gentoo resync : 11.01.2018

11 files changed, 259 insertions, 0 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index f27e2dc34985..63826002c21f 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/fastx_toolkit/Manifest b/sci-biology/fastx_toolkit/Manifest
new file mode 100644
index 000000000000..033337cdcfdd
--- /dev/null
+++ b/sci-biology/fastx_toolkit/Manifest
@@ -0,0 +1,5 @@
+AUX fastx_toolkit-0.0.14-fix-build-system.patch 1885 BLAKE2B f97c5e847be5e746df5b5b37d69a3b5f410e97136ed8a294b846efddb4d3ee599835b393abb5251b7230c56f109f3a7ee6f3b5092e0f37cd849e3deda3cf9229 SHA512 72fd5048a9cda4a0afb9af7ee040ed2efa5941f6f4103d0fd83465f89f636c5282381122690dd581138318ab2d2327837e4412ab9e06cd2aeeabd6db82cbf83e
+AUX fastx_toolkit-0.0.14-gcc7.patch 225 BLAKE2B 72f7b80d0cdd3ade66ae3a83340e8b31d6f8f3b71901953ae8f56e856787b546700036c1331aad884175e2a4d659588ab80097244970b764092f87ffb08d1f44 SHA512 b0e679d367f50b8f29aa759c55e2d31e859b84e53da32ef92263b258bd6163d19c44b1ed68085b1a3600e8fb19cddee9cbb5019d6050da6c028cfc291ade504c
+DIST fastx_toolkit-0.0.14.tar.bz2 543018 BLAKE2B d61456252ada507efd4cc45ff2f0d54f7a6c55b185d41eb5f5accd7e73184b8b80b2c415b38f8e4ccd687ae715191785a89e64f790fe598ba477901c12d514a1 SHA512 e1df1486e853b3ecee71e677cd6e86246a3993174016111eb84910625dc7ec11d37aff75de7ccefad1e019e75fe72050d6529add2116b759d5056b8096286c05
+EBUILD fastx_toolkit-0.0.14.ebuild 687 BLAKE2B db00581b41017886ce6c560788cb6efb3f0a45663f3cb215dfba85267c276354d418a2d036ca757f1d675af7503430b0c39fa39f9593524c7120495f432c2c38 SHA512 0254e55a40f055eb18a31a0bd0bae97e1e6c190bf73094f591cdaea15ba413d00f2f9589369eaeaa60f93f135889a1da79ae81ae32fdb765ed162bbbce152f86
+MISC metadata.xml 339 BLAKE2B 5f3ac1398bae32aa61a3024e52c0e35065f9554d4a40830c5d694594df49f395c16614848b435e3bc5b33ad7443f6076cc1953c94add034911b1f13473be1002 SHA512 a6d032fe81daa4726fcde93dc62aac141d8f0a8bae090cd3bef43c837fddc8de10ba81870c30a0e34fec0f663f8d985dd56a451ffc9fbdcfcd05c2a318221e0b
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 000000000000..d9012a54e166
--- /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 000000000000..a8b22579f737
--- /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 000000000000..e47717785517
--- /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 000000000000..880cea0165ff
--- /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>
diff --git a/sci-biology/libgtextutils/Manifest b/sci-biology/libgtextutils/Manifest
new file mode 100644
index 000000000000..dc3c8bb842ae
--- /dev/null
+++ b/sci-biology/libgtextutils/Manifest
@@ -0,0 +1,5 @@
+AUX libgtextutils-0.6.1-fix-build-system.patch 1719 BLAKE2B 993f1e68f960853a264d5e9b9cd1352df123424f4cfbf79f2cbb4451ff6ec0fed985a1b184bfe200e036ef65a07f7e4e258f731cc12d708ed68f278b2934904c SHA512 9889fe99addb820f049800fa8aec414c28d87bbaae209af0e45614d4592d578a7309376aa69f58e7c9879ad64a20be417e9d05ebf45ec4af2729c591517e610e
+AUX libgtextutils-0.6.1-gcc6.patch 724 BLAKE2B 14ebd0ab5ec4685688caa922dacccdaad9101af0814a93b08f0c9ba5e50ac6a02291528b6ad3d61b48a2f29a25b63e421690f19109351f4472cc118886ca0e10 SHA512 74ec8fafc699cadc5d40f5284cd42cfb8c949744b7a16bbf8142c8db71ad6c921551da03f260e82bfe84b69dd5fbd2261031fe22aee6b3396515b1f66576a530
+DIST libgtextutils-0.6.1.tar.bz2 273459 BLAKE2B 81b1e9b467287ed9551fc53abddf5757efb2dd1c98f0388e2128535fbe70b706badd5702a5b5c3cb19a34c26ffa218c9c41caf9f17770a015b09fc13fabe4d53 SHA512 0bc392385f9e6c345dff82b3fb04f322e8aceca769e15a3a87da6c718b6e9a7e1de082940d4bb0339a4c3a86f706fde0de047df459682aa9ea216d6e5c17eab6
+EBUILD libgtextutils-0.6.1.ebuild 623 BLAKE2B 5bd2ff34a6898b662e6e624a77682a358b9340c6b94b9dfa40bec0637d4074ec648ca6146ee870f9cf5a8141028d23aedc55407aea04fbf2b69d62699d69d547 SHA512 e72eaddb48422afe71140394825964e6778a339ea182d614178061eb294dada1b81e7b5221a1a19d9d2ac720200f6eb4a7eab09f6ef1b7425ce7dda491add449
+MISC metadata.xml 379 BLAKE2B b5f42185a237d0dd1dcbf6c5ae9e007f0a2f875ab0e7c4e6bb8cca07b6f24248d449541e0f455687a0876d7286bc8fbd08e72df88cffc69d255d22788fbadc05 SHA512 9b77656bd047462678494259c168f2214238c909e4dd19ff822cf182e442ce385a3375158fcc0a1be53303a4828e6339ea379f9de60851c894b8d57c0a099aea
diff --git a/sci-biology/libgtextutils/files/libgtextutils-0.6.1-fix-build-system.patch b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-fix-build-system.patch
new file mode 100644
index 000000000000..f7f608b792d2
--- /dev/null
+++ b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-fix-build-system.patch
@@ -0,0 +1,61 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -15,7 +15,7 @@
+ 
+ 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])
+ 
+ # dynamic library version
+@@ -25,12 +25,12 @@
+ 
+ AC_PROG_CC
+ AC_PROG_CXX
+-AC_PROG_LIBTOOL
++LT_INIT
+ 
+ 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 "${enableval}" in
+   yes) wall=true ;;
+   no)  wall=false ;;
+@@ -42,22 +42,6 @@
+   CXXFLAGS="${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="${CFLAGS} -DDEBUG -g -O1"
+-  CXXFLAGS="${CFLAGS} -DDEBUG -g -O1"
+-else
+-  CFLAGS="${CFLAGS} -O3"
+-  CXXFLAGS="${CFLAGS} -O3"
+-fi
+ 
+ 
+ dnl --enable-tuple-parser-check
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -9,7 +9,7 @@
+ # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ 
+ EXTRA_DIST = reconf configure
+-SUBDIRS = m4 src doc tests
++SUBDIRS = src doc tests
+ 
+ pkgconfigdir = $(libdir)/pkgconfig
+ pkgconfig_DATA = gtextutils.pc
diff --git a/sci-biology/libgtextutils/files/libgtextutils-0.6.1-gcc6.patch b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-gcc6.patch
new file mode 100644
index 000000000000..490b4be9b91b
--- /dev/null
+++ b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-gcc6.patch
@@ -0,0 +1,22 @@
+From d8bb66d26288293ebde7f8d88979c13c208ffce5 Mon Sep 17 00:00:00 2001
+From: Assaf Gordon <assafgordon@gmail.com>
+Date: Mon, 14 Aug 2017 11:52:09 -0600
+Subject: [PATCH] text_line_reader: adjust to new compilers
+
+Fixes https://github.com/agordon/libgtextutils/issues/10 .
+---
+ src/gtextutils/text_line_reader.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/gtextutils/text_line_reader.cpp b/src/gtextutils/text_line_reader.cpp
+index fede933..f0984d5 100644
+--- a/src/gtextutils/text_line_reader.cpp
++++ b/src/gtextutils/text_line_reader.cpp
+@@ -44,6 +44,6 @@ bool TextLineReader::next_line()
+ 	if (input_stream.eof())
+ 		return false;
+ 
+-	return input_stream ;
++	return input_stream.good() ;
+ }
+ 
diff --git a/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild b/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild
new file mode 100644
index 000000000000..8f0455e5322c
--- /dev/null
+++ b/sci-biology/libgtextutils/libgtextutils-0.6.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Gordon Text utils Library"
+HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit/"
+SRC_URI="http://hannonlab.cshl.edu/fastx_toolkit/${P}.tar.bz2"
+
+LICENSE="AGPL-3"
+SLOT="0/0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+PATCHES=(
+	"${FILESDIR}"/${P}-fix-build-system.patch
+	"${FILESDIR}"/${P}-gcc6.patch
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf --disable-static
+}
+
+src_install() {
+	default
+
+	# package installs .pc files
+	find "${D}" -name '*.la' -delete || die
+}
diff --git a/sci-biology/libgtextutils/metadata.xml b/sci-biology/libgtextutils/metadata.xml
new file mode 100644
index 000000000000..138cb7705c0a
--- /dev/null
+++ b/sci-biology/libgtextutils/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+</pkgmetadata>