kallisto: Update plist, clean up and test

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Oct 25 15:53:00 2018 -0500
Changeset:	891f09f38955acfa9a0c8308dd464e7cbabde11f

Modified Files:
	kallisto/Makefile
	kallisto/PLIST
	kallisto/distinfo
Added Files:
	kallisto/patches/patch-CMakeLists.txt
	kallisto/patches/patch-src_CMakeLists.txt

Log Message:
kallisto: Update plist, clean up and test

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=891f09f38955acfa9a0c8308dd464e7cbabde11f

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

diffstat:
 kallisto/Makefile                         | 10 ++--------
 kallisto/PLIST                            |  2 ++
 kallisto/distinfo                         |  2 ++
 kallisto/patches/patch-CMakeLists.txt     | 28 ++++++++++++++++++++++++++++
 kallisto/patches/patch-src_CMakeLists.txt | 30 ++++++++++++++++++++++++++++++
 5 files changed, 64 insertions(+), 8 deletions(-)

diffs:
diff --git a/kallisto/Makefile b/kallisto/Makefile
index 970773b9b8..a39a16fdb9 100644
--- a/kallisto/Makefile
+++ b/kallisto/Makefile
@@ -14,30 +14,24 @@ GITHUB_TAG=	v${PV}
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://pachterlab.github.io/kallisto/about.html
 COMMENT=	Quantify abundances of transcripts from RNA-Seq data
-# Check this
 LICENSE=	2-clause-bsd
 
-# Test and change if necessary.
-# MAKE_JOBS_SAFE=	no
-
-# Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	pax
 USE_CMAKE=	yes
 
-CXXFLAGS+=	-I${PREFIX}/include
+# CXXFLAGS+=	-I${PREFIX}/include
 
 PV=		0.44.0
 DATADIR=	${PREFIX}/share/kallisto
 
-# Specify which directories to create before install.
-# You should only need this if using your own install target.
 INSTALLATION_DIRS=	bin ${DATADIR}
 
 post-install:
 	${INSTALL_SCRIPT} ${FILESDIR}/kallisto-test ${DESTDIR}${PREFIX}/bin
 	cd ${WRKSRC} && pax -rw test ${DESTDIR}${DATADIR}
 
+.include "../../biology/htslib/buildlink3.mk"
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../archivers/szip/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
diff --git a/kallisto/PLIST b/kallisto/PLIST
index 897025dc87..dbae922335 100644
--- a/kallisto/PLIST
+++ b/kallisto/PLIST
@@ -3,6 +3,8 @@ bin/kallisto
 bin/kallisto-test
 share/kallisto/test/README.md
 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/transcripts.fasta.gz
+share/kallisto/test/transcripts.gtf.gz
diff --git a/kallisto/distinfo b/kallisto/distinfo
index c31edcde4f..1a3c78ce68 100644
--- a/kallisto/distinfo
+++ b/kallisto/distinfo
@@ -4,3 +4,5 @@ SHA1 (kallisto-0.44.0.tar.gz) = 77f4e5ec4f94ed222ece07fee2792dfe0e8f096f
 RMD160 (kallisto-0.44.0.tar.gz) = 15888692b43c7aed659d27e7d21659b54d51aece
 SHA512 (kallisto-0.44.0.tar.gz) = 7809257c2aa9ccca98e34cb16e12ce00ceb691600430ae689d4fdcdd7a43850ec940b6868550399bf3cef1136af8a6e6320ecd5215ee4aee6a136d1e27c062c2
 Size (kallisto-0.44.0.tar.gz) = 2242173 bytes
+SHA1 (patch-CMakeLists.txt) = 6624f6dd544d3d310dc103c64d5bada17e8c2381
+SHA1 (patch-src_CMakeLists.txt) = 2ef72024591c5216fbf44fb7cdfa4a8330b0c81a
diff --git a/kallisto/patches/patch-CMakeLists.txt b/kallisto/patches/patch-CMakeLists.txt
new file mode 100644
index 0000000000..3f79ba35b7
--- /dev/null
+++ b/kallisto/patches/patch-CMakeLists.txt
@@ -0,0 +1,28 @@
+$NetBSD$
+
+# Unbundle htslib
+
+--- CMakeLists.txt.orig	2018-10-17 23:58:06 UTC
++++ CMakeLists.txt
+@@ -35,21 +35,6 @@ ELSE(LINK MATCHES shared)
+ 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 ${PROJECT_SOURCE_DIR}/ext/htslib/configure 
+-        --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
+-    BUILD_COMMAND make lib-static
+-    INSTALL_COMMAND ""
+-)
+-
+-include_directories(${htslib_PREFIX}/src/htslib)
+-
+-
+-
+ # add_compile_options(-Wdeprecated-register)
+ 
+ add_subdirectory(src)
diff --git a/kallisto/patches/patch-src_CMakeLists.txt b/kallisto/patches/patch-src_CMakeLists.txt
new file mode 100644
index 0000000000..11280e311e
--- /dev/null
+++ b/kallisto/patches/patch-src_CMakeLists.txt
@@ -0,0 +1,30 @@
+$NetBSD$
+
+# Unbundle htslib
+
+--- src/CMakeLists.txt.orig	2018-10-17 23:58:22 UTC
++++ 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 ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
++target_link_libraries(kallisto kallisto_core pthread hts)
+ 
+ if(LINK MATCHES static)
+     set(BUILD_SHARED_LIBS OFF)
+@@ -56,4 +54,4 @@ else()
+ endif(LINK MATCHES static)
+ 
+ 
+-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
+\ No newline at end of file
++install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")