kallisto: Test biology/kallisto with libaec in place of szip
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Makefile
1
Makefile
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@ -1688,6 +1688,7 @@ SUBDIR+= kacst-ttf
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SUBDIR+= kactivitymanagerd
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SUBDIR+= kahakai
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SUBDIR+= kalarmcal
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SUBDIR+= kallisto
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SUBDIR+= kamera
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SUBDIR+= kannel-gateway
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SUBDIR+= kapacitor
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@ -0,0 +1,4 @@
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Kallisto is a program for quantifying abundances of transcripts from RNA-Seq
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data, or more generally of target sequences using high-throughput sequencing
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reads. It is based on the novel idea of pseudoalignment for rapidly determining
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the compatibility of reads with targets, without the need for alignment.
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@ -0,0 +1,38 @@
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# $NetBSD: Makefile,v 1.1 2018/12/21 19:00:56 bacon Exp $
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DISTNAME= kallisto-${PV}
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=pachterlab/}
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GITHUB_TAG= v${PV}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= https://pachterlab.github.io/kallisto/
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COMMENT= Quantify abundances of transcripts from RNA-Seq data
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LICENSE= 2-clause-bsd
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USE_LANGUAGES= c c++
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USE_TOOLS+= pax
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USE_CMAKE= yes
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SUBST_CLASSES+= test
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SUBST_STAGE.test= post-build
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SUBST_FILES.test= kallisto-test
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SUBST_SED.test= -e 's|/usr/local/share/kallisto|${DATADIR}|g'
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PV= 0.45.0
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DATADIR= ${PREFIX}/share/kallisto
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INSTALLATION_DIRS= bin ${DATADIR}
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post-extract:
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${CP} ${FILESDIR}/kallisto-test ${WRKSRC}
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post-install:
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${INSTALL_SCRIPT} ${WRKSRC}/kallisto-test ${DESTDIR}${PREFIX}/bin
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cd ${WRKSRC} && pax -rw test ${DESTDIR}${DATADIR}
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.include "../../biology/htslib/buildlink3.mk"
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.include "../../devel/hdf5/buildlink3.mk"
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.include "../../wip/libaec/buildlink3.mk"
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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@ -0,0 +1,10 @@
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@comment $NetBSD: PLIST,v 1.1 2018/12/21 19:00:56 bacon Exp $
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bin/kallisto
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bin/kallisto-test
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share/kallisto/test/README.md
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share/kallisto/test/Snakefile
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share/kallisto/test/chrom.txt
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share/kallisto/test/reads_1.fastq.gz
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share/kallisto/test/reads_2.fastq.gz
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share/kallisto/test/transcripts.fasta.gz
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share/kallisto/test/transcripts.gtf.gz
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@ -0,0 +1,8 @@
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$NetBSD: distinfo,v 1.1 2018/12/21 19:00:56 bacon Exp $
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SHA1 (kallisto-0.45.0.tar.gz) = ab0890c5d675d678dbcf415a86512b4694b3a4a6
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RMD160 (kallisto-0.45.0.tar.gz) = f482f7525dde0bfc2425cf803812c1c7748c882e
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SHA512 (kallisto-0.45.0.tar.gz) = b120c36ccb4725b19307c3e90c7f9b73b87efc53f08d3f2c12fc2e4b7afc3c03c52ba07dff623c9c8ad5a7e89c1eeb907389ccf3e4440236e81a0611500639e2
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Size (kallisto-0.45.0.tar.gz) = 2250430 bytes
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SHA1 (patch-CMakeLists.txt) = 2817091347e35898fec0bab77e8d9cc5ca5fff3f
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SHA1 (patch-src_CMakeLists.txt) = 2ef72024591c5216fbf44fb7cdfa4a8330b0c81a
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@ -0,0 +1,45 @@
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#!/bin/sh
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##########################################################################
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# Script description:
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# Run standard kallisto test data
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#
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# History:
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# Date Name Modification
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# 2016-03-21 J Bacon Begin
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##########################################################################
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usage()
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{
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printf "Usage: $0 test-directory\n"
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exit 1
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}
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##########################################################################
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# Main
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##########################################################################
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if [ $# != 1 ]; then
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usage
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fi
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dir="$1"
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if [ -e "$dir" ]; then
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printf "$dir already exists. Remove it first or choose a different name.\n"
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exit 1
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fi
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cp -iR /usr/local/share/kallisto/test/ "$dir"
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cd "$dir"
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kallisto index -i transcripts.idx transcripts.fasta.gz
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kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
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ls -l output
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more output/abundance.tsv
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cat << EOM
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See https://pachterlab.github.io/kallisto/starting.html for instructions
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on interpreting the output above.
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EOM
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@ -0,0 +1,28 @@
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$NetBSD: patch-CMakeLists.txt,v 1.1 2018/12/21 19:00:56 bacon Exp $
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# Unbundle htslib
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--- CMakeLists.txt.orig 2018-12-19 17:13:04.000000000 +0000
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+++ CMakeLists.txt
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@@ -35,21 +35,6 @@ ELSE(LINK MATCHES shared)
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ENDIF(LINK MATCHES static)
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-include(ExternalProject)
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-ExternalProject_Add(htslib
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- PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
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- SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
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- BUILD_IN_SOURCE 1
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- CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure
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- --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
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- BUILD_COMMAND make lib-static
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- INSTALL_COMMAND ""
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-)
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-
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-include_directories(${htslib_PREFIX}/src/htslib)
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-
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-
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-
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# add_compile_options(-Wdeprecated-register)
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add_subdirectory(src)
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@ -0,0 +1,30 @@
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$NetBSD: patch-src_CMakeLists.txt,v 1.1 2018/12/21 19:00:56 bacon Exp $
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# Unbundle htslib
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--- src/CMakeLists.txt.orig 2018-10-17 23:58:22 UTC
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+++ src/CMakeLists.txt
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@@ -3,15 +3,13 @@ file(GLOB headers *.h *.hpp)
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list(REMOVE_ITEM sources main.cpp)
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-include_directories(../ext/htslib)
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-
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add_library(kallisto_core ${sources} ${headers})
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target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
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add_executable(kallisto main.cpp)
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find_package( Threads REQUIRED )
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-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
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+target_link_libraries(kallisto kallisto_core pthread hts)
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if(LINK MATCHES static)
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set(BUILD_SHARED_LIBS OFF)
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@@ -56,4 +54,4 @@ else()
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endif(LINK MATCHES static)
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-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
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\ No newline at end of file
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+install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
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