reinit the tree, so we can have metadata

6 files changed, 180 insertions, 0 deletions

diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
new file mode 100644
index 000000000000..3b001600d840
--- /dev/null
+++ b/sci-biology/mira/Manifest
@@ -0,0 +1,9 @@
+AUX mira-4.0.2-boost-1.50.patch 1444 SHA256 5790acf4a0a19f314285abb7bcf4b0ac38594346790eaee38cb20598ee083be4 SHA512 647efc785a76369524e264b611773d9f5101c13981c98a8bfa03d2633c74ff9e16253b48a506624cf75d1b11852ae8573d6446f584a951b8c5cdec1cd23552f5 WHIRLPOOL 8beeb1a1828ad721655290c4fffc09416073edf0ca13f2295b9a5b26c22380534a6d2713a8ce991388f7d64286149ccda331811b6049320b1dfa076c17415084
+AUX mira-4.0.2-cmath.patch 295 SHA256 44f98a0c58d670d30c69b8c6159fd019e1377da4a5fc8f0797b5891286713861 SHA512 7c45bf5dd987c06c76bbacc1bd6f1137f1c6ea23eecf01643ee335216341714a0607b4468d9241c4084bed6d32e453c8bb1cb48997164769aa33223fb59edd88 WHIRLPOOL 99a653497e8ca9da7ebe11d91d0bc6553f2609a1996607b642ed6a9415c71d1da0bf0194f271d2211a17841b07b2cdd88a9b690ae438c8d811d931f7988122f7
+AUX mira-4.0.2-cout.patch 735 SHA256 674daadda7a2e3b560237b1b4990d9184286be3ba7b03c3d080268b46bb0d096 SHA512 9d1aa493d20481d0a7e3eaefba36dc29d7903f70c9a445b6e0ea478d04124e8a81de37c437f0fb28c0a395562db7e78217cf09e500fd4a1f2a1f929c1d4d2a5a WHIRLPOOL 565380db81da08694536d141c5b74b3140f955f5aab98060d40b331bd8faa087d94378f6afc8777bad36466dca0ff7d44f2febe7d5e1bfa99a06a4e12f76b5ac
+DIST mira-4.0.2.tar.bz2 10368046 SHA256 a32cb2b21e0968a5536446287c895fe9e03d11d78957554e355c1080b7b92a80 SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e WHIRLPOOL d038472f9b129e97883f59c471df51f07315ee38eda5a9e804cdd2d33988306162b1bb1dde2cb7fd510c82be5734240dfd69364d39865a47af439762c7154747
+DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
+EBUILD mira-4.0.2.ebuild 2596 SHA256 2ad115b8c1108130d8d53227843603ff9a7f7908e09b595d1b9137d75ef83c60 SHA512 d39da2d62806f3d8efb5f998b363c7309d9e2254a3f084497e2fc7c86858804e55247b9deea1460b1c1dc017f7cf587174ee3c23ad62158d74c447de16bfae0a WHIRLPOOL 571773d44e31be5f974abccb989e95723f8fe4d0584aacb86d89712239dc87f27e55caed456be0526c538a2850d291e3626aa59d2e5bd1f96216d4319185a39a
+MISC ChangeLog 3215 SHA256 932523a09fa5a0ca0cd8a91db43c773c14c12418e4c77944e495dfd3032b30dd SHA512 5c957aa95250c5a1acb53614f51f09cfa99e109b1a968064af088451edb46eb51cc56f80237770837cc60c2b182a1df01b08cd78fcc4b1a7afc8302b40a535df WHIRLPOOL c377dae8df89a237241880daa5fdbcc00d28d4b3a6fbae474ef2451326711fd338c650a642a7e38c811ffddba1cbcf0f9f52a23107cefdbaea5a7355e3f32673
+MISC ChangeLog-2015 4470 SHA256 40a66fa59c1d4434e70367580bf573a7bf29b9d01ab8cc5b3d5827ef171c3502 SHA512 ddd76e13a8cc27331d4352c7c3206fb96e29de7a4ff4fc47f4f7cd1f3cc2fd4b53947476d320397f87d4f5273754e78cdf300719575fdf3e04669e374d7e3c02 WHIRLPOOL 8298602a4f9da18ba845b60d24b787b2727adce4057db6b91c61dc783b9f0493540e17255f43a233f37ddedf74b96aec4c1119ac14d65ff6f12404879dbc034e
+MISC metadata.xml 355 SHA256 516431894fbce903b3fe5539ea04820656e23c48dcd642e808a1af66ee8a23a6 SHA512 9d9037805b94622cb468553fa27c948de2849ac4c6dc1eafae8c3261554b5e97b631fe77e4e589eff613822d316b2843bcab0c47547b202651c8a804a516554e WHIRLPOOL ae8d0b1704c5d654d5669cfdea0ac0e7c14831c833ac00aa6d647f3ab523520d164dc42e8774ce7947a751f0b5da3f590f43826331bc9aafc914f49de913ce90
diff --git a/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch
new file mode 100644
index 000000000000..50f83c9021dc
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch
@@ -0,0 +1,22 @@
+ax_boost_regex.m4 |    4 ++--
+1 file changed, 2 insertions(+), 2 deletions(-)
+
+--- mira-4.0.2/m4/ax_boost_regex.m4
++++ mira-4.0.2/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@
+                 for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
+                      ax_lib=${libextension}
+ 				    AC_CHECK_LIB($ax_lib, exit,
+-                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+                                  [link_regex="no"])
+ 				done
+                 if test "x$link_regex" != "xyes"; then
+                 for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
+                      ax_lib=${libextension}
+ 				    AC_CHECK_LIB($ax_lib, exit,
+-                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+                                  [link_regex="no"])
+ 				done
+                 fi
diff --git a/sci-biology/mira/files/mira-4.0.2-cmath.patch b/sci-biology/mira/files/mira-4.0.2-cmath.patch
new file mode 100644
index 000000000000..a4a020177af7
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-cmath.patch
@@ -0,0 +1,14 @@
+--- mira-4.0.2/src/mira/ads.C
++++ mira-4.0.2/src/mira/ads.C
+@@ -31,10 +31,11 @@
+  * Routines for computing scores and some other classification number are
+  *  provided, too.
+  *
+  */
+ 
++#include <cmath>
+ 
+ #include "ads.H"
+ 
+ #include "errorhandling/errorhandling.H"
+ #include "util/dptools.H"
diff --git a/sci-biology/mira/files/mira-4.0.2-cout.patch b/sci-biology/mira/files/mira-4.0.2-cout.patch
new file mode 100644
index 000000000000..78e7168cb49d
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-cout.patch
@@ -0,0 +1,27 @@
+ src/progs/quirks.C | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/progs/quirks.C b/src/progs/quirks.C
+index 47e5ee8..060b6f3 100644
+--- a/src/progs/quirks.C
++++ b/src/progs/quirks.C
+@@ -25,6 +25,8 @@
+ 
+ #include <boost/filesystem.hpp>
+ 
++#include <iostream>
++
+ // make the "tcmalloc: large alloc" messages from TCMallom disappear
+ // by setting the reporting environment variable to a very large value
+ // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1
+--- a/src/mira/parameters.C
++++ b/src/mira/parameters.C
+@@ -2222,7 +2222,7 @@
+     MIRANOTIFY(Notify::FATAL, "File not found: " << pfile);
+   }
+ 
+-  parse(fin, Pv, nullptr);
++  parse(fin, Pv, false);
+ 
+   fin.close();
+ 
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
new file mode 100644
index 000000000000..0704cef4806d
--- /dev/null
+++ b/sci-biology/mira/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-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="sourceforge">mira-assembler</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild
new file mode 100644
index 000000000000..fd95fbfb2a78
--- /dev/null
+++ b/sci-biology/mira/mira-4.0.2.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+MIRA_3RDPARTY_PV="06-07-2012"
+MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
+
+inherit autotools eutils multilib
+
+DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina"
+HOMEPAGE="http://www.chevreux.org/projects_mira.html"
+SRC_URI="
+	https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
+	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+#	https://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
+#	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+S="${WORKDIR}"/"${PN}"-"${MY_PV}"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="doc"
+
+CDEPEND="
+	dev-libs/boost[threads]
+	dev-util/google-perftools"
+DEPEND="${CDEPEND}
+	sys-devel/flex
+	app-editors/vim-core
+	dev-libs/expat"
+RDEPEND="${CDEPEND}"
+
+#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
+#	THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
+DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
+
+PATCHES=(
+	"${FILESDIR}/${PN}-4.0.2-boost-1.50.patch"
+	"${FILESDIR}/${PN}-4.0.2-cout.patch"
+	"${FILESDIR}/${PN}-4.0.2-cmath.patch"
+)
+
+src_prepare() {
+	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
+
+	default
+
+	sed \
+		-e "s:-O[23]::g" \
+		-e "s:-funroll-loops::g" \
+		-i configure.ac || die
+
+	eautoreconf
+
+	# Remove C++ source files that upstream built with flex.
+	local f
+	local PREBUILT_CXX_LEXER_FILES=(
+		"${S}"/src/caf/caf_flexer.cc
+		"${S}"/src/io/exp_flexer.cc
+		"${S}"/src/mira/parameters_flexer.cc
+	)
+
+	for f in "${PREBUILT_CXX_LEXER_FILES[@]}"; do
+		if [[ -f ${f} ]] ; then
+			rm "${f}" || die "Failed to remove ${f}"
+		else
+			die "${f} not found"
+		fi
+	done
+}
+
+src_configure() {
+	econf \
+		--with-boost="${EPREFIX}/usr/$(get_libdir)" \
+		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
+		--with-boost-thread=boost_thread-mt
+}
+
+#src_compile() {
+#	base_src_compile
+#	# TODO: resolve docbook incompatibility for building docs
+#	if use doc; then emake -C doc clean docs || die; fi
+#}
+
+src_install() {
+	default
+
+	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+	dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
+}
+
+pkg_postinst() {
+	einfo "Documentation is no longer built, you can find it at:"
+	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
+}