reinit the tree, so we can have metadata

6 files changed, 157 insertions, 0 deletions

diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest
new file mode 100644
index 000000000000..adca26eb831f
--- /dev/null
+++ b/sci-biology/mcl/Manifest
@@ -0,0 +1,10 @@
+AUX mcl-14.137-qa-implicit-declarations.patch 786 SHA256 ee30112d296b8ebbfd1b7f9b831aaed715aead47cab1c8756e9a68e05462b6e2 SHA512 e1388441e06075e951a1ff9994a8e9fe1083042c09e072c68e9abb20dc4a83498eb4cb71aa71d738268a50a0e03ee8e7976df9bbb304b8c90314d682bb8625d3 WHIRLPOOL fd024ef468fd8557f6e931b147c4a280c679482d8d55b80325146a1b1347f2212a6c4d02a90a90c46bd892e7a4e716cae332827486ebf58ff4c4aa2be8ab492d
+DIST mcl-08-312.tar.gz 2749006 SHA256 0061da0661e99f783d97e6ae10149fe5ce11fa332b24cc8a4a491a072867bb6e SHA512 9f89f81af398710ebb9135c93653d892fc9daef360d70f3b890a3133d8a17dddffe568b110d3370602cead895562bc0dc5a71020834b3b3e9b6d2abf4bf64b0b WHIRLPOOL 6d00665c545edb55605fb0438cc79a412150e68b9c63ffc51c93f8f8c33b9bcd6e4e5e435b3be89a64407a0a8f6f1b8e77567f653e45c08f1675dbf2b9e0b59e
+DIST mcl-12-135.tar.gz 2970824 SHA256 3f5e0e7ad1074c7c4ef0139aa3318f92971fede7292dc3571eca2fd1da20a283 SHA512 97234e88f3430f223e1f303577b2b8853f40de6b204de415466719f691f529a795b17bf2fd48d4cc73d05900c87a10ba9afabbe54bce9367ee59215e7db0a8f5 WHIRLPOOL 1505643a460ba5bd6b834d070278a108fba57c9dc2a90a72a8e0726bd54a1b8fe3e4792a63397d58db62b036d22c325db2dd76f696a8692473987395c556a279
+DIST mcl-14-137.tar.gz 3035491 SHA256 b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497 SHA512 7e399e571de60da5e1ba9e643b7f0cd98fe484cc8cef517222a57322b5c7a04afa675c7cf0ab88b5801efa9565e5e67a14c4914987964308391d88dd4be1bea2 WHIRLPOOL 6a4afda86cc91c3ddacb64740f020cec2235e22411430281cde9106fb8399663c7854eb1ba5f477624d825280a7762cf5a3f7c6ec824a784a7e200e92d42a168
+EBUILD mcl-08.312.ebuild 678 SHA256 4dba82220a12bd139e76a72622b3896c30db75ebf907a7ceb0f5b4a88a9bac6c SHA512 e628f2226efd505d191efdaac7a9f83e896d5b97455833aa7a6846fc7a8c8a1079fcc60fc343606252e839a3a2820dc6ab53ad84d57ae582f339b840bfbe9cc6 WHIRLPOOL 6780bc68f9f644f98faa82162b69032366f33c9f0ac3ecd8026aa411a2decda8e7620663e4535ca3328250eed4609cbf2cbfaa258db959a9d49799aa6f57dedc
+EBUILD mcl-12.135.ebuild 678 SHA256 4dba82220a12bd139e76a72622b3896c30db75ebf907a7ceb0f5b4a88a9bac6c SHA512 e628f2226efd505d191efdaac7a9f83e896d5b97455833aa7a6846fc7a8c8a1079fcc60fc343606252e839a3a2820dc6ab53ad84d57ae582f339b840bfbe9cc6 WHIRLPOOL 6780bc68f9f644f98faa82162b69032366f33c9f0ac3ecd8026aa411a2decda8e7620663e4535ca3328250eed4609cbf2cbfaa258db959a9d49799aa6f57dedc
+EBUILD mcl-14.137.ebuild 651 SHA256 6fe7f4adc04598fb1df491d4048a8a51d620799cdd047ad6f226b01d09fbf92f SHA512 042277297965d4796d0805dad2a951e8bd467630c7904fe1a5211616fc2a620c041ea6093bbaf10e6fed17037bccd7013afcfb0260e69c09bd1cdc3ca2f76f53 WHIRLPOOL effe1116b79cf9c2b8194bb69e048242860443a01d27889c151f6750e780ba116455fd598240feba62a7385897be7b7b879834dc0edd4c801320f8b8b5066f4c
+MISC ChangeLog 2694 SHA256 b9b528bf475eb8d8d0f8cfce2efcd07e83b408ec8a3cf1b783755860412ff6c8 SHA512 a0256b62909e040eb9a9b01b379e49812ec776c353f5bb82ccda08a4aba5c6a7c98efd0e5144363c580f257ae58c3eb20fc4033d93b25fb5ccbd9cbd1496c184 WHIRLPOOL ec83d61d3a139b8ae37c02121fcfa08acd42503f299aa0a0ad4150989f98053ddf01f26cd23cfc31e646d1ddc3c7a449ea243233f984209d721ccdd381c77c9e
+MISC ChangeLog-2015 910 SHA256 af9af086bd09e35b484f10cb43a649c4a398ae12ba7ee99de86786c312f182d9 SHA512 e615f431461784a2fef5c9ef7f445ef40bda238ed47f07a277acae33ec2e629b68d98cde0a9ea99cb3f32923ec71508fcc4047c36dea9e70f2fd81ac99301354 WHIRLPOOL 4f6659d92ee95f174e567038cf33bf7e5c99b36fb29b98f50275c3924b2f33d30ad76c5fd711a96eb3262bc2de0974c8690fbb487c50d6633039a7309599e4f5
+MISC metadata.xml 351 SHA256 fecfcf8c3f170513b7e1d3dd8f505846f2728a2f9d4eb14bdb4260788ca05f5f SHA512 cbd1dc5b22ba9761f793edffa5adc3a5c99fe99569301bbba219f04ba21c603e8a3c183d04ab6838ebab3777b2855a2d46a69908e683f5183a5a22872dd429dd WHIRLPOOL 1773bdfcb553cb970fc1cf94fde6526c72187e15a30aca6823954e355cac413c414b7f2746e16875635c30299b6f918e779de8b0b5084439ceab633323f56b61
diff --git a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch
new file mode 100644
index 000000000000..df4309874d48
--- /dev/null
+++ b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch
@@ -0,0 +1,27 @@
+Fix QA issues related to implicit declarations.
+
+* QA Notice: Package triggers severe warnings which indicate that it
+*            may exhibit random runtime failures.
+* clmadjust.c:184:10: warning: implicit declaration of function ‘mcxFree’ [-Wimplicit-function-declaration]
+* mcxi.c:42:16: warning: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration]
+
+--- mcl-14-137/src/shcl/clmadjust.c
++++ mcl-14-137/src/shcl/clmadjust.c
+@@ -14,6 +14,7 @@
+ #include "report.h"
+ #include "clmadjust.h"
+ 
++#include "util/alloc.h"
+ #include "util/io.h"
+ #include "util/types.h"
+ #include "util/err.h"
+--- mcl-14-137/src/shmcx/mcxi.c
++++ mcl-14-137/src/shmcx/mcxi.c
+@@ -8,6 +8,7 @@
+ */
+ 
+ #include <stdio.h>
++#include <unistd.h>
+ 
+ #include "stack.h"
+ #include "glob.h"
diff --git a/sci-biology/mcl/mcl-08.312.ebuild b/sci-biology/mcl/mcl-08.312.ebuild
new file mode 100644
index 000000000000..fb0bf237a671
--- /dev/null
+++ b/sci-biology/mcl/mcl-08.312.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+MY_P="${PN}-${PV/./-}"
+
+DESCRIPTION="A Markov Cluster Algorithm implementation"
+HOMEPAGE="http://micans.org/mcl/"
+SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+blast"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	find \
+		-name Makefile.am \
+		-exec sed \
+			-e '/docdir/d' \
+			-e '/exampledir/s:doc::g' \
+			-i '{}' + || die
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=( $(use_enable blast) )
+	autotools-utils_src_configure
+}
diff --git a/sci-biology/mcl/mcl-12.135.ebuild b/sci-biology/mcl/mcl-12.135.ebuild
new file mode 100644
index 000000000000..fb0bf237a671
--- /dev/null
+++ b/sci-biology/mcl/mcl-12.135.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+MY_P="${PN}-${PV/./-}"
+
+DESCRIPTION="A Markov Cluster Algorithm implementation"
+HOMEPAGE="http://micans.org/mcl/"
+SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+blast"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	find \
+		-name Makefile.am \
+		-exec sed \
+			-e '/docdir/d' \
+			-e '/exampledir/s:doc::g' \
+			-i '{}' + || die
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=( $(use_enable blast) )
+	autotools-utils_src_configure
+}
diff --git a/sci-biology/mcl/mcl-14.137.ebuild b/sci-biology/mcl/mcl-14.137.ebuild
new file mode 100644
index 000000000000..e48198deca29
--- /dev/null
+++ b/sci-biology/mcl/mcl-14.137.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools
+
+MY_P="${PN}-${PV/./-}"
+
+DESCRIPTION="A Markov Cluster Algorithm implementation"
+HOMEPAGE="http://micans.org/mcl/"
+SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+blast"
+
+PATCHES=("${FILESDIR}/${P}-qa-implicit-declarations.patch")
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	find \
+		-name Makefile.am \
+		-exec sed \
+			-e '/docdir/d' \
+			-e '/exampledir/s:doc::g' \
+			-i '{}' + || die
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf $(use_enable blast)
+}
diff --git a/sci-biology/mcl/metadata.xml b/sci-biology/mcl/metadata.xml
new file mode 100644
index 000000000000..a8e52b205b3a
--- /dev/null
+++ b/sci-biology/mcl/metadata.xml
@@ -0,0 +1,13 @@
+<?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>
+  <use>
+    <flag name="blast">
+		add support for NCBI BLAST data
+	</flag>
+  </use>
+</pkgmetadata>