proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

15 files changed, 552 insertions, 0 deletions

diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
new file mode 100644
index 000000000000..1c17d7b94a74
--- /dev/null
+++ b/sci-biology/psipred/Manifest
@@ -0,0 +1,7 @@
+DIST psipred3.3.tar.gz 1239746 SHA256 133eef16ba4ac6ff5e10a757290ef794552833f42ed8251ff866ae56d9527c40 SHA512 38f5dd0f6eb6fc38888f9a850604b95904a8626d6862eb0b2a389caaf49af8f81436aa78a087da22281113d8afad2d28e5109ddade7d17718c1028eed8325b7e WHIRLPOOL d3883df88bde12a0f5ba6e195dc37b7104db36d16b5846b978fb045def6c4452edce4361dcced27ed36937bbd8d0e8dd4391b8592dca390941b3450e49cc5d34
+DIST psipred3.4.tar.gz 1102416 SHA256 c0eb8877313eb0564d34fc4d0e2d8d22e09d84d245e41008227560a10e64da9d SHA512 1bc7ac41a213766139324540ba6952538f2890749ecf217d771b4ce59e25231857d38c237ea573674f11a82300750e9a3ff628ec0156864863a9528a144cd919 WHIRLPOOL bdb47f296db1172df08f84b8cf18782e8585a8bc49f190b9783192db0e9d632bd6660437e8a35c24bb5970ca7a556b368c5a93373772f20d4be9a98ef963b902
+DIST psipred3.5.tar.gz 1101579 SHA256 107979a6bee968ba1df1ac1ee63bc1611105b83a7d519ab814f848ed955b76d8 SHA512 a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2 WHIRLPOOL fb07fdf550af6c9942e131a4856942c74adb3a7954c433ac7bc27680d9ab2b3db82a5178a15bcea224f7bb0da3cd84c94a4e9188be4fcbd49851037f631732e3
+DIST psipred31.tar.gz 746797 SHA256 2150696cae281bc942a18fc5f1e2057ed70cb6ee7b492c9594cbd99b8f6987dd SHA512 a04482fc5a08de03b2c1ac3eafbc289d476906811ef2557681f00e3ba865488c6061a194c5e12fe3ff38d31f42f13f4e783de1ca4a04508dd38a93c3ad848710 WHIRLPOOL 288d161698726a944b40acb3e2c355e61bad3644bf5edca40fd5e478f9d37e3acc9a91ee199fbadea680ab3a8c974eb8f80dd700dfe790e84d8a862148538dff
+DIST psipred32.tar.gz 747120 SHA256 0775b0f07df87b2afd4989a378fc9b47f462507a264aaf2d56dd0243d9d00343 SHA512 49660d1c3cb9aa4c3ab13e721e23b83d70d0b6ecb772b08bd1058d3293dbcc9642d63092dd9746aa2a3a9085a13ba91e9849172d36954228a4f7a16e6e81050d WHIRLPOOL 24413200771fcee89c123fad25033b3230de3fdd82016ad7d084ddb096c081c46537f35c06578dad84a79a62c493e03b8f7b51be296b04d9568ea00b94293360
+DIST psipred321.tar.gz 747151 SHA256 5e88f2402e333be401b3022937b0167a33203f6289a84dd344941546f550f1f8 SHA512 b742f5fd3151bd624452bf37761fa66d364ea5b28d9d005ae6ce6f52fc6f2b17df31d6f1e600bd6c57776a1812f22b1eafbca781b430811a010d74f157a75cd1 WHIRLPOOL bb7111851ffe533b30fd6b77fb1ae396f0dd6506ce941944974c3b5c73c41d1a5b04c5af3d7e697aeb0640c03168b78d8832747940ed0de087df784d2d27e9f1
+DIST tdbdata.tar.gz 40241247 SHA256 87b7743538898f6cdf89cc5c18e1ecd040bc6223a01821d2bfc3109f4571851f SHA512 f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c WHIRLPOOL 37bc0912c6a71d1396489161465c690fb63d28167694d2e43553b6684c1f1f88866b2bf71f9531c7a7f41fc8ca81a6c93c2895ed498a07e3c4836f8c8bf4a34e
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/files/3.0-path.patch b/sci-biology/psipred/files/3.0-path.patch
new file mode 100644
index 000000000000..ebf9b2a61f4e
--- /dev/null
+++ b/sci-biology/psipred/files/3.0-path.patch
@@ -0,0 +1,38 @@
+diff --git a/runpsipred b/runpsipred
+index e133686..6ad57cc 100755
+--- a/runpsipred
++++ b/runpsipred
+@@ -14,13 +14,13 @@
+ set dbname = uniref90
+ 
+ # Where the NCBI programs have been installed
+-set ncbidir = /usr/local/bin
++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+ 
+ # 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/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/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-fgets.patch b/sci-biology/psipred/files/3.1-fgets.patch
new file mode 100644
index 000000000000..e58d677258e0
--- /dev/null
+++ b/sci-biology/psipred/files/3.1-fgets.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
+index 4d8e5ff..0d82483 100644
+--- a/src/sspred_avpred.c
++++ b/src/sspred_avpred.c
+@@ -213,7 +213,7 @@ predict(int argc, char **argv)
+ int             getmtx(FILE *lfil)
+ {
+     int             aa, i, j, naa;
+-    char            buf[256], *p;
++    char            buf[65536], *p;
+     
+     if (fscanf(lfil, "%d", &naa) != 1)
+ 	fail("Bad mtx file - no sequence length!");
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/files/3.2-fgets.patch b/sci-biology/psipred/files/3.2-fgets.patch
new file mode 100644
index 000000000000..ec06d141ee34
--- /dev/null
+++ b/sci-biology/psipred/files/3.2-fgets.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
+index 37b1332..4f04ab6 100644
+--- a/src/sspred_avpred.c
++++ b/src/sspred_avpred.c
+@@ -223,7 +223,7 @@ predict(int argc, char **argv)
+ int             getmtx(FILE *lfil)
+ {
+     int             aa, i, j, naa;
+-    char            buf[256], *p;
++    char            buf[65536], *p;
+     
+     if (fscanf(lfil, "%d", &naa) != 1)
+ 	fail("Bad mtx file - no sequence length!");
diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml
new file mode 100644
index 000000000000..655b161c218d
--- /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-biology</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/psipred/psipred-3.1.ebuild b/sci-biology/psipred/psipred-3.1.ebuild
new file mode 100644
index 000000000000..b81c4149b568
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+	rm -f bin/*
+	epatch \
+		"${FILESDIR}"/${PV}-Makefile.patch \
+		"${FILESDIR}"/${PV}-path.patch \
+		"${FILESDIR}"/${PV}-fgets.patch
+	eprefixify runpsipred*
+}
+
+src_compile() {
+	emake -C src CC=$(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"
+}
diff --git a/sci-biology/psipred/psipred-3.2.1.ebuild b/sci-biology/psipred/psipred-3.2.1.ebuild
new file mode 100644
index 000000000000..6b2158ef81e9
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.2.1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+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="test"
+
+RDEPEND="
+	sci-biology/ncbi-tools
+	|| ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+	rm -f bin/*
+	epatch \
+		"${FILESDIR}"/3.1-Makefile.patch \
+		"${FILESDIR}"/3.1-path.patch \
+		"${FILESDIR}"/3.2-fgets.patch
+	eprefixify runpsipred*
+}
+
+src_compile() {
+	emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+	emake -C src DESTDIR="${D}" install
+	dobin runpsipred* bin/* BLAST+/runpsipred*
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc README
+	newdoc BLAST+/README README-blast
+}
+
+pkg_postinst() {
+	elog "Please use the update_blastdb.pl in order to"
+	elog "maintain your own local blastdb"
+}
diff --git a/sci-biology/psipred/psipred-3.2.ebuild b/sci-biology/psipred/psipred-3.2.ebuild
new file mode 100644
index 000000000000..418179c41278
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+	rm -f bin/*
+	epatch \
+		"${FILESDIR}"/3.1-Makefile.patch \
+		"${FILESDIR}"/3.1-path.patch \
+		"${FILESDIR}"/${PV}-fgets.patch
+	eprefixify runpsipred*
+}
+
+src_compile() {
+	emake -C src CC=$(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"
+}
diff --git a/sci-biology/psipred/psipred-3.3.ebuild b/sci-biology/psipred/psipred-3.3.ebuild
new file mode 100644
index 000000000000..3727fc29ad25
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.3.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils prefix toolchain-funcs versionator
+
+#MY_P="${PN}$(delete_all_version_separators)"
+MY_P="${PN}${PV}"
+
+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
+	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	sci-biology/ncbi-tools
+	|| ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	rm -f bin/*
+	epatch \
+		"${FILESDIR}"/3.1-Makefile.patch \
+		"${FILESDIR}"/3.1-path.patch \
+		"${FILESDIR}"/3.2-fgets.patch
+	eprefixify runpsipred*
+	emake -C src clean
+}
+
+src_compile() {
+	emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+	emake -C src DESTDIR="${D}" install
+	dobin runpsipred* bin/* BLAST+/runpsipred*
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc README
+}
+
+pkg_postinst() {
+	elog "Please use the update_blastdb.pl in order to"
+	elog "maintain your own local blastdb"
+}
diff --git a/sci-biology/psipred/psipred-3.4.ebuild b/sci-biology/psipred/psipred-3.4.ebuild
new file mode 100644
index 000000000000..95d859b7898d
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.4.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils prefix toolchain-funcs versionator
+
+#MY_P="${PN}$(delete_all_version_separators)"
+MY_P="${PN}${PV}"
+
+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
+	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	app-shells/tcsh
+	sci-biology/ncbi-tools
+	|| ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	rm -f bin/*
+	epatch \
+		"${FILESDIR}"/3.1-Makefile.patch \
+		"${FILESDIR}"/3.1-path.patch \
+		"${FILESDIR}"/3.2-fgets.patch
+	eprefixify runpsipred*
+	emake -C src clean
+}
+
+src_compile() {
+	emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+	emake -C src DESTDIR="${D}" install
+	dobin runpsipred* bin/* BLAST+/runpsipred*
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc README
+}
+
+pkg_postinst() {
+	elog "Please use the update_blastdb.pl in order to"
+	elog "maintain your own local blastdb"
+}
diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild
new file mode 100644
index 000000000000..95d859b7898d
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.5.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils prefix toolchain-funcs versionator
+
+#MY_P="${PN}$(delete_all_version_separators)"
+MY_P="${PN}${PV}"
+
+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
+	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	app-shells/tcsh
+	sci-biology/ncbi-tools
+	|| ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	rm -f bin/*
+	epatch \
+		"${FILESDIR}"/3.1-Makefile.patch \
+		"${FILESDIR}"/3.1-path.patch \
+		"${FILESDIR}"/3.2-fgets.patch
+	eprefixify runpsipred*
+	emake -C src clean
+}
+
+src_compile() {
+	emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+	emake -C src DESTDIR="${D}" install
+	dobin runpsipred* bin/* BLAST+/runpsipred*
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc README
+}
+
+pkg_postinst() {
+	elog "Please use the update_blastdb.pl in order to"
+	elog "maintain your own local blastdb"
+}