reinit the tree, so we can have metadata

4 files changed, 107 insertions, 0 deletions

diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest
new file mode 100644
index 000000000000..127cef1fa218
--- /dev/null
+++ b/sci-biology/elph/Manifest
@@ -0,0 +1,6 @@
+AUX elph-1.0.1-fix-build-system.patch 1303 SHA256 5f1212cfd7fac3d15c969eee62fe9423c5d609a29a75a9f8cd599236fb188ba8 SHA512 d39611f80cd2e67e94f3d1dd7eb1dfe59ac3b221956ab72f3951b5716825387e7d3ed04608e75abfc43ae2cbc53ace474e602ddbd93441c2da74f04516ba2ba5 WHIRLPOOL 86dace4f513f6f0b41621e58ac783224916bf84031bed1223bc43566217b3474153814a9e023b7b9812e7f3ea63ade97bef8ed4d7da201440d0e0fab78e8d654
+DIST ELPH-1.0.1.tar.gz 113476 SHA256 6d944401d2457d75815a34dbb5780f05df569eb1edfd00909b33c4c4c4ff40b9 SHA512 a76cdcdaa1dc406fb0f1204b6a40ffc9f4c0840611b960a3d4299d447446e5bbf941abe7f70cee38f69a64862e186133fd60c1aac18b4b58d86f2ed5c4dd7d72 WHIRLPOOL 598dc3f95c93e5e36bcd20de3c985c22d650462ab27df31af54ca5b5b50c0a60fcc47637a41c449bdf7e572cee097289916aca4f0de79b804854d233ff3e20ff
+EBUILD elph-1.0.1-r1.ebuild 658 SHA256 2843414d1f6279497e5577d0dfb9c8c2d32d3238fbc8f75336d23174948ba176 SHA512 ae25927fb71058c7543083735082e025defb746ea89f633e0bfa99291507e3a59ccdb05f51924b62a393dbaa40e727e83e83dc6e88b3acbe8e368cd856bd4121 WHIRLPOOL 4a84c71f80348508d1c6b825467da7f3a5df8f09d2e749fa4bcac972645dafcae8d26d3678f0b65283b00f14c696ef9fcb9998f0c7d2cc07e052e1e9d44b84d5
+MISC ChangeLog 2531 SHA256 d80ad382c93ebf13e79e3e0a159157d34bc781e995b42be22e3b850bed8c8f98 SHA512 2042496398adafd39319f7867c612a820275b984f825eaaecc3723468defa3aa0fd2f29613095fe13a844120d994493a78e861b1197a087ecae43e58ca7fe7c2 WHIRLPOOL 321afb35bca0963738f488b39bc6eaed74f3727763c826eef2094463937fd94abb3b2140c5c9e1df110fce9cc8bff767a1e53e30b48ea5851e252fa401a3c80e
+MISC ChangeLog-2015 2410 SHA256 8f02ff022a059a9636b9d5fccb171cceb654c973c343eaff4dc5bc853d5634e6 SHA512 238c2d7ff81cfae365e2488bc5cb617af65b2f539f53c3e60fc1084302b578df46066ef60496f6c33265d97d0df526ed50fc6dbb8444c15913a8247f089f28bc WHIRLPOOL 808a8e0b99fde5bc1a2434bbf705a758e64faa7bbc876ac019ff71e62d14f819c3374323b50a707dc63f1f77c3f035c4aa3dabf4011a38a4fc79c25f1969374a
+MISC metadata.xml 617 SHA256 577bac45e9296a2f04abd14bc8849a994b15f133958ecf4247a371dff4e25187 SHA512 d1998f0590fd4c555dcea00c1865da9258ba2a98bf7a1779703aca47ae01523cad74866e90fa612d16193c3974226519d4f5768180a3ae0646af2eb9fcbd1c2c WHIRLPOOL 82ff4415edbf7177606a2931079c0e0b137c91d5ed514f2fbf137eb112c82368bc66defd419a7ae5aa3c450ce986f0a7acb26ed5e10b89a188548bec049db887
diff --git a/sci-biology/elph/elph-1.0.1-r1.ebuild b/sci-biology/elph/elph-1.0.1-r1.ebuild
new file mode 100644
index 000000000000..c166dd93e41d
--- /dev/null
+++ b/sci-biology/elph/elph-1.0.1-r1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program"
+LICENSE="Artistic"
+HOMEPAGE="http://cbcb.umd.edu/software/ELPH/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+S=${WORKDIR}/${PN^^}/sources
+
+PATCHES=( "${FILESDIR}/${PN}-1.0.1-fix-build-system.patch" )
+
+src_configure() {
+	tc-export CC CXX
+}
+
+src_install() {
+	dobin elph
+
+	cd "${WORKDIR}"/ELPH || die
+	dodoc VERSION
+	newdoc Readme.ELPH README
+}
diff --git a/sci-biology/elph/files/elph-1.0.1-fix-build-system.patch b/sci-biology/elph/files/elph-1.0.1-fix-build-system.patch
new file mode 100644
index 000000000000..9afbb68666d6
--- /dev/null
+++ b/sci-biology/elph/files/elph-1.0.1-fix-build-system.patch
@@ -0,0 +1,55 @@
+Make build system respect user variables
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,42 +1,26 @@
+-CLASSDIR := .
+-
+-# Directories to search for header files
+-SEARCHDIRS := -I- -I${CLASSDIR}
+-
+-
+-SYSTYPE :=     $(shell uname)
+-
+-# C compiler
+-
+-CC      := g++
+-CFLAGS  = -Wall ${SEARCHDIRS} -fno-exceptions -fno-rtti -D_REENTRANT -g
++my_CPPFLAGS = -D_REENTRANT -I.
+ 
+ %.o : %.c
+-	${CC} ${CFLAGS} -c $< -o $@
++	$(CC) -Wall $(CFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
+ 
+ %.o : %.cc
+-	${CC} ${CFLAGS} -c $< -o $@
++	$(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
+ 
+ %.o : %.C
+-	${CC} ${CFLAGS} -c $< -o $@
++	$(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
+ 
+ %.o : %.cpp
+-	${CC} ${CFLAGS} -c $< -o $@
++	$(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
+ 
+ %.o : %.cxx
+-	${CC} ${CFLAGS} -c $< -o $@
++	$(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
+ 
+ # C/C++ linker
+-
+-LINKER    := g++
+-LDFLAGS    =
+-LOADLIBES := 
+-
+ .PHONY : all
+ all:    elph
+ 
+-elph:  ./elph.o ${CLASSDIR}/motif.o ${CLASSDIR}/GBase.o ${CLASSDIR}/GString.o ${CLASSDIR}/GArgs.o
+-	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
++elph: elph.o motif.o GBase.o GString.o GArgs.o
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^
+ 
+ # target for removing all object files
+ 
diff --git a/sci-biology/elph/metadata.xml b/sci-biology/elph/metadata.xml
new file mode 100644
index 000000000000..979dde87e15d
--- /dev/null
+++ b/sci-biology/elph/metadata.xml
@@ -0,0 +1,15 @@
+<?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>
+	<longdescription>
+		ELPH is a general-purpose Gibbs sampler for finding motifs in a set of
+		DNA or protein sequences. The program takes as input a set containing
+		anywhere from a few dozen to thousands of sequences, and searches
+		through them for the most common motif, assuming that each sequence
+		contains one copy of the motif.
+	</longdescription>
+</pkgmetadata>