reinit the tree, so we can have metadata

4 files changed, 87 insertions, 0 deletions

diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
new file mode 100644
index 000000000000..6851a54f2a38
--- /dev/null
+++ b/sci-biology/poa/Manifest
@@ -0,0 +1,6 @@
+AUX 2-respect-flags.patch 743 SHA256 12178e90b6ed7a70e6d436f0ad391e151b2b0a5b36d31133016acc6a6bbded6c SHA512 496415d501040057155ba2ba261564fc00dc764626c8d41081f5463b0b40f9eae978bb8a81db15cf90f193c4ca9fe8725a2876ed175e15d37a983196b70e192f WHIRLPOOL fdf2268b3c0811c8e07b018d9d23c504c4bbdec33da6884399e2c7b031dd16a4594cd07fce2f297fcdc2ce44f8082aa71890b3166c1fc3bc59424aaf0b44076c
+DIST poaV2.tar.gz 62612 SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2 SHA512 2a54b025f0a74ff4c01828f3e4b9e8e135bffe26d08f651f981bc95a64196173b5d887ef988a25c1f5fbf89333b4771622d5dc93946d66e7ec9abacb6167595c WHIRLPOOL 971baf2e60406f56b2d15b597f3471fd4efee8f76288df859cc1b81d8449424be3542d30f3b4c9a9f5d1f7eb05318967fba5413e17db510b25253fdd377fe741
+EBUILD poa-2-r1.ebuild 932 SHA256 89e485e8589f6ec88343c67657a47519db6b102756b8756cef580ff3bcd3146d SHA512 f371f3d321065905ea469b9473c40b000de43f62c3eac78e2ea9e5e3ec03d2dfa21083267be1159570ddecde325400d1c381a100831b5f56086e5465acf6e29a WHIRLPOOL 5106cf9aecfb3b7efa27241f3efc37baae2fb55727f8dced96b9eeab08b0ad4771c3ff4e530de39acf5b3e6e90db53a2c9764f372cdcda45096227f7543da1ee
+MISC ChangeLog 2477 SHA256 cd3314f464a39912b70d833554dfe5146c0a31bc7ecd3381da00223593daa067 SHA512 06d2b3f422024d52e5a157cddf1550321c13129cfb5f93cbf1905cf08a173dc39a1d28592b0d077c410300be73b5b65157d8ae6e802efd2e86acb805808cf0e7 WHIRLPOOL 25e0916834cab77263889c5f583c4872d4135a0b7c72028d4a9f723a2b1d6363ee2d434dace74566e0f859dec871dc49fa454bb290de4bcbd87e91b8b3058114
+MISC ChangeLog-2015 817 SHA256 1de38231da7348f93a4ce0a70e3777668cf3b276ef48a6da76dca4a4a1458347 SHA512 29ac954a78cdece0447a24cac32fc1cd7dceb68e9bbb6c0eed1caa285cfda16152f78f985f7165ac36ef2a1b82e4b92b590fb9c4efec5d0cf20aac55782529c1 WHIRLPOOL 603f706ededbd456b069ca1bcb5a7582b9cf632fd2ab8e9fd30f78d5a76cce74ee93c27c77a3289ad5ded467823dc4fd07f4fa89bc53c8da338e8f250b5e3788
+MISC metadata.xml 347 SHA256 54cbfd5f930bb079143854733d16c6c5988226321dc34863dfce508279847275 SHA512 8610e747bbc86428757f77ed688520cdd9efeabc08e08f99ce74d98e7763f3f8cb7648b1eea01bc4db79ae16a650cb119b82022d1ac41e8fcbd6a6b40385e580 WHIRLPOOL fc0da5a6f4a5a4e1bc83c12cfb5c1616f839e9d71bb61daf2749b7d26ef0c576ce46073f11382602a0bce24f1ab31816b08961b75824f5175c8386b10fdf0776
diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/2-respect-flags.patch
new file mode 100644
index 000000000000..bdd638cf64b7
--- /dev/null
+++ b/sci-biology/poa/files/2-respect-flags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index a65bed0..713a7ab 100644
+--- a/Makefile
++++ b/Makefile
+@@ -26,9 +26,10 @@ LIBOBJECTS= \
+ 	stringptr.o
+ 
+ 
+-CC = gcc
++CC ?= gcc
+ #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
++OPT_CFLAGS = -g
++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+ # -I$(HOME)/lib/include
+ # -DREPORT_MAX_ALLOC
+ 
+@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS)
+ 
+ # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!!
+ poa: $(OBJECTS) liblpo.a
+-	$(CC) -o $@ $(OBJECTS) -lm liblpo.a
++	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a
+ 
+ what:
+ 	@echo poa: partial-order based sequence alignment program
diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml
new file mode 100644
index 000000000000..229e2f246a80
--- /dev/null
+++ b/sci-biology/poa/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="sourceforge">poamsa</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild
new file mode 100644
index 000000000000..c53fcd5f5f24
--- /dev/null
+++ b/sci-biology/poa/poa-2-r1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils
+
+MY_P="${PN}V${PV}"
+
+DESCRIPTION="Fast multiple sequence alignments using partial-order graphs"
+HOMEPAGE="http://bioinfo.mbi.ucla.edu/poa/"
+SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz"
+
+# According to SF project page
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="static-libs"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-respect-flags.patch
+}
+
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		OPT_CFLAGS="${CFLAGS}" \
+		poa
+}
+
+src_install() {
+	dobin "${S}"/poa "${S}"/make_pscores.pl
+	use static-libs && dolib.a "${S}"/liblpo.a
+	dodoc "${S}"/README "${S}"/multidom.*
+	insinto /usr/share/poa
+	doins "${S}"/*.mat
+}
+
+pkg_postinst() {
+	elog "poa requires a score matrix as the first argument."
+	elog "This package installs two examples to ${EROOT}usr/share/poa/."
+}