reinit the tree, so we can have metadata

7 files changed, 171 insertions, 0 deletions

diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest
new file mode 100644
index 000000000000..81152dbf720b
--- /dev/null
+++ b/sci-biology/cufflinks/Manifest
@@ -0,0 +1,9 @@
+AUX cufflinks-2.2.1-boost-1.65-tr1-removal.patch 344 SHA256 284c120453ec82ed194cdff6cd6344ac9fcf3dfba9c960483313be077241838e SHA512 774558e93cf57ca9e9361df2271119474c8726573ff4467af4836db863d87ff0f38fe7048c9287227f18d3541891bb7b433b5fa33567616eeecda2bb5b057e9a WHIRLPOOL a984c72436d307ecaf68efa5e6367d377912d616c4f35625df2471361a02ef2009d0f5d42355ac856852a3d30ecd390a1e9916bc67496df23637ebd5e6914afa
+AUX cufflinks-2.2.1-flags.patch 1132 SHA256 3f86cd6ef757bc597bf4a511c119f176d4bb1bc06b3098791849446329f42a2e SHA512 58ea036d55d0b4835a56ea66afc2359bdb3e022f1fda3cab8402e4a2d7c6eab00fae96c739f89a25ca1e7528dad02f20c5c944a198c1eeca245e8995fbaa8f12 WHIRLPOOL 40db49fef766bf43508fc9748b31dce0098fc2cbd330106dd8156ccab39bbad5f5d15027fa126b6fe7eae082a10355319cca1b223e170d3ab99b8f587a8d935f
+AUX cufflinks-2.2.1-gcc6.patch 344 SHA256 eb3df22fac5dc390ee72fcb2d1dd794d744acc08456a37d6343ead6348bc7786 SHA512 1e8fc2e717c464e39aecf2c434857e962a809fd2a9f84bfca2b7230d5150d464262b579f1a8c13970767e929562d04994d60002834c98c204e089d2d2a8381c0 WHIRLPOOL 3bb3f042c3f1d2e9c3c58a57ef7f519063241f6526dc4ac464a7668d8ad41aff19d4b7e1a945f45ce28bab886bf7081d13a95fe423458442146d2894361d8c8a
+AUX cufflinks-2.2.1-samtools-legacy.patch 1105 SHA256 384370accab11dee8b3bfa6f31a6e506bf6b1f1c82906d4d72194f58dd69b453 SHA512 80c6eaadcfe6919d61b63efc83d3d618e939c3a1cd5e4977f936c41656a96c7c2dd71a1309d6b0422b1bf248a366643a62f011b30b37b4001efae5da04acaadf WHIRLPOOL af190cdf446331dffbdc9d247ed7574e855ccd0287b81d1e7c83c709eadd7fc60276dd5fdfed26f61cf52053a1ae444cf5d0c72b5b59bb8f9d3eb7799bbfbb3f
+DIST cufflinks-2.2.1.tar.gz 766280 SHA256 e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b WHIRLPOOL bd40e6612f3c16466cf14efe706e38663c61d01661f901d9fdb140d0419e47e2ff10515dc7a0ff81da081e87af6d5d393d88cc4d036e8b921491fb5a790ae224
+EBUILD cufflinks-2.2.1-r2.ebuild 1187 SHA256 048bbaf1af91038ed6af53b08cd78bfd0c7856c3741205a48c7abcbda3e52646 SHA512 8894ed39cc003b86660453968ad4ba7013153e16ec22f7818dce541bcdfd241693139ad45996b8b42edce5412de1413f4ad0966bf5b04c5e9a39476458d14a82 WHIRLPOOL ba3d9678f81e1a13646e0461fa53946a86088902c38fb68fd7c74bdb57cada5a6f77bcd655025d57783f4370e0854828ca482e51e78b53e30f512795fc4acbe6
+MISC ChangeLog 3543 SHA256 39d8c4ff13a6022567504b432e48ba6aacb4a902831b958917fe2d2522d7adf9 SHA512 2cc7d3924bf6276b0e748203ad96af4fc70fd52a61f05bb12b38bbb61b09ac1d51834260e5240fb1079253ccd05099f326961b2e3c8907209d40d114fadc1a81 WHIRLPOOL d892bb756e9b707829b709330a67b3ef7c550d3c7bfa34b0ab7eac49cd6ce7dda103e74c464d3592832b91f9cb880160c99ec2e90e4f47aa09f1e8e3707a8aa4
+MISC ChangeLog-2015 2124 SHA256 a1c5876fc85bd35681d61a2f8679365f556de35dfec2e9605e18b0e0016fabef SHA512 ed23958452e90447dd9f58c8bb2ab65d367bd44cf74f09ea00840a40afb3ba1c97c2df888bde5e46c05ed96cce7e2a54bdce0d491928dd0c1d01a6872c88036b WHIRLPOOL 3d087552cc441da6d0ae23f1532e04a79e7aa8862088d74079fd823f26e66a806637a56f547b8f674d5a602d160c1ab51157772bd726f765e0373141154c437d
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
new file mode 100644
index 000000000000..89f8484fad6a
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools flag-o-matic python-single-r1 toolchain-funcs
+
+DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq"
+HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
+SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	sci-biology/samtools:0.1-legacy
+	>=dev-libs/boost-1.62.0:=
+	${PYTHON_DEPS}"
+DEPEND="
+	${RDEPEND}
+	dev-cpp/eigen:3
+	virtual/pkgconfig"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-samtools-legacy.patch
+	"${FILESDIR}"/${P}-flags.patch
+	"${FILESDIR}"/${P}-gcc6.patch
+	"${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch
+)
+
+src_prepare() {
+	default
+	python_fix_shebang src/cuffmerge
+
+	eautoreconf
+}
+
+src_configure() {
+	# keep in sync with Boost
+	append-cxxflags -std=c++14
+	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
+
+	econf \
+		--disable-optim \
+		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \
+		--with-bam="${EPREFIX}/usr/" \
+		$(use_enable debug) \
+		PYTHON="${PYTHON}"
+}
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch
new file mode 100644
index 000000000000..42a906e7a83a
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch
@@ -0,0 +1,14 @@
+Boost 1.65 removed the TR1 headers.
+Bug: https://bugs.gentoo.org/show_bug.cgi?id=630654
+
+--- a/src/biascorrection.h
++++ b/src/biascorrection.h
+@@ -15,7 +15,7 @@
+ #include <vector>
+ #include <list>
+ #include <string>
+-#include <boost/tr1/unordered_map.hpp>
++#include <boost/unordered_map.hpp>
+ #include <boost/thread.hpp>
+ #include "common.h"
+ 
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
new file mode 100644
index 000000000000..47784088fab9
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
@@ -0,0 +1,28 @@
+ configure.ac | 7 ++++---
+ 1 file changed, 4 insertions(+), 3 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 96ffbac..e88b8e4 100755
+--- a/configure.ac
++++ b/configure.ac
+@@ -61,7 +61,8 @@ AC_CANONICAL_HOST
+ 
+ # set CFLAGS and CXXFLAGS
+ user_CFLAGS=${CFLAGS}
+-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024"
++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized"
++generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024"
+ ext_CFLAGS=""
+ debug_CFLAGS=""
+ #echo "${host_cpu}-${host_os}"
+@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling,      [  --enable-profiling        enable profiling with
+ 	  [ext_LDFLAGS="-lprofiler -ltcmalloc"], [])
+ 	  
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
+-CXXFLAGS="$CFLAGS"
+-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
++CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}"
++CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
+ user_LDFLAGS="$LDFLAGS"
+ LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
+ 
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch
new file mode 100644
index 000000000000..6ee9bcf456d4
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch
@@ -0,0 +1,14 @@
+--- a/src/lemon/error.h
++++ b/src/lemon/error.h
+@@ -67,9 +67,9 @@
+     }
+ 
+     ExceptionMember& operator=(const ExceptionMember& copy) {
+-      if (ptr.get() == 0) return;
++      if (ptr.get() == 0) return *this;
+       try {
+-	if (!copy.valid()) return;
++	if (!copy.valid()) return *this;
+  	*ptr = copy.get();
+       } catch (...) {}
+     }
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch
new file mode 100644
index 000000000000..374ce519ef86
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch
@@ -0,0 +1,44 @@
+Modify the buildsystem to work with the legacy version of samtools,
+which can coexist with the most recent version of samtools.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=577854
+
+--- cufflinks-2.2.1/ax_bam.m4
++++ cufflinks-2.2.1/ax_bam.m4
+@@ -102,7 +102,7 @@
+ 
+ 	AC_LANG_PUSH(C++)
+      	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+-	@%:@include <bam/bam.h>
++	@%:@include <bam-0.1-legacy/bam.h>
+ 	]], [[
+ 	]])],[
+         AC_MSG_RESULT(yes)
+@@ -171,7 +171,7 @@
+ 
+ 		AC_LANG_PUSH(C++)
+ 	     	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+-		@%:@include <bam/version.hpp>
++		@%:@include <bam-0.1-legacy/version.hpp>
+ 		]], [[
+ 		]])],[
+         	AC_MSG_RESULT(yes)
+@@ -189,7 +189,7 @@
+ 			AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).])
+ 		fi
+ 	else
+-		BAM_LIB="-lbam"
++		BAM_LIB="-lbam-0.1-legacy"
+ 		AC_SUBST(BAM_CPPFLAGS)
+ 		AC_SUBST(BAM_LDFLAGS)
+ 		AC_SUBST(BAM_LIB)
+--- cufflinks-2.2.1/src/hits.h
++++ cufflinks-2.2.1/src/hits.h
+@@ -18,7 +18,7 @@
+ 
+ #include <boost/shared_ptr.hpp>
+ 
+-#include <bam/sam.h>
++#include <bam-0.1-legacy/sam.h>
+ 
+ #include "common.h"
+ #include "multireads.h"
diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/cufflinks/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>