Sun Feb 27 01:57:27 2022 UTC ()
biology/kallisto: Update to 0.48.0

Long awaited bug fix release
Also unbundled htslib
Changes: https://github.com/pachterlab/kallisto/tags


(bacon)
diff -r1.3 -r1.4 pkgsrc/biology/kallisto/Makefile
diff -r1.2 -r1.3 pkgsrc/biology/kallisto/PLIST
diff -r1.4 -r1.5 pkgsrc/biology/kallisto/distinfo
diff -r0 -r1.3 pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt
diff -r0 -r1.3 pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt
diff -r0 -r1.1 pkgsrc/biology/kallisto/patches/patch-src_kseq.h
cvs diff -r1.3 -r1.4 pkgsrc/biology/kallisto/Makefile (expand / switch to unified diff)

--- pkgsrc/biology/kallisto/Makefile 2020/07/23 19:22:00 1.3
+++ pkgsrc/biology/kallisto/Makefile 2022/02/27 01:57:27 1.4
@@ -1,38 +1,39 @@ @@ -1,38 +1,39 @@
1# $NetBSD: Makefile,v 1.3 2020/07/23 19:22:00 bacon Exp $ 1# $NetBSD: Makefile,v 1.4 2022/02/27 01:57:27 bacon Exp $
2 2
3DISTNAME= kallisto-0.46.1 3DISTNAME= kallisto-0.48.0
4CATEGORIES= biology 4CATEGORIES= biology
5MASTER_SITES= ${MASTER_SITE_GITHUB:=pachterlab/} 5MASTER_SITES= ${MASTER_SITE_GITHUB:=pachterlab/}
6GITHUB_TAG= v${PKGVERSION_NOREV} 6GITHUB_TAG= v${PKGVERSION_NOREV}
7 7
8MAINTAINER= bacon@NetBSD.org 8MAINTAINER= bacon@NetBSD.org
9HOMEPAGE= https://pachterlab.github.io/kallisto/ 9HOMEPAGE= https://pachterlab.github.io/kallisto/
10COMMENT= Quantify abundances of transcripts from RNA-Seq data 10COMMENT= Quantify abundances of transcripts from RNA-Seq data
11LICENSE= 2-clause-bsd 11LICENSE= 2-clause-bsd
12 12
13USE_TOOLS+= autoconf gmake pax 13USE_TOOLS+= autoconf gmake pax
14USE_LANGUAGES= c c++ 14USE_LANGUAGES= c c++
15USE_CMAKE= yes 15USE_CMAKE= yes
16 16
17SUBST_CLASSES+= test 17SUBST_CLASSES+= test
18SUBST_STAGE.test= pre-configure 18SUBST_STAGE.test= pre-configure
19SUBST_FILES.test= kallisto-test 19SUBST_FILES.test= kallisto-test
20SUBST_SED.test= -e 's|/usr/local/share/kallisto|${DATADIR}|g' 20SUBST_SED.test= -e 's|/usr/local/share/kallisto|${DATADIR}|g'
21 21
22CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON 22CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON
23MAKE_JOBS_SAFE= no # Doesn't finished bundled htslib first 
24INSTALLATION_DIRS+= ${DATADIR} 23INSTALLATION_DIRS+= ${DATADIR}
25 24
26DATADIR= ${PREFIX}/share/kallisto 25DATADIR= ${PREFIX}/share/kallisto
27 26
28post-extract: 27post-extract:
29 ${CP} ${FILESDIR}/kallisto-test ${WRKSRC} 28 ${CP} ${FILESDIR}/kallisto-test ${WRKSRC}
 29 ${RM} -rf ${WRKSRC}/ext/htslib
30 30
31post-install: 31post-install:
32 ${INSTALL_SCRIPT} ${WRKSRC}/kallisto-test ${DESTDIR}${PREFIX}/bin 32 ${INSTALL_SCRIPT} ${WRKSRC}/kallisto-test ${DESTDIR}${PREFIX}/bin
33 cd ${WRKSRC} && pax -rw test ${DESTDIR}${DATADIR} 33 cd ${WRKSRC} && pax -rw test ${DESTDIR}${DATADIR}
34 34
35.include "../../devel/hdf5/buildlink3.mk" 35.include "../../devel/hdf5/buildlink3.mk"
36.include "../../archivers/libaec/buildlink3.mk" 36.include "../../archivers/libaec/buildlink3.mk"
37.include "../../devel/zlib/buildlink3.mk" 37.include "../../devel/zlib/buildlink3.mk"
 38.include "../../biology/htslib/buildlink3.mk"
38.include "../../mk/bsd.pkg.mk" 39.include "../../mk/bsd.pkg.mk"
cvs diff -r1.2 -r1.3 pkgsrc/biology/kallisto/PLIST (expand / switch to unified diff)

--- pkgsrc/biology/kallisto/PLIST 2020/07/23 19:22:00 1.2
+++ pkgsrc/biology/kallisto/PLIST 2022/02/27 01:57:27 1.3
@@ -1,10 +1,12 @@ @@ -1,10 +1,12 @@
1@comment $NetBSD: PLIST,v 1.2 2020/07/23 19:22:00 bacon Exp $ 1@comment $NetBSD: PLIST,v 1.3 2022/02/27 01:57:27 bacon Exp $
2bin/kallisto 2bin/kallisto
3bin/kallisto-test 3bin/kallisto-test
4share/kallisto/test/README.md 4share/kallisto/test/README.md
5share/kallisto/test/Snakefile 5share/kallisto/test/Snakefile
6share/kallisto/test/chrom.txt 6share/kallisto/test/chrom.txt
7share/kallisto/test/reads_1.fastq.gz 7share/kallisto/test/reads_1.fastq.gz
8share/kallisto/test/reads_2.fastq.gz 8share/kallisto/test/reads_2.fastq.gz
 9share/kallisto/test/sc_reads_1.fastq.gz
 10share/kallisto/test/sc_reads_2.fastq.gz
9share/kallisto/test/transcripts.fasta.gz 11share/kallisto/test/transcripts.fasta.gz
10share/kallisto/test/transcripts.gtf.gz 12share/kallisto/test/transcripts.gtf.gz
cvs diff -r1.4 -r1.5 pkgsrc/biology/kallisto/distinfo (expand / switch to unified diff)

--- pkgsrc/biology/kallisto/distinfo 2021/10/26 10:03:40 1.4
+++ pkgsrc/biology/kallisto/distinfo 2022/02/27 01:57:27 1.5
@@ -1,5 +1,8 @@ @@ -1,5 +1,8 @@
1$NetBSD: distinfo,v 1.4 2021/10/26 10:03:40 nia Exp $ 1$NetBSD: distinfo,v 1.5 2022/02/27 01:57:27 bacon Exp $
2 2
3BLAKE2s (kallisto-0.46.1.tar.gz) = 8468937c3735b7bd476db90557b0fd590b65de46b6bc80a58387702b6c34d86a 3BLAKE2s (kallisto-0.48.0.tar.gz) = c31cdd71591d4784e5b48560dd2c8ed19f8baa77317f0c05441a75f7deb39d64
4SHA512 (kallisto-0.46.1.tar.gz) = 53a4db8fd5e0585693d8cd683651b4bdcc84c724a19e80a6162f1844fd491eb2d4e3180be2d9aabea7d49c9cbe0a05250f41da7d1de89d5d6cb6a8806f1afb7d 4SHA512 (kallisto-0.48.0.tar.gz) = 6325660c18c98b591bfa0f293f55f13fa45b58acf86dead3b0c9cd88942c9d3dfa548cf0b8f05fb89697845b7047627b8fcdfba4237a5876463311a6f7127feb
5Size (kallisto-0.46.1.tar.gz) = 2254560 bytes 5Size (kallisto-0.48.0.tar.gz) = 2706838 bytes
 6SHA1 (patch-CMakeLists.txt) = 9c96f53ec2e280b7f778ae04b002783559730df7
 7SHA1 (patch-src_CMakeLists.txt) = dde489a9299207d189d3f94b875bb1929c958897
 8SHA1 (patch-src_kseq.h) = c35bca57fb85367e8646a4b771449da7dbfbb439
File Added: pkgsrc/biology/kallisto/patches/patch-CMakeLists.txt
$NetBSD: patch-CMakeLists.txt,v 1.3 2022/02/27 01:57:27 bacon Exp $

# Unbundle htslib

--- CMakeLists.txt.orig	2022-02-26 16:36:13.527572702 +0000
+++ CMakeLists.txt
@@ -43,15 +43,6 @@ ENDIF(LINK MATCHES static)
 
 
 include(ExternalProject)
-ExternalProject_Add(htslib
-    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
-    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
-    BUILD_IN_SOURCE 1
-    CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure 
-        --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
-    BUILD_COMMAND make lib-static
-    INSTALL_COMMAND ""
-)
 
 include_directories(${htslib_PREFIX}/src/htslib)
File Added: pkgsrc/biology/kallisto/patches/patch-src_CMakeLists.txt
$NetBSD: patch-src_CMakeLists.txt,v 1.3 2022/02/27 01:57:27 bacon Exp $

# Unbundle htslib

--- src/CMakeLists.txt.orig	2022-02-26 16:35:26.912550601 +0000
+++ src/CMakeLists.txt
@@ -3,15 +3,13 @@ file(GLOB headers *.h *.hpp)
 
 list(REMOVE_ITEM sources main.cpp)
 
-include_directories(../ext/htslib)
-
 add_library(kallisto_core ${sources} ${headers})
 target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
 add_executable(kallisto main.cpp)
 
 find_package( Threads REQUIRED )
-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
+target_link_libraries(kallisto kallisto_core pthread hts)
 
 if(LINK MATCHES static)
     set(BUILD_SHARED_LIBS OFF)
@@ -62,4 +60,4 @@ else()
 endif(LINK MATCHES static)
 
 
-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
\ No newline at end of file
+install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
File Added: pkgsrc/biology/kallisto/patches/patch-src_kseq.h
$NetBSD: patch-src_kseq.h,v 1.1 2022/02/27 01:57:27 bacon Exp $

# Unbundle htslib

--- src/kseq.h.orig	2022-02-26 16:37:08.929391121 +0000
+++ src/kseq.h
@@ -27,6 +27,8 @@ SOFTWARE.
 #include <ctype.h>
 #include <string.h>
 #include <stdlib.h>
+// Prevent redefinition of kstring_t below
+#include <htslib/kstring.h>
 
 #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
 #define KS_SEP_TAB   1 // isspace() && !' '