reinit the tree, so we can have metadata

8 files changed, 285 insertions, 0 deletions

diff --git a/sci-biology/infernal/Manifest b/sci-biology/infernal/Manifest
new file mode 100644
index 000000000000..d97cb531ca8b
--- /dev/null
+++ b/sci-biology/infernal/Manifest
@@ -0,0 +1,10 @@
+AUX infernal-1.0.2-ldflags.patch 444 SHA256 db5d7d514d949dbe6f9e47961cc3e3e57898d6292fc6eb3675d69705737cecad SHA512 95f953bbf57a78f40df51bbfdab62e715905aa2bc57d4ca75e380c81d34c88d0177e6fe51933c908bf6e6f513b8c38ffeeb7c8f1802773c7c9773a36388b81d0 WHIRLPOOL 6c78e220702819ffe4ea25210a9b57052a37a24bed626cbc9970108358e76c0a5e3430ae44fcc92df78e3d8483f015e018f17928c999a359e3b4f8122596e5b0
+AUX infernal-1.0.2-overflows.patch 540 SHA256 692f1fecbb8e210e8b958d3a50584b4073ec129b6647da83f282e06949cb66ab SHA512 c8bafb2c10d09cae24f882d5238b6ae974669d59e0ee583bcedb13e81c88ea9859c1f78343d5be91a5cca05a3dc07ffe6436b33e201a46baf349795da5eec906 WHIRLPOOL ab0dd02643040650a40b717ec9f597c664bff9735e5ddc51a567dc9f4fc26a192f09212ee9ac0e10ade1061391517017416dde59dc4ccfef7d5876803dd6e739
+AUX infernal-1.0.2-parallel-build.patch 659 SHA256 79e8142c0970c7de12ebf2264b9ae1973dc9d1e76d672d0ffc2790a5aa95096b SHA512 d67271d858f60a5378d61892cd5c354ac95234620437621f3bf770e8829fa866a451ee031f530f502385044d7622f0fe88827614e95ab35ac6cbf8384d21e9c5 WHIRLPOOL 1513e00ecb5884ea3f1729f60862b3c3ee88b7686f331b8c2b00f078eb8ab5e2592510c7eee344516a559fcdaa8dd88ced11a212a15dee5806bb0361b1539722
+AUX infernal-1.0.2-perl-5.16-2.patch 4206 SHA256 db663878a8d139f1832ddbec54131c518cdbac1fa8d298e80cee529fb3eddd0f SHA512 9784f31c18f6c53b15c0454d3a41db27c3f433ac3d3030bc113e9f9e8194fb51109de5055d038a3c639b1c4142d6fd0010825df484a857c9f072f43d8cadcb44 WHIRLPOOL d8ce80893fe2abeb537daa0a759a432649f677d9cc9f77ff597b4a1bfb8d90b45ca4bae0043cd0fb889f6a14b0caa90d3d7cec9516f53d24e6b441fbfeb4dfe3
+AUX infernal-1.0.2-respect-DESTDIR.patch 396 SHA256 179a5e9fdb5f298cbab69f9dcbf3b97df7242702268e433e7bfeadcdee16379e SHA512 6847c87e45a34a68d179fbf8c9965af502cc9e52aa1f5ed800332dfb52e97ca3f2cb87a7dc4c3adb2d85f63567f15b084a50c7139f5ab03b0cf2b0711d023ec4 WHIRLPOOL 36981fcb327727c24364bc73ad3f80dc03628996c6c115677f676e02b1704d970329c3f87b812300d1897975373996ef54c3c4da343c2884fa29bdd8e880196f
+DIST infernal-1.0.2.tar.gz 15205421 SHA256 c4f89ac2e865c8b04a53a647703d88f96c31bb1d47d3e06f4b6090d7d15643ad SHA512 0399be14c17f053574e95d8c5b9eaf990545795a9268e20f0940e11a8e78fc49beb4b23994e9ea427764fbb29e9b39f6da9cb1d85eb4b56d354057b48515c4af WHIRLPOOL c4fa3326eb1b36252ce41ca1aeca68bed4373061ca6bc2bfc0af62c0805bfa1747272fbf223b8d47194853ae5cbe7af11d47493c258264503ea6aa7b142a6b60
+EBUILD infernal-1.0.2-r1.ebuild 924 SHA256 db7e48034d9bca2ca4f0a385eb4451ed06d15029c45c9c76b4774f3b38869f3e SHA512 816308be6a7e57e30f7c22e0c37662cde9b234501e324889e7e21e4d0e779cc6bb113490f10ce1aba3aeff46bdf9668442878e3cea4d5ad171beeb0e9fe6832c WHIRLPOOL 51a7a1e7d6f615f2fd283ef8471181791b342b7dc7ef62d2093ec87ed06ae41f7f79a6b87a2dc47a416a02a8039a4d744d405205e2fe8b05fa7c1116969b8409
+MISC ChangeLog 2606 SHA256 479570cc326272ca6f0a2d16121de71e902d5e838def774c132b6dd6216ffe69 SHA512 c20696de2b14dc6720ccf55229941b69dc295c848b9236d902694e43425aed06389a90f3ce82e0bda9868028b49bf39cf847fe35089cb9d043e04340ce86cdde WHIRLPOOL 0340e76d90c707d2cc187e263cb6d5dde99d0724566a48c4188ad96b10d940858ef8a69d0d88a0884e55fc68f7ca126054a29c1bffd7c4620e469973b54e7e9d
+MISC ChangeLog-2015 2575 SHA256 98f684e2671e5dcef3a9572874849d0bf01b8794e7ada1611c491816d8b8ef40 SHA512 371c177a61a11365b50244977c04f1d19cd3ae77425b11f29e39cb9e6ecc5a389cd4fcd0e24bf7fc9086874a03b64208ddac40c2d4ecb893296218a490ecc0ae WHIRLPOOL 3e6552a94f52d170421f1bce77fca59259cca376c1043f10e47c3274ba16089fbff2261817b88773d284b0ca0cd2d51e5078a7b43e973e6712197ab546c93a27
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch
new file mode 100644
index 000000000000..f688dce152ed
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch
@@ -0,0 +1,15 @@
+Respect LDFLAGS
+
+http://bugs.gentoo.org/show_bug.cgi?id=338177
+
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -86,7 +86,7 @@
+ all: 	$(PROGS) 
+ 
+ $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS}
+-	$(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
+ 
+ 
+ #################################################################
diff --git a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch
new file mode 100644
index 000000000000..67190c4c1d42
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch
@@ -0,0 +1,15 @@
+Fix buffer overflow
+
+http://bugs.gentoo.org/show_bug.cgi?id=338179
+
+--- a/easel/esl_getopts.c
++++ b/easel/esl_getopts.c
+@@ -1270,7 +1270,7 @@
+ 		   "Arg looks like option? Use %.24s%.24s if you really mean it.",
+ 		   g->opt[opti].name, *ret_optarg);
+       } else 
+-	ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name);
++	ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name);
+ 
+       g->optstring = NULL;   /* An optchar that takes an arg must terminate an optstring. */
+     }
diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch
new file mode 100644
index 000000000000..67ffa6fda7f6
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch
@@ -0,0 +1,31 @@
+Fix parallel build 
+
+http://bugs.gentoo.org/show_bug.cgi?id=311919
+
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -82,9 +82,10 @@
+ all: core 
+ 
+ core:
+-	(cd easel;     make CC="$(CC)" CFLAGS="$(CFLAGS)"; make)
+-	(cd src;       make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module)
+-	(cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)")
++	$(MAKE) -C easel
++	$(MAKE) -C src 
++	$(MAKE) -C src module
++	$(MAKE) -C testsuite
+ 
+ #.PHONY: $(RIGFILTERS)
+ #$(RIGFILTERS): core
+--- a/easel/Makefile.in
++++ b/easel/Makefile.in
+@@ -132,7 +132,7 @@
+ 	esl_wuss.o
+ 
+ all: libeasel.a
+-	(cd miniapps; make)
++	$(MAKE) -C miniapps
+ 
+ .c.o: 
+ 	${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $<		
diff --git a/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch
new file mode 100644
index 000000000000..c96dcae7b296
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch
@@ -0,0 +1,147 @@
+ benchmarks/cmsearch-rmark/sre.pl   | 4 +---
+ easel/devkit/autodoc               | 4 ++--
+ easel/devkit/esl-dependencies      | 4 ++--
+ easel/devkit/sqc                   | 7 +++----
+ easel/testsuite/coverage_report.pl | 4 ++--
+ easel/testsuite/driver_report.pl   | 4 ++--
+ easel/testsuite/valgrind_report.pl | 4 ++--
+ 7 files changed, 14 insertions(+), 17 deletions(-)
+
+diff --git a/benchmarks/cmsearch-rmark/sre.pl b/benchmarks/cmsearch-rmark/sre.pl
+index 9136717..e4df233 100644
+--- a/benchmarks/cmsearch-rmark/sre.pl
++++ b/benchmarks/cmsearch-rmark/sre.pl
+@@ -6,8 +6,6 @@
+ 
+ package SRE_perlstuff;
+ 
+-require "importenv.pl";
+-
+ # Function: tempname
+ #
+ # Returns a unique temporary filename. 
+@@ -26,7 +24,7 @@ require "importenv.pl";
+ #
+ sub main'tempname {
+     local ($dir, $name);
+-    if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";}
++    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";}
+ 
+     foreach $suffix ("aa".."zz") {
+ 	$name = "$dir/sre$suffix$$";
+diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
+old mode 100755
+new mode 100644
+index 045ce36..22268f6
+--- a/easel/devkit/autodoc
++++ b/easel/devkit/autodoc
+@@ -49,8 +49,8 @@
+ #
+ # SRE, Tue Nov 30 19:43:47 2004
+ 
+-require  "getopts.pl";
+-&Getopts('n:t');
++use Getopt::Std;
++getopts('n:t');
+ $cfile = shift;
+ 
+ if ($opt_t) { $show_api_table = 1; }
+diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
+old mode 100755
+new mode 100644
+index a4dc126..b61fa7a
+--- a/easel/devkit/esl-dependencies
++++ b/easel/devkit/esl-dependencies
+@@ -13,8 +13,8 @@
+ # SRE, Mon Jun 11 11:15:31 2007
+ # SVN $Id$
+ 
+-require "getopts.pl"
+-&Getopts('1afr');
++use Getopt::Std;
++getopts('1afr');
+ 
+ if ($opt_1) { $show_summary_table = 1; }
+ if ($opt_a) { $list_augfiles      = 1; }
+diff --git a/easel/devkit/sqc b/easel/devkit/sqc
+old mode 100755
+new mode 100644
+index 81d03de..6201d3d
+--- a/easel/devkit/sqc
++++ b/easel/devkit/sqc
+@@ -176,12 +176,11 @@
+ # SRE, Tue Aug  6 11:16:39 2002
+ # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $
+ 
+-require "getopts.pl";
+-require "importenv.pl";
++use Getopt::Std;
+ 
+ # Parse our command line
+ #
+-&Getopts('mp:r:v');
++getopts('mp:r:v');
+ if ($opt_m) { $do_memtest = 1;    }
+ if ($opt_p) { push @prepdirs, $opt_p; }
+ if ($opt_r) { push @olddirs,  $opt_r; }
+@@ -510,7 +509,7 @@ check_ccmalloc_status
+ #
+ sub tempname {
+     my ($dir, $name, $suffix);
+-    if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
++    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
+ 
+     foreach $suffix ("aa".."zz") {
+         $name = "$dir"."esltmp".$suffix.$$;
+diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
+old mode 100755
+new mode 100644
+index 9c77791..024ed34
+--- a/easel/testsuite/coverage_report.pl
++++ b/easel/testsuite/coverage_report.pl
+@@ -16,9 +16,9 @@
+ #
+ # SRE, Thu Mar  1 19:22:57 2007 (Janelia)
+ # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $
+-require  "getopts.pl";
++use Getopt::Std;
+ $have_sloccount = 1;
+-&Getopts('cs');
++getopts('cs');
+ if ($opt_c) { $do_recompile     = 1; }
+ if ($opt_s) { $have_sloccount   = 0; }
+ 
+diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl
+old mode 100755
+new mode 100644
+index d1b4a9a..db4378f
+--- a/easel/testsuite/driver_report.pl
++++ b/easel/testsuite/driver_report.pl
+@@ -19,8 +19,8 @@
+ # SRE, Fri Mar  2 10:01:44 2007 (Janelia)
+ # SVN $Id: driver_report.pl 231 2008-03-25 14:43:57Z eddys $
+ 
+-require  "getopts.pl";
+-&Getopts('c');
++use Getopt::Std;
++getopts('c');
+ if ($opt_c) { $do_recompile = 1; }
+ 
+ if ($ENV{'CC'}     ne "") { $CC     = $ENV{'CC'};     } else { $CC       = "gcc"; } 
+diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl
+old mode 100755
+new mode 100644
+index 186a392..07026a0
+--- a/easel/testsuite/valgrind_report.pl
++++ b/easel/testsuite/valgrind_report.pl
+@@ -10,8 +10,8 @@
+ #
+ # SRE, Fri Mar  2 08:37:48 2007 [Janelia]
+ # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $
+-require  "getopts.pl";
+-&Getopts('c');
++use Getopt::Std;
++getopts('c');
+ if ($opt_c) { $do_recompile = 1; }
+ 
+ if ($ENV{'CC'}     ne "") { $CC     = $ENV{'CC'};     } else { $CC       = "gcc"; } 
diff --git a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch
new file mode 100644
index 000000000000..ea465e592ffa
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch
@@ -0,0 +1,16 @@
+Build system does not respect DESTDIR by default.
+
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -203,9 +203,9 @@
+ # "make install" installs the programs in BINDIR
+ #
+ install:
+-	mkdir -p ${BINDIR}
++	mkdir -p $(DESTDIR)${BINDIR}
+ 	for file in $(PROGS); do\
+-		cp src/$$file $(BINDIR)/;\
++		cp src/$$file $(DESTDIR)$(BINDIR)/;\
+ 	done
+ #	if test -d $(RIGFILTERS); then\
+ #	   for file in $(RFPROGS); do\
diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
new file mode 100644
index 000000000000..e906c23024ff
--- /dev/null
+++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="Inference of RNA alignments"
+HOMEPAGE="http://infernal.janelia.org/"
+SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="mpi"
+KEYWORDS="amd64 x86"
+
+RDEPEND="mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-parallel-build.patch
+	"${FILESDIR}"/${P}-overflows.patch
+	"${FILESDIR}"/${P}-perl-5.16-2.patch
+	"${FILESDIR}"/${P}-ldflags.patch
+	"${FILESDIR}"/${P}-respect-DESTDIR.patch
+)
+
+src_configure() {
+	econf $(use_enable mpi)
+}
+
+src_install() {
+	DOCS=( 00README* Userguide.pdf documentation/release-notes )
+	default
+
+	pushd documentation/manpages >/dev/null || die
+	local i
+	for i in *.man; do
+		newman "${i}" "${i/.man/.1}"
+	done
+	popd >/dev/null || die
+
+	insinto /usr/share/${PN}
+	doins -r benchmarks tutorial intro matrices
+}
diff --git a/sci-biology/infernal/metadata.xml b/sci-biology/infernal/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/infernal/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>