moved from sci-chemistry to sci-biology

Package-Manager: portage-2.2_rc63/cvs/Linux x86_64

6 files changed, 158 insertions, 0 deletions

diff --git a/sci-biology/psipred/ChangeLog b/sci-biology/psipred/ChangeLog
new file mode 100644
index 000000000000..340315e55790
--- /dev/null
+++ b/sci-biology/psipred/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/psipred
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.1 2010/02/28 10:31:18 jlec Exp $
+
+*psipred-2.6.1 (28 Feb 2010)
+
+  28 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/2.6.1-Makefile.patch, +files/2.6.1-path.patch,
+  +psipred-2.6.1.ebuild, +metadata.xml:
+  moved from sci-chemistry to sci-biology
+
diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
new file mode 100644
index 000000000000..bb42170228b3
--- /dev/null
+++ b/sci-biology/psipred/Manifest
@@ -0,0 +1,16 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 2.6.1-Makefile.patch 1295 RMD160 38eb08b77f15db26d60eb9ad5b603df3927f9471 SHA1 4aa02b3f7868e113501538da5cc88b80987029b4 SHA256 f50dc85ad2e630fbe8e3a15315cd7dca0e0349a7e8e83d80b36fb9a4cf7a3d97
+AUX 2.6.1-path.patch 1114 RMD160 b0982bb972daccd9e4d3dbc0668ad80084929a33 SHA1 d0e1f4a20f114312ab8fcf8faa58b5eb29f7fa1d SHA256 0b2c0cf62c9c8b5fc21ac0c6b537aac52dcf617ffd2bd99724f1ac980efce7a5
+DIST psipred261.tar.gz 873613 RMD160 744e984a21145b6caf312f68de66501ba0ac2d39 SHA1 db3af95091ed745fc956153239016d042e44b62d SHA256 0b39c075493d43e63952535dfed5341d0b81a99e4fb72d5431676d657d027126
+EBUILD psipred-2.6.1.ebuild 1188 RMD160 a828327a6186d856ac8b8d02af63ebe323aab6fc SHA1 2c02f74b663f5d58b47a6ace99df02195bd83f86 SHA256 e4d9d7d73bffc6a1f04b99831dd3cfac3b7a707991ad718706ce61d2d19d2ec5
+MISC ChangeLog 432 RMD160 fca8f0897af4499d86638fbbd0245d4113b131ed SHA1 12faf94062d973467919b8ab951821c668371f18 SHA256 be498ed3320370445ba412c78f6a58241af8f142424d11b25780f114cdf01ded
+MISC metadata.xml 216 RMD160 04a6fc4e2160b439296b52aa97d5b7d83af75508 SHA1 9561c9e6eada6aac9b503407917900529ce703e9 SHA256 24f5c205c2655ef27138c8aa087701626f5b4c666229c9ef7fe814e63ea2e776
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAkuKRf8ACgkQgAnW8HDreRaOZACghviGuGJ7qzP0Cc182fH1B3uv
+HHgAn227h7ZN9Pu+cCS+BgESvLD5XMnZ
+=3QJ7
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/psipred/files/2.6.1-Makefile.patch b/sci-biology/psipred/files/2.6.1-Makefile.patch
new file mode 100644
index 000000000000..0a6df743ec83
--- /dev/null
+++ b/sci-biology/psipred/files/2.6.1-Makefile.patch
@@ -0,0 +1,42 @@
+--- src/Makefile	2008-03-09 22:59:51.000000000 +0100
++++ src/Makefile.new	2009-04-09 12:31:38.669457918 +0200
+@@ -6,9 +6,7 @@
+ #### CFLAGS	Flags to pass to C compiler.
+ 
+ INCDIR		= .
+-CC		= cc
+ 
+-CFLAGS		= -O
+ LIBS		= -lm
+ 
+ all:		psipred psipass2 seq2mtx pfilt
+@@ -20,13 +18,13 @@
+ 		/bin/rm -f psipred psipass2 seq2mtx pfilt
+ 
+ psipred:	sspred_avpred.c ssdefs.h sspred_net.h
+-		$(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred
++		$(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred
+ 
+ psipass2:	sspred_hmulti.c ssdefs.h sspred_net2.h
+-		$(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
++		$(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
+ 
+ seq2mtx:	seq2mtx.c
+-		$(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
++		$(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
+ 
+ pfilt:		pfilt.c
+-		$(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt
++		$(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt
+--- src/Makefile	2009-04-09 12:34:41.636939862 +0200
++++ src/Makefile.new	2009-04-09 12:36:03.796098341 +0200
+@@ -12,7 +12,8 @@
+ all:		psipred psipass2 seq2mtx pfilt
+ 
+ install:
+-		/bin/cp psipred psipass2 seq2mtx pfilt ../bin
++		/bin/mkdir -p $(DESTDIR)/usr/bin
++		/bin/cp psipred psipass2 seq2mtx pfilt $(DESTDIR)/usr/bin
+ 
+ clean:
+ 		/bin/rm -f psipred psipass2 seq2mtx pfilt
diff --git a/sci-biology/psipred/files/2.6.1-path.patch b/sci-biology/psipred/files/2.6.1-path.patch
new file mode 100644
index 000000000000..9b8d6b9fecfa
--- /dev/null
+++ b/sci-biology/psipred/files/2.6.1-path.patch
@@ -0,0 +1,34 @@
+--- runpsipred	2008-04-05 00:14:36.000000000 +0200
++++ runpsipred.new	2009-04-09 12:40:46.376203036 +0200
+@@ -14,13 +14,13 @@
+ set dbname = nr
+ 
+ # Where the NCBI programs have been installed
+-set ncbidir = /usr/local/bin
++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+ 
+ # Where the PSIPRED V2 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+ 
+ # Where the PSIPRED V2 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+ 
+ set basename = $1:r
+ set rootname = $basename:t
+--- runpsipred_single	2008-04-05 00:14:38.000000000 +0200
++++ runpsipred_single.new	2009-04-09 12:41:10.086067082 +0200
+@@ -10,10 +10,10 @@
+ # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
+ 
+ # Where the PSIPRED V2 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+ 
+ # Where the PSIPRED V2 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+ 
+ set basename = $1:r
+ set rootname = $basename:t
diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml
new file mode 100644
index 000000000000..c6856dc7f2cf
--- /dev/null
+++ b/sci-biology/psipred/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>jlec@gentoo.org</email>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/psipred/psipred-2.6.1.ebuild b/sci-biology/psipred/psipred-2.6.1.ebuild
new file mode 100644
index 000000000000..2ac04814cdfe
--- /dev/null
+++ b/sci-biology/psipred/psipred-2.6.1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-2.6.1.ebuild,v 1.1 2010/02/28 10:31:18 jlec Exp $
+
+EAPI="3"
+
+inherit eutils prefix toolchain-funcs versionator
+
+MY_P="${PN}$(delete_all_version_separators)"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	sci-biology/ncbi-tools
+	sci-biology/ncbi-tools++"
+
+S="${WORKDIR}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-Makefile.patch
+	epatch "${FILESDIR}"/${PV}-path.patch
+	eprefixify runpsipred*
+}
+
+src_compile() {
+	emake -C src CC=$(tc-getCC) || die "emake failed"
+}
+
+src_install() {
+	emake -C src DESTDIR="${D}" install || die "installation failed"
+	dobin runpsipred* || die
+	insinto /usr/share/${PN}
+	doins -r data || die "failed to install data"
+	dodoc README || die "nothing to read"
+}
+
+pkg_postinst() {
+	elog "Please use the update_blastdb.pl in order to"
+	elog "maintain your own local blastdb"
+}