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