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kallisto: Remove following commit
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Fri Dec 21 14:50:12 2018 -0600
Changeset: 9511535079bc7771c84341f27dd0ceca176623fa
Modified Files:
Makefile
Removed Files:
kallisto/DESCR
kallisto/Makefile
kallisto/PLIST
kallisto/distinfo
kallisto/files/kallisto-test
kallisto/patches/patch-CMakeLists.txt
kallisto/patches/patch-src_CMakeLists.txt
Log Message:
kallisto: Remove following commit
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9511535079bc7771c84341f27dd0ceca176623fa
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 -
kallisto/DESCR | 4 ---
kallisto/Makefile | 38 --------------------------
kallisto/PLIST | 10 -------
kallisto/distinfo | 8 ------
kallisto/files/kallisto-test | 45 -------------------------------
kallisto/patches/patch-CMakeLists.txt | 28 -------------------
kallisto/patches/patch-src_CMakeLists.txt | 30 ---------------------
8 files changed, 164 deletions(-)
diffs:
diff --git a/Makefile b/Makefile
index 6ac003847e..2a34747455 100644
--- a/Makefile
+++ b/Makefile
@@ -1649,7 +1649,6 @@ SUBDIR+= kacst-ttf
SUBDIR+= kactivitymanagerd
SUBDIR+= kahakai
SUBDIR+= kalarmcal
-SUBDIR+= kallisto
SUBDIR+= kamera
SUBDIR+= kannel-gateway
SUBDIR+= kate
diff --git a/kallisto/DESCR b/kallisto/DESCR
deleted file mode 100644
index de9c8d8c3d..0000000000
--- a/kallisto/DESCR
+++ /dev/null
@@ -1,4 +0,0 @@
-Kallisto is a program for quantifying abundances of transcripts from RNA-Seq
-data, or more generally of target sequences using high-throughput sequencing
-reads. It is based on the novel idea of pseudoalignment for rapidly determining
-the compatibility of reads with targets, without the need for alignment.
diff --git a/kallisto/Makefile b/kallisto/Makefile
deleted file mode 100644
index eef1448ab0..0000000000
--- a/kallisto/Makefile
+++ /dev/null
@@ -1,38 +0,0 @@
-# $NetBSD$
-
-DISTNAME= kallisto-${PV}
-CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_GITHUB:=pachterlab/}
-GITHUB_TAG= v${PV}
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= https://pachterlab.github.io/kallisto/
-COMMENT= Quantify abundances of transcripts from RNA-Seq data
-LICENSE= 2-clause-bsd
-
-USE_LANGUAGES= c c++
-USE_TOOLS+= pax
-USE_CMAKE= yes
-
-SUBST_CLASSES+= test
-SUBST_STAGE.test= post-build
-SUBST_FILES.test= kallisto-test
-SUBST_SED.test= -e 's|/usr/local/share/kallisto|${DATADIR}|g'
-
-PV= 0.45.0
-DATADIR= ${PREFIX}/share/kallisto
-
-INSTALLATION_DIRS= bin ${DATADIR}
-
-post-extract:
- ${CP} ${FILESDIR}/kallisto-test ${WRKSRC}
-
-post-install:
- ${INSTALL_SCRIPT} ${WRKSRC}/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"
-.include "../../mk/bsd.pkg.mk"
diff --git a/kallisto/PLIST b/kallisto/PLIST
deleted file mode 100644
index dbae922335..0000000000
--- a/kallisto/PLIST
+++ /dev/null
@@ -1,10 +0,0 @@
-@comment $NetBSD$
-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
deleted file mode 100644
index faae34d6ad..0000000000
--- a/kallisto/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD$
-
-SHA1 (kallisto-0.45.0.tar.gz) = ab0890c5d675d678dbcf415a86512b4694b3a4a6
-RMD160 (kallisto-0.45.0.tar.gz) = f482f7525dde0bfc2425cf803812c1c7748c882e
-SHA512 (kallisto-0.45.0.tar.gz) = b120c36ccb4725b19307c3e90c7f9b73b87efc53f08d3f2c12fc2e4b7afc3c03c52ba07dff623c9c8ad5a7e89c1eeb907389ccf3e4440236e81a0611500639e2
-Size (kallisto-0.45.0.tar.gz) = 2250430 bytes
-SHA1 (patch-CMakeLists.txt) = 2817091347e35898fec0bab77e8d9cc5ca5fff3f
-SHA1 (patch-src_CMakeLists.txt) = 2ef72024591c5216fbf44fb7cdfa4a8330b0c81a
diff --git a/kallisto/files/kallisto-test b/kallisto/files/kallisto-test
deleted file mode 100644
index f0b7695224..0000000000
--- a/kallisto/files/kallisto-test
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/bin/sh
-
-##########################################################################
-# Script description:
-# Run standard kallisto test data
-#
-# History:
-# Date Name Modification
-# 2016-03-21 J Bacon Begin
-##########################################################################
-
-usage()
-{
- printf "Usage: $0 test-directory\n"
- exit 1
-}
-
-
-##########################################################################
-# Main
-##########################################################################
-
-if [ $# != 1 ]; then
- usage
-fi
-
-dir="$1"
-if [ -e "$dir" ]; then
- printf "$dir already exists. Remove it first or choose a different name.\n"
- exit 1
-fi
-
-cp -iR /usr/local/share/kallisto/test/ "$dir"
-cd "$dir"
-kallisto index -i transcripts.idx transcripts.fasta.gz
-kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
-ls -l output
-more output/abundance.tsv
-
-cat << EOM
-
-See https://pachterlab.github.io/kallisto/starting.html for instructions
-on interpreting the output above.
-
-EOM
diff --git a/kallisto/patches/patch-CMakeLists.txt b/kallisto/patches/patch-CMakeLists.txt
deleted file mode 100644
index fb2e62ac5b..0000000000
--- a/kallisto/patches/patch-CMakeLists.txt
+++ /dev/null
@@ -1,28 +0,0 @@
-$NetBSD$
-
-# Unbundle htslib
-
---- CMakeLists.txt.orig 2018-12-19 17:13:04.000000000 +0000
-+++ 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 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(${htslib_PREFIX}/src/htslib)
--
--
--
- # add_compile_options(-Wdeprecated-register)
-
- add_subdirectory(src)
diff --git a/kallisto/patches/patch-src_CMakeLists.txt b/kallisto/patches/patch-src_CMakeLists.txt
deleted file mode 100644
index 11280e311e..0000000000
--- a/kallisto/patches/patch-src_CMakeLists.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-$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}")
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