Imported from sci overlay

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

7 files changed, 163 insertions, 5 deletions

diff --git a/sci-chemistry/mars/Manifest b/sci-chemistry/mars/Manifest
index ca4662e471a1..e6a57dd72e2b 100644
--- a/sci-chemistry/mars/Manifest
+++ b/sci-chemistry/mars/Manifest
@@ -2,13 +2,13 @@
 Hash: SHA1
 
 DIST mars-1.1.3_linux.tar.Z 2682055 RMD160 28e87604fd5cb5951fe983d9883743eb589d896e SHA1 89c97332dd0edd89875422809c5d0d63863f9ac3 SHA256 728182f1204ec7a8a16e781c6bc0a8dc1346f8b92af24905c58a1fb0a7aa7acb
-EBUILD mars-1.1.3.ebuild 971 RMD160 6512dfd667f53398688f2db250d4aa852e6e16a6 SHA1 40fae08bcaabd29323fedf1ce2463918984d5aab SHA256 6d3351b191d33f2da25665306515b8ce3262287373b02ade773c8152eed0942e
-MISC ChangeLog 357 RMD160 f6418d99aebe6ad8a26d3fed376f98356e28252e SHA1 361fe4cf4c5fe7a02365d906654945531372b787 SHA256 31b3f0720404fcfdc793fb8d9663dfb6a982cf59b4baed95ccefcfa4ca050ad9
+EBUILD mars-1.1.3.ebuild 1014 RMD160 5bc1ebf429786cb840cac6b32e6b8b9f7b4daf6b SHA1 e748527f404a31f1b5af3feb46432630dfc8cdc2 SHA256 f3cf8734d1375e66b0a5c78f7a91df67bc172f12d9ec55724ef45ea60f1a66a3
+MISC ChangeLog 479 RMD160 ff27e1ec2d44bb9658bdcc5263582ec34885ef72 SHA1 b688b1c8cbf68a4efb7b247d8032bd26a2753ccd SHA256 4d0323de8d70567c10dfceb45143dbb22200bd32d6df43b737cea496badb9098
 MISC metadata.xml 216 RMD160 04a6fc4e2160b439296b52aa97d5b7d83af75508 SHA1 9561c9e6eada6aac9b503407917900529ce703e9 SHA256 24f5c205c2655ef27138c8aa087701626f5b4c666229c9ef7fe814e63ea2e776
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 Version: GnuPG v2.0.14 (GNU/Linux)
 
-iEYEARECAAYFAkuE4LQACgkQgAnW8HDreRYo3QCeKYFFx/saNGG+kFysWZyH5F9d
-WekAoLBN06JkivI4v0BxGVqv6pba0qPI
-=uqvI
+iEYEARECAAYFAkuI7eMACgkQgAnW8HDreRZWDQCfUi9SEMYX/wpfFd8F1yzDQXIq
+imkAnisoqAgmbPh3bPGlf1BoY1jFzNyC
+=HM+k
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/psipred/ChangeLog b/sci-chemistry/psipred/ChangeLog
new file mode 100644
index 000000000000..5f810721a4da
--- /dev/null
+++ b/sci-chemistry/psipred/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/psipred
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/psipred/ChangeLog,v 1.1 2010/02/27 10:01:52 jlec Exp $
+
+*psipred-2.6.1 (27 Feb 2010)
+
+  27 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:
+  Imported from sci overlay
+
diff --git a/sci-chemistry/psipred/Manifest b/sci-chemistry/psipred/Manifest
new file mode 100644
index 000000000000..ed39be74fcc8
--- /dev/null
+++ b/sci-chemistry/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 1190 RMD160 008fa643f0f3f316a042cdd6778a575aa5616547 SHA1 bdbcbec9edc958cab329e5a1ad6f081814570a38 SHA256 461f0d1a5998f3a01e5cba2b3de99c7197840f86c36325e86eccac55f4b0d595
+MISC ChangeLog 422 RMD160 d6f53c966022c6460301e3ba87c2fc4a4dff0d85 SHA1 87dbddb22cf1f35f9be4e1cbc443d53dd0e31a2e SHA256 51fd30919266cb0a0daec0796c29ac51972545ea79aceacf4fc61e755eebef30
+MISC metadata.xml 216 RMD160 04a6fc4e2160b439296b52aa97d5b7d83af75508 SHA1 9561c9e6eada6aac9b503407917900529ce703e9 SHA256 24f5c205c2655ef27138c8aa087701626f5b4c666229c9ef7fe814e63ea2e776
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
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+fu0AnAhtknEo6XWx9NFWE90WOCx4mieu
+=oO/0
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/psipred/files/2.6.1-Makefile.patch b/sci-chemistry/psipred/files/2.6.1-Makefile.patch
new file mode 100644
index 000000000000..0a6df743ec83
--- /dev/null
+++ b/sci-chemistry/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-chemistry/psipred/files/2.6.1-path.patch b/sci-chemistry/psipred/files/2.6.1-path.patch
new file mode 100644
index 000000000000..9b8d6b9fecfa
--- /dev/null
+++ b/sci-chemistry/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-chemistry/psipred/metadata.xml b/sci-chemistry/psipred/metadata.xml
new file mode 100644
index 000000000000..c6856dc7f2cf
--- /dev/null
+++ b/sci-chemistry/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-chemistry/psipred/psipred-2.6.1.ebuild b/sci-chemistry/psipred/psipred-2.6.1.ebuild
new file mode 100644
index 000000000000..8f324553d994
--- /dev/null
+++ b/sci-chemistry/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-chemistry/psipred/psipred-2.6.1.ebuild,v 1.1 2010/02/27 10:01:52 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"
+}