sci-biology/fastx_toolkit: Initial addition

Package-Manager: Portage-2.3.19, Repoman-2.3.6

diff --git a/sci-biology/fastx_toolkit/Manifest b/sci-biology/fastx_toolkit/Manifest
new file mode 100644 (file)
index 0000000..abb3cfa
--- /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 (file)
index 0000000..d9012a5
--- /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 (file)
index 0000000..a8b2257
--- /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 (file)
index 0000000..e477177
--- /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 (file)
index 0000000..880cea0
--- /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>sci@gentoo.org</email>
+               <name>Gentoo Science Project</name>
+       </maintainer>
+       <upstream>
+               <remote-id type="github">agordon/fastx_toolkit</remote-id>
+       </upstream>
+</pkgmetadata>