biology/kallisto: Update to 0.48.0

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

6 files changed, 81 insertions, 8 deletions

diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index 730338ac22d..3f95c200ce1 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.3 2020/07/23 19:22:00 bacon Exp $
+# $NetBSD: Makefile,v 1.4 2022/02/27 01:57:27 bacon Exp $
 
-DISTNAME=	kallisto-0.46.1
+DISTNAME=	kallisto-0.48.0
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=pachterlab/}
 GITHUB_TAG=	v${PKGVERSION_NOREV}
@@ -20,13 +20,13 @@ SUBST_FILES.test=	kallisto-test
 SUBST_SED.test=		-e 's|/usr/local/share/kallisto|${DATADIR}|g'
 
 CMAKE_ARGS+=		-DUSE_HDF5:BOOL=ON
-MAKE_JOBS_SAFE=		no	# Doesn't finished bundled htslib first
 INSTALLATION_DIRS+=	${DATADIR}
 
 DATADIR=		${PREFIX}/share/kallisto
 
 post-extract:
 	${CP} ${FILESDIR}/kallisto-test ${WRKSRC}
+	${RM} -rf ${WRKSRC}/ext/htslib
 
 post-install:
 	${INSTALL_SCRIPT} ${WRKSRC}/kallisto-test ${DESTDIR}${PREFIX}/bin
@@ -35,4 +35,5 @@ post-install:
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../archivers/libaec/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../biology/htslib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/kallisto/PLIST b/biology/kallisto/PLIST
index 870b133476a..ebe03604392 100644
--- a/biology/kallisto/PLIST
+++ b/biology/kallisto/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2020/07/23 19:22:00 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2022/02/27 01:57:27 bacon Exp $
 bin/kallisto
 bin/kallisto-test
 share/kallisto/test/README.md
@@ -6,5 +6,7 @@ share/kallisto/test/Snakefile
 share/kallisto/test/chrom.txt
 share/kallisto/test/reads_1.fastq.gz
 share/kallisto/test/reads_2.fastq.gz
+share/kallisto/test/sc_reads_1.fastq.gz
+share/kallisto/test/sc_reads_2.fastq.gz
 share/kallisto/test/transcripts.fasta.gz
 share/kallisto/test/transcripts.gtf.gz
diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo
index 8b290aafc15..2ac49ae0baf 100644
--- a/biology/kallisto/distinfo
+++ b/biology/kallisto/distinfo
@@ -1,5 +1,8 @@
-$NetBSD: distinfo,v 1.4 2021/10/26 10:03:40 nia Exp $
+$NetBSD: distinfo,v 1.5 2022/02/27 01:57:27 bacon Exp $
 
-BLAKE2s (kallisto-0.46.1.tar.gz) = 8468937c3735b7bd476db90557b0fd590b65de46b6bc80a58387702b6c34d86a
-SHA512 (kallisto-0.46.1.tar.gz) = 53a4db8fd5e0585693d8cd683651b4bdcc84c724a19e80a6162f1844fd491eb2d4e3180be2d9aabea7d49c9cbe0a05250f41da7d1de89d5d6cb6a8806f1afb7d
-Size (kallisto-0.46.1.tar.gz) = 2254560 bytes
+BLAKE2s (kallisto-0.48.0.tar.gz) = c31cdd71591d4784e5b48560dd2c8ed19f8baa77317f0c05441a75f7deb39d64
+SHA512 (kallisto-0.48.0.tar.gz) = 6325660c18c98b591bfa0f293f55f13fa45b58acf86dead3b0c9cd88942c9d3dfa548cf0b8f05fb89697845b7047627b8fcdfba4237a5876463311a6f7127feb
+Size (kallisto-0.48.0.tar.gz) = 2706838 bytes
+SHA1 (patch-CMakeLists.txt) = 9c96f53ec2e280b7f778ae04b002783559730df7
+SHA1 (patch-src_CMakeLists.txt) = dde489a9299207d189d3f94b875bb1929c958897
+SHA1 (patch-src_kseq.h) = c35bca57fb85367e8646a4b771449da7dbfbb439
diff --git a/biology/kallisto/patches/patch-CMakeLists.txt b/biology/kallisto/patches/patch-CMakeLists.txt
new file mode 100644
index 00000000000..70aaa3cbe12
--- /dev/null
+++ b/biology/kallisto/patches/patch-CMakeLists.txt
@@ -0,0 +1,22 @@
+$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(${htslib_PREFIX}/src/htslib)
+ 
diff --git a/biology/kallisto/patches/patch-src_CMakeLists.txt b/biology/kallisto/patches/patch-src_CMakeLists.txt
new file mode 100644
index 00000000000..f721fef7213
--- /dev/null
+++ b/biology/kallisto/patches/patch-src_CMakeLists.txt
@@ -0,0 +1,30 @@
+$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 "${CMAKE_INSTALL_BINDIR}")
diff --git a/biology/kallisto/patches/patch-src_kseq.h b/biology/kallisto/patches/patch-src_kseq.h
new file mode 100644
index 00000000000..695c202aa74
--- /dev/null
+++ b/biology/kallisto/patches/patch-src_kseq.h
@@ -0,0 +1,15 @@
+$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() && !' '