Version Bump

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

5 files changed, 139 insertions, 5 deletions

diff --git a/sci-biology/psipred/ChangeLog b/sci-biology/psipred/ChangeLog
index 970c787dc9e5..b947e301b829 100644
--- a/sci-biology/psipred/ChangeLog
+++ b/sci-biology/psipred/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.2 2010/05/06 18:27:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.3 2010/05/16 11:23:30 jlec Exp $
+
+*psipred-3.1 (16 May 2010)
+
+  16 May 2010; Justin Lecher <jlec@gentoo.org> +files/3.1-Makefile.patch,
+  +psipred-3.1.ebuild, +files/3.1-path.patch:
+  Version bump
 
 *psipred-3.0 (06 May 2010)
 *psipred-2.6.1-r1 (06 May 2010)
diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
index 02f3379d5b4e..435d36a879eb 100644
--- a/sci-biology/psipred/Manifest
+++ b/sci-biology/psipred/Manifest
@@ -4,16 +4,20 @@ 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
 AUX 3.0-path.patch 1124 RMD160 985bc8a52db2df5b7ea0529f69e43d440621829d SHA1 db74c92afa9f9b2849fe65a61259bb8cfc5f9ee4 SHA256 2dc3b531f1bc1ab7e2426b0ec95ff67ec93ac8376e017215b3b2dcd5b1c8804d
+AUX 3.1-Makefile.patch 1103 RMD160 a9ccbf9602a7afa2875a5e43a5e27bec4b17709a SHA1 989fbe7b175ea161c0a314e4c78c3e065d0116b5 SHA256 de49b937edc714ba84ea2ae0900ea92b73c58048fafb8d616e8dfa44b548e927
+AUX 3.1-path.patch 1128 RMD160 2281327e849146a6dc38f035501727e0a30d2d59 SHA1 579b36644c4fd9a23f72177b8ed63e80ccebf751 SHA256 0b91a360760bd27f4ba43639d32e891d5576595451e1f7285632fc9ad38a80fa
 DIST psipred261.tar.gz 873613 RMD160 744e984a21145b6caf312f68de66501ba0ac2d39 SHA1 db3af95091ed745fc956153239016d042e44b62d SHA256 0b39c075493d43e63952535dfed5341d0b81a99e4fb72d5431676d657d027126
 DIST psipred30.tar.gz 724315 RMD160 6aabe85bff8d3a60d3e80d6646ba391c23716edc SHA1 c7d6c4a5a4cc2fe52acb7b2b24eb3b7780c7afca SHA256 24a70fa859ade37d634f2fa8e047061d107ac96ffba8ea96b5bab186f402e62c
+DIST psipred31.tar.gz 746797 RMD160 921f0a0cc8b88a0d8deeaccf05231447122f4237 SHA1 f4ce00879a3dd787df9015636184d777e54d5905 SHA256 2150696cae281bc942a18fc5f1e2057ed70cb6ee7b492c9594cbd99b8f6987dd
 EBUILD psipred-2.6.1-r1.ebuild 1204 RMD160 e45a3e88e973ae58cd553e7d627f6b684b197d43 SHA1 d814f149f3ea10d36a74d111a2369f57a7823d95 SHA256 d66c6f9d91a47e07ceb00e593579a2d351bdffd7aa7ed7478dfbf6c8ce02a4d6
 EBUILD psipred-3.0.ebuild 1199 RMD160 6e1a35188b15cf3f77053df03445e2470c290f3f SHA1 4a8caf825bafe4e5b092b1d2fc56d59944673951 SHA256 12a8bf0ebe5d37922f87b04ec0820903bec0592dd550ff9b963b85bb89b84b90
-MISC ChangeLog 695 RMD160 64938fae5e94d2cef55a148b9b220a5d9f703e4b SHA1 4a8eaad0ecf488e165af93628dee6f99836080fa SHA256 f207ce434b8078e7b3a7d930a91052345f4f07886aa6c393eb5fa4f47c7aa953
+EBUILD psipred-3.1.ebuild 1224 RMD160 a3f28901894c035726e37917b0b0092e52bd6168 SHA1 6a6d52c165c26a2f60300210bef7bbd024a0f1c3 SHA256 d4667bc4a25fbe7ad888415a62c06cbbaa672542df563d7422ee7b69f690aaea
+MISC ChangeLog 859 RMD160 a3d2f967909d0ffb8bd7bcbe1ff7bc89514daa9d SHA1 e8a41836bf2d0b9e4ec99c7d78319dc4da93213c SHA256 dad6495fa6d20b01ae6b7c730634fa066f6c077b564dc5047f5dd47c5c93aaa2
 MISC metadata.xml 216 RMD160 04a6fc4e2160b439296b52aa97d5b7d83af75508 SHA1 9561c9e6eada6aac9b503407917900529ce703e9 SHA256 24f5c205c2655ef27138c8aa087701626f5b4c666229c9ef7fe814e63ea2e776
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diff --git a/sci-biology/psipred/files/3.1-Makefile.patch b/sci-biology/psipred/files/3.1-Makefile.patch
new file mode 100644
index 000000000000..0c70b6868565
--- /dev/null
+++ b/sci-biology/psipred/files/3.1-Makefile.patch
@@ -0,0 +1,38 @@
+diff --git a/src/Makefile b/src/Makefile
+index abed8af..26061fa 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -6,9 +6,9 @@
+ #### CFLAGS	Flags to pass to C compiler.
+ 
+ INCDIR		= .
+-CC		= cc
++CC		?= gcc
+ 
+-CFLAGS		= -O
++CFLAGS		?= -O2
+ LIBS		= -lm
+ 
+ all:		psipred psipass2 chkparse seq2mtx pfilt
+@@ -20,16 +20,16 @@ clean:
+ 		/bin/rm -f psipred psipass2 chkparse 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
+ 
+ chkparse:	chkparse.c
+-		$(CC) $(CFLAGS) chkparse.c $(LIBS) -o chkparse
++		$(CC) $(CFLAGS) $(LDFLAGS) chkparse.c $(LIBS) -o chkparse
+ 
+ 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
diff --git a/sci-biology/psipred/files/3.1-path.patch b/sci-biology/psipred/files/3.1-path.patch
new file mode 100644
index 000000000000..564e9c8a1ef9
--- /dev/null
+++ b/sci-biology/psipred/files/3.1-path.patch
@@ -0,0 +1,38 @@
+diff --git a/runpsipred b/runpsipred
+index 4ccf44e..34dee99 100755
+--- a/runpsipred
++++ b/runpsipred
+@@ -14,13 +14,13 @@
+ set dbname = uniref90filt
+ 
+ # 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
+diff --git a/runpsipred_single b/runpsipred_single
+index 1f7680b..7bd5bc3 100755
+--- a/runpsipred_single
++++ b/runpsipred_single
+@@ -10,10 +10,10 @@
+ # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
+ 
+ # Where the PSIPRED V3 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+ 
+ # Where the PSIPRED V3 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/psipred-3.1.ebuild b/sci-biology/psipred/psipred-3.1.ebuild
new file mode 100644
index 000000000000..3201132f6781
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.1.ebuild
@@ -0,0 +1,48 @@
+# 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-3.1.ebuild,v 1.1 2010/05/16 11:23:30 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="${WORKDIR}"
+
+src_prepare() {
+	rm -f bin/*
+	epatch "${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="${D}" install || die "installation failed"
+	dobin runpsipred* bin/* BLAST+/runpsipred* || die
+	insinto /usr/share/${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"
+}