commit: 84dea31f7c0f129fa53d5a2db54895dd2255d15b Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Wed Jan 10 09:51:17 2018 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Wed Jan 10 09:52:26 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=84dea31f
sci-biology/fastx_toolkit: Initial addition Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/fastx_toolkit/Manifest | 1 + .../fastx_toolkit/fastx_toolkit-0.0.14.ebuild | 34 ++++++++++++ .../fastx_toolkit-0.0.14-fix-build-system.patch | 63 ++++++++++++++++++++++ .../files/fastx_toolkit-0.0.14-gcc7.patch | 10 ++++ sci-biology/fastx_toolkit/metadata.xml | 11 ++++ 5 files changed, 119 insertions(+) diff --git a/sci-biology/fastx_toolkit/Manifest b/sci-biology/fastx_toolkit/Manifest new file mode 100644 index 00000000000..abb3cfa08ae --- /dev/null +++ b/sci-biology/fastx_toolkit/Manifest @@ -0,0 +1 @@ +DIST fastx_toolkit-0.0.14.tar.bz2 543018 BLAKE2B d61456252ada507efd4cc45ff2f0d54f7a6c55b185d41eb5f5accd7e73184b8b80b2c415b38f8e4ccd687ae715191785a89e64f790fe598ba477901c12d514a1 SHA512 e1df1486e853b3ecee71e677cd6e86246a3993174016111eb84910625dc7ec11d37aff75de7ccefad1e019e75fe72050d6529add2116b759d5056b8096286c05 diff --git a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild new file mode 100644 index 00000000000..d9012a54e16 --- /dev/null +++ b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Tools for Short Read FASTA/FASTQ file processing" +HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit"; +SRC_URI="https://github.com/agordon/fastx_toolkit/releases/download/${PV}/${P}.tar.bz2"; + +LICENSE="AGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + sci-biology/libgtextutils + virtual/pkgconfig" +RDEPEND=" + dev-perl/PerlIO-gzip + dev-perl/GDGraph + sci-biology/libgtextutils:= + sci-visualization/gnuplot" + +PATCHES=( + "${FILESDIR}"/${P}-fix-build-system.patch + "${FILESDIR}"/${P}-gcc7.patch +) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-fix-build-system.patch b/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-fix-build-system.patch new file mode 100644 index 00000000000..a8b22579f73 --- /dev/null +++ b/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-fix-build-system.patch @@ -0,0 +1,63 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -14,12 +14,12 @@ + [fastx_toolkit]) + AC_CONFIG_AUX_DIR(config) + AC_CONFIG_MACRO_DIR([m4]) +-AM_CONFIG_HEADER(config.h) ++AC_CONFIG_HEADERS([config.h]) + AM_INIT_AUTOMAKE([dist-bzip2]) + + AC_PROG_CC + AC_PROG_CXX +-AC_PROG_LIBTOOL ++LT_INIT + AX_C_LONG_LONG + AX_CXX_HEADER_STDCXX_TR1 + AX_CXX_COMPILE_STDCXX_11([noext],[optional]) +@@ -31,9 +31,9 @@ + PKG_CHECK_MODULES([GTEXTUTILS],[gtextutils]) + + dnl --enable-wall +-EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror" ++EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal" + AC_ARG_ENABLE(wall, +-[ --enable-wall Enable many common GCC warnings (-Wall,-Wextra, -Werror etc., default enabled)], ++[ --enable-wall Enable many common GCC warnings (-Wall,-Wextra etc., default enabled)], + [case "${enableval}" in + yes) wall=true ;; + no) wall=false ;; +@@ -45,22 +45,6 @@ + CXXFLAGS="${CXXFLAGS} ${EXTRA_CHECKS}" + fi + +-dnl --enable-debug +-AC_ARG_ENABLE(debug, +-[ --enable-debug Enable debug mode (default enabled)], +-[case "${enableval}" in +- yes) debug=true ;; +- no) debug=false ;; +- *) AC_MSG_ERROR(bad value ${enableval} for --enable-debug) ;; +-esac],[debug=true]) +-if test "$debug" = "true" +-then +- CFLAGS="${CFLAGS} -DDEBUG -g -O1" +- CXXFLAGS="${CXXFLAGS} -DDEBUG -g -O1" +-else +- CFLAGS="${CFLAGS} -O3" +- CXXFLAGS="${CXXFLAGS} -O3" +-fi + + dnl 'all-static' marco copied from subversion's configure.ac + dnl Check for --enable-all-static option +--- a/Makefile.am ++++ b/Makefile.am +@@ -10,7 +10,7 @@ + + EXTRA_DIST = reconf configure README install_galaxy_files.sh + +-SUBDIRS = m4 src doc galaxy scripts build_scripts ++SUBDIRS = src doc galaxy scripts build_scripts + + ACLOCAL_AMFLAGS = -I m4 + diff --git a/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-gcc7.patch b/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-gcc7.patch new file mode 100644 index 00000000000..e4771778551 --- /dev/null +++ b/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-gcc7.patch @@ -0,0 +1,10 @@ +--- a/src/fasta_formatter/fasta_formatter.cpp ++++ b/src/fasta_formatter/fasta_formatter.cpp +@@ -103,6 +103,7 @@ + switch(opt) { + case 'h': + usage(); ++ exit(EXIT_SUCCESS); + + case 'i': + input_filename = optarg; diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml new file mode 100644 index 00000000000..880cea0165f --- /dev/null +++ b/sci-biology/fastx_toolkit/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>s...@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">agordon/fastx_toolkit</remote-id> + </upstream> +</pkgmetadata>
