commit: f58ff05630e47bad8736bd30d9e6985fe0910754
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 20:56:53 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 20:56:53 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f58ff056
avoid file collision on /usr/bin/extract (bug #247394)
Package-Manager: portage-2.2.18
sci-biology/glimmer/ChangeLog | 47 ++++++
.../glimmer/files/glimmer-3.02-glibc210.patch | 24 +++
.../glimmer/files/glimmer-3.02-jobserver-fix.patch | 22 +++
.../glimmer/files/glimmer-3.02-ldflags.patch | 88 ++++++++++
.../files/glimmer-3.02-rename_extract.patch | 185 +++++++++++++++++++++
sci-biology/glimmer/glimmer-3.02-r3.ebuild | 53 ++++++
sci-biology/glimmer/metadata.xml | 5 +
7 files changed, 424 insertions(+)
diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
new file mode 100644
index 0000000..c3d61e9
--- /dev/null
+++ b/sci-biology/glimmer/ChangeLog
@@ -0,0 +1,47 @@
+# ChangeLog for sci-biology/glimmer
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.10
2013/03/11 15:17:43 jlec Exp $
+
+ 11 Mar 2013; Justin Lecher <j...@gentoo.org> metadata.xml:
+ Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
+
+ 16 Jul 2010; Markos Chandras <hwoar...@gentoo.org> glimmer-3.02-r2.ebuild:
+ Stable on amd64 wrt bug #328415
+
+ 16 Jul 2010; Christian Faulhammer <fa...@gentoo.org>
+ glimmer-3.02-r2.ebuild:
+ stable x86, bug 328415
+
+*glimmer-3.02-r2 (03 Apr 2010)
+
+ 03 Apr 2010; Justin Lecher <j...@gentoo.org> +glimmer-3.02-r2.ebuild,
+ +files/glimmer-3.02-jobserver-fix.patch:
+ jobserver fix, #299482, Thanks Myckel Habets
+ LDFLAGS/CFLAGS etc repected
+
+ 03 Jan 2010; Pacho Ramos <pa...@gentoo.org> glimmer-3.02-r1.ebuild:
+ amd64 stable, bug 298762
+
+ 29 Dec 2009; Christian Faulhammer <fa...@gentoo.org>
+ glimmer-3.02-r1.ebuild:
+ stable x86, bug 298762
+
+ 28 Dec 2009; Andrey Kislyuk <wea...@gentoo.org>
+ +files/glimmer-3.02-glibc210.patch, glimmer-3.02-r1.ebuild:
+ QA fixes, including bug 298223
+
+*glimmer-3.02-r1 (04 Jan 2009)
+
+ 04 Jan 2009; weaver <wea...@gentoo.org> -glimmer-3.02.ebuild,
+ +glimmer-3.02-r1.ebuild:
+ Collision block, bug 247394
+
+ 30 Sep 2008; Jeremy Olexa <darks...@gentoo.org> glimmer-3.02.ebuild:
+ add ~amd64 kw based on Chad's testing. bug #239162
+
+*glimmer-3.02 (07 Sep 2008)
+
+ 07 Sep 2008; weaver <wea...@gentoo.org> +metadata.xml,
+ +glimmer-3.02.ebuild:
+ Import from science overlay
+
diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
new file mode 100644
index 0000000..f6051ec
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
@@ -0,0 +1,24 @@
+diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc
+--- glimmer3.02-orig/src/Common/gene.cc 2009-12-28 13:34:21.577437056
+0000
++++ glimmer3.02/src/Common/gene.cc 2009-12-28 13:36:06.914974685 +0000
+@@ -443,7 +443,7 @@
+ // Return a subscript corresponding to character ch .
+
+ {
+- char * p;
++ const char * p;
+
+ p = strchr (CONVERSION_STRING, tolower (ch));
+ if (p == NULL)
+diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc
+--- glimmer3.02-orig/src/ICM/icm.cc 2009-12-28 13:34:21.577437056 +0000
++++ glimmer3.02/src/ICM/icm.cc 2009-12-28 13:36:44.649451803 +0000
+@@ -1981,7 +1981,7 @@
+ // model) for character ch .
+
+ {
+- char * p;
++ const char * p;
+
+ p = strchr (ALPHA_STRING, tolower (Filter (ch)));
+ if (p == NULL)
diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
new file mode 100644
index 0000000..91498b1
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch
@@ -0,0 +1,22 @@
+diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile
+--- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100
+@@ -2,12 +2,12 @@
+
+
+ all:
+- @ TGT=objs
+- @ $(dosubdirs)
+- @ TGT=libs
+- @ $(dosubdirs)
+- @ TGT=progs
+- @ $(dosubdirs)
++ @+ TGT=objs
++ @+ $(dosubdirs)
++ @+ TGT=libs
++ @+ $(dosubdirs)
++ @+ TGT=progs
++ @+ $(dosubdirs)
+
+
+ install: all
diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
new file mode 100644
index 0000000..0a04fbe
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch
@@ -0,0 +1,88 @@
+diff --git a/src/c_make.gen b/src/c_make.gen
+index 414dead..84c3030 100644
+--- a/src/c_make.gen
++++ b/src/c_make.gen
+@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc
+ #### Do not redefine if (a) passed in on command line, or (b)
+ #### defined in an environment variable.
+
+-ifneq "$(origin CC)" "environment"
+-CC = cc
+-endif
+-
+-ifneq "$(origin CPPFLAGS)" "environment"
+-CPPFLAGS=
+-endif
+-
+-ifneq "$(origin CFLAGS)" "environment"
+-CFLAGS =
+-endif
+-
+-ifneq "$(origin CDEFS)" "environment"
+-CDEFS =
+-endif
+-
+-ifneq "$(origin CXX)" "environment"
+-CXX = g++
+-endif
+-
+-ifneq "$(origin CXXFLAGS)" "environment"
+-CXXFLAGS=
+-endif
+-
+-ifneq "$(origin CXXDEFS)" "environment"
+-CXXDEFS= -D__cplusplus
+-endif
+-
+-ifneq "$(origin AR)" "environment"
+-AR = ar
+-endif
+-
+-ifneq "$(origin ARFLAGS)" "environment"
+-ARFLAGS = rvs
+-endif
+-
+-ifneq "$(origin LDFLAGS)" "environment"
+-LDFLAGS =
+-endif
++CC ?= cc
++CXX ?= g++
++CXXFLAGS ?=
++CXXDEFS = -D__cplusplus
++AR ?= ar
++ARFLAGS ?= rvs
+
+ #### Delete default suffix rules
+ .SUFFIXES:
+@@ -359,13 +326,13 @@ $(PROGS):
+ cd $(LOCAL_OBJ); \
+ if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
+ $(LD_DIRS) $(filter-out lib%.a, $+) \
+- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
+ true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
+ else \
+ cd $(LOCAL_OBJ); \
+ if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
+ $(LD_DIRS) $(filter-out lib%.a, $+) \
+- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
+ true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
+ fi ;
+
+diff --git a/src/c_make.glm b/src/c_make.glm
+index 0decc17..b82131c 100644
+--- a/src/c_make.glm
++++ b/src/c_make.glm
+@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen
+
+ SUBDIRS = Common ICM Glimmer Util
+
+-CFLAGS = -g -Wall
+-CXXFLAGS = -g -Wall
+-
+-LDFLAGS = -g -lm
++LIBS = -lm
+
+
+ #AS_BUILD_DIR =$(LOCAL_WORK)
diff --git a/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch
b/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch
new file mode 100644
index 0000000..07c8cd3
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch
@@ -0,0 +1,185 @@
+diff -r -u glimmer3.02.old/docs/notes.tex glimmer3.02/docs/notes.tex
+--- glimmer3.02.old/docs/notes.tex 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/docs/notes.tex 2015-05-25 22:41:39.450340098 +0200
+@@ -306,7 +306,7 @@
+ The script would then run the commands:
+ \BSV\begin{verbatim}
+ long-orfs -n -t 1.15 genom.seq run1.longorfs
+- extract -t genom.seq run1.longorfs > run1.train
++ glimmer_extract -t genom.seq run1.longorfs > run1.train
+ build-icm -r run1.icm < run1.train
+ glimmer3 -o50 -g110 -t30 genom.seq run1.icm run1
+ \end{verbatim}\ESV
+@@ -330,9 +330,9 @@
+ \end{verbatim}\ESV
+ The script would then run the commands:
+ \BSV\begin{verbatim}
+- extract -t genom.seq train.coords > run2.train
++ glimmer_extract -t genom.seq train.coords > run2.train
+ build-icm -r run2.icm < run2.train
+- upstream-coords.awk 25 0 train.coords | extract genom.seq - > run2.upstream
++ upstream-coords.awk 25 0 train.coords | glimmer_extract genom.seq - >
run2.upstream
+ elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
+ set startuse = `start-codon-distrib -3 genom.seq train.coords`
+ glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse genom.seq run2.icm run2
+@@ -358,11 +358,11 @@
+ The script would then run the commands:
+ \BSV\begin{verbatim}
+ long-orfs -n -t 1.15 genom.seq run3.longorfs
+- extract -t genom.seq run3.longorfs > run3.train
++ glimmer_extract -t genom.seq run3.longorfs > run3.train
+ build-icm -r run3.icm < run3.train
+ glimmer3 -o50 -g110 -t30 genom.seq run3.icm run3.run1
+ tail +2 run3.run1.predict > run3.coords
+- upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
++ upstream-coords.awk 25 0 run3.coords | glimmer_extract genom.seq - >
run3.upstream
+ elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
+ set startuse = `start-codon-distrib -3 genom.seq run3.coords`
+ glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
+@@ -1081,12 +1081,12 @@
+ \Pg{entropy-score}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
+ \eq
+
+-\subsubsection{\Pg{extract} Program}
++\subsubsection{\Pg{glimmer_extract} Program}
+ This program reads a genome sequence and a list of coordinates
+ for it and outputs a multi-fasta file of the regions specified
+ by the coordinates. Output goes to standard output.
+ \bq
+- \Pg{extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
++ \Pg{glimmer_extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
+ \eq
+
+ \subsubsection{\Pg{multi-extract} Program}
+diff -r -u glimmer3.02.old/sample-run/g3-from-scratch.csh
glimmer3.02/sample-run/g3-from-scratch.csh
+--- glimmer3.02.old/sample-run/g3-from-scratch.csh 2006-06-12
21:46:35.000000000 +0200
++++ glimmer3.02/sample-run/g3-from-scratch.csh 2015-05-25 22:40:18.450338748
+0200
+@@ -50,7 +50,7 @@
+ step2:
+ # Extract the training sequences from the genome file
+ echo "Step 2 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+diff -r -u glimmer3.02.old/sample-run/g3-from-training.csh
glimmer3.02/sample-run/g3-from-training.csh
+--- glimmer3.02.old/sample-run/g3-from-training.csh 2006-06-12
21:46:35.000000000 +0200
++++ glimmer3.02/sample-run/g3-from-training.csh 2015-05-25
22:40:18.450338748 +0200
+@@ -42,7 +42,7 @@
+ step1:
+ # Extract the training sequences from the genome file
+ echo "Step 1 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $coords > $tag.train
++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+@@ -66,7 +66,7 @@
+ # upstream of the start locations in $coords
+ echo "Step 3 of ${numsteps}: Making PWM from upstream regions"
+ $awkpath/upstream-coords.awk 25 0 $coords \
+- | $glimmerpath/extract $genome - > $tag.upstream
++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
+ $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
+ if ($status != 0) then
+ echo "Failed to create PWM"
+diff -r -u glimmer3.02.old/sample-run/g3-iterated.csh
glimmer3.02/sample-run/g3-iterated.csh
+--- glimmer3.02.old/sample-run/g3-iterated.csh 2006-06-13 14:15:28.000000000
+0200
++++ glimmer3.02/sample-run/g3-iterated.csh 2015-05-25 22:40:18.450338748
+0200
+@@ -57,7 +57,7 @@
+ step2:
+ # Extract the training sequences from the genome file
+ echo "Step 2 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+@@ -103,7 +103,7 @@
+ # upstream of the start locations in $tag.coords
+ echo "Step 6 of ${numsteps}: Making PWM from upstream regions"
+ $awkpath/upstream-coords.awk 25 0 $tag.coords \
+- | $glimmerpath/extract $genome - > $tag.upstream
++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
+ $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
+ if ($status != 0) then
+ echo "Failed to create PWM"
+diff -r -u glimmer3.02.old/scripts/g3-from-scratch.csh
glimmer3.02/scripts/g3-from-scratch.csh
+--- glimmer3.02.old/scripts/g3-from-scratch.csh 2006-06-12
21:40:14.000000000 +0200
++++ glimmer3.02/scripts/g3-from-scratch.csh 2015-05-25 22:44:44.190343177
+0200
+@@ -50,7 +50,7 @@
+ step2:
+ # Extract the training sequences from the genome file
+ echo "Step 2 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+diff -r -u glimmer3.02.old/scripts/g3-from-training.csh
glimmer3.02/scripts/g3-from-training.csh
+--- glimmer3.02.old/scripts/g3-from-training.csh 2006-06-12
21:40:14.000000000 +0200
++++ glimmer3.02/scripts/g3-from-training.csh 2015-05-25 22:44:44.190343177
+0200
+@@ -42,7 +42,7 @@
+ step1:
+ # Extract the training sequences from the genome file
+ echo "Step 1 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $coords > $tag.train
++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+@@ -66,7 +66,7 @@
+ # upstream of the start locations in $coords
+ echo "Step 3 of ${numsteps}: Making PWM from upstream regions"
+ $awkpath/upstream-coords.awk 25 0 $coords \
+- | $glimmerpath/extract $genome - > $tag.upstream
++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
+ $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
+ if ($status != 0) then
+ echo "Failed to create PWM"
+diff -r -u glimmer3.02.old/scripts/g3-iterated.csh
glimmer3.02/scripts/g3-iterated.csh
+--- glimmer3.02.old/scripts/g3-iterated.csh 2006-06-13 14:15:46.000000000
+0200
++++ glimmer3.02/scripts/g3-iterated.csh 2015-05-25 22:44:44.190343177
+0200
+@@ -57,7 +57,7 @@
+ step2:
+ # Extract the training sequences from the genome file
+ echo "Step 2 of ${numsteps}: Extracting training sequences"
+-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
+ if ($status != 0) then
+ echo "Failed to extract training sequences"
+ exit
+@@ -103,7 +103,7 @@
+ # upstream of the start locations in $tag.coords
+ echo "Step 6 of ${numsteps}: Making PWM from upstream regions"
+ $awkpath/upstream-coords.awk 25 0 $tag.coords \
+- | $glimmerpath/extract $genome - > $tag.upstream
++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
+ $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
+ if ($status != 0) then
+ echo "Failed to create PWM"
+diff -r -u glimmer3.02.old/src/Util/Makefile glimmer3.02/src/Util/Makefile
+--- glimmer3.02.old/src/Util/Makefile 2006-06-12 21:40:14.000000000 +0200
++++ glimmer3.02/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200
+@@ -8,7 +8,7 @@
+ SOURCES = $(UTIL_SRCS)
+ OBJECTS = $(UTIL_OBJS)
+
+-PROGS = entropy-profile entropy-score extract multi-extract
start-codon-distrib \
++PROGS = entropy-profile entropy-score glimmer_extract multi-extract
start-codon-distrib \
+ uncovered window-acgt
+
+ LIBRARIES =
+diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc
+--- glimmer3.02.old/src/Util/extract.cc 2006-06-12 21:40:14.000000000
+0200
++++ glimmer3.02/src/Util/extract.cc 2015-05-25 22:44:01.760342470 +0200
+@@ -297,7 +297,7 @@
+
+ {
+ fprintf (stderr,
+- "USAGE: extract [options] <sequence-file> <coords>\n"
++ "USAGE: glimmer_extract [options] <sequence-file> <coords>\n"
+ "\n"
+ "Read fasta-format <sequence-file> and extract from it the\n"
+ "subsequences specified by <coords>. By default, <coords>\n"
diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild
b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
new file mode 100644
index 0000000..c8a09d8
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header:
/var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r2.ebuild,v 1.3
2010/07/16 17:29:32 hwoarang Exp $
+
+EAPI="2"
+
+inherit eutils
+
+MY_PV=${PV//./}
+
+DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
+HOMEPAGE="http://ccb.jhu.edu/software/glimmer";
+SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz";
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh
+ !app-crypt/pkcrack
+ !media-libs/libextractor"
+
+S="${WORKDIR}/${PN}${PV}"
+
+src_prepare() {
+ sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
+ -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die
"failed to rewrite paths"
+ # Fix Makefile to die on failure
+ sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen ||
die
+ # GCC 4.3 include fix
+ sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh
|| die
+ # avoid file collision on /usr/bin/extract #247394
+ epatch "${FILESDIR}/${P}-glibc210.patch"
+ epatch "${FILESDIR}/${P}-jobserver-fix.patch"
+ epatch "${FILESDIR}/${P}-ldflags.patch"
+ epatch "${FILESDIR}/${P}-rename_extract.patch"
+}
+
+src_compile() {
+ emake -C src || die
+}
+
+src_install() {
+ rm -f bin/test
+ dobin bin/* || die
+
+ insinto /usr/share/${PN}/scripts
+ doins scripts/* || die
+
+ dodoc glim302notes.pdf
+}
diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/glimmer/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
