +1,9 @@
 # $NetBSD: Makefile,v 1.1 2018/12/21 19:00:56 bacon Exp $
 
-DISTNAME=	kallisto-${PV}
+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/
@@ -11,7 +11,7 @@ COMMENT=	Quantify abundances of transcripts from RNA-Seq data
 LICENSE=	2-clause-bsd
 
 USE_LANGUAGES=	c c++
-USE_TOOLS+=	pax
+USE_TOOLS+=	autoconf autoreconf automake gmake pax
 USE_CMAKE=	yes
 
 SUBST_CLASSES+=		test
@@ -19,10 +19,10 @@ SUBST_STAGE.test=	post-build
 SUBST_FILES.test=	kallisto-test
 SUBST_SED.test=		-e 's|/usr/local/share/kallisto|${DATADIR}|g'
 
-PV=		0.46.0
 DATADIR=	${PREFIX}/share/kallisto
 
 INSTALLATION_DIRS=	bin ${DATADIR}
+MAKE_JOBS_SAFE=		no
 
 post-extract:
 	${CP} ${FILESDIR}/kallisto-test ${WRKSRC}
@@ -31,7 +31,7 @@ post-install:
 	${INSTALL_SCRIPT} ${WRKSRC}/kallisto-test ${DESTDIR}${PREFIX}/bin
 	cd ${WRKSRC} && pax -rw test ${DESTDIR}${DATADIR}
 
-.include "../../biology/htslib/buildlink3.mk"
+# .include "../../biology/htslib/buildlink3.mk"
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../wip/libaec/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
diff --git a/kallisto/distinfo b/kallisto/distinfo
index 4998500be3..5aeefd98fa 100644
--- a/kallisto/distinfo
+++ b/kallisto/distinfo
@@ -1,8 +1,9 @@
 $NetBSD$
 
-SHA1 (kallisto-0.46.0.tar.gz) = bbbb6984e94cb12ef8419971c23b643cff99f343
-RMD160 (kallisto-0.46.0.tar.gz) = 7619aaaf4488298cbc593d1b412b3ae740dcccff
-SHA512 (kallisto-0.46.0.tar.gz) = 747aacc2b0e3d2f7e299d849e8cb9262ad16acf446350f2c993b342980dec087c6b9b46b7b5fc95159d3059fbd5b7e7e72fe8da90635e7870303e295393732e3
-Size (kallisto-0.46.0.tar.gz) = 2252729 bytes
+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
 SHA1 (patch-CMakeLists.txt) = 2817091347e35898fec0bab77e8d9cc5ca5fff3f
 SHA1 (patch-src_CMakeLists.txt) = 2ef72024591c5216fbf44fb7cdfa4a8330b0c81a
+SHA1 (patch-src_kseq.h) = d56e9d69bd1799ffec59e468979dab2fca15b168