InCvs

6 files changed, 0 insertions, 225 deletions

diff --git a/sci-libs/rosetta-fragments/ChangeLog b/sci-libs/rosetta-fragments/ChangeLog
deleted file mode 100644
index d9b0e8b9a..000000000
--- a/sci-libs/rosetta-fragments/ChangeLog
+++ /dev/null
@@ -1,11 +0,0 @@
-# ChangeLog for sci-libs/rosetta-fragments
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*rosetta-fragments-3.0 (09 Apr 2009)
-
-  09 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +files/3.0-chemshift.patch, +files/3.0-nnmake.patch, +metadata.xml,
-  +rosetta-fragments-3.0.ebuild:
-  Initial checkin to sci
-
diff --git a/sci-libs/rosetta-fragments/Manifest b/sci-libs/rosetta-fragments/Manifest
deleted file mode 100644
index 26c79d942..000000000
--- a/sci-libs/rosetta-fragments/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX 3.0-chemshift.patch 952 RMD160 783195efb0952657dd47aab8e448a9b4044e623a SHA1 997c62e47832f1643bfa584a013d950ee2af6e2f SHA256 e453052bfe4b6927d9911661c4e791e256fd88473ab53b7e9faa254a1701db48
-AUX 3.0-nnmake.patch 5861 RMD160 3e3ed271cce1f5856cf13d808f673743f5680d39 SHA1 1a43e8a093d41805b4287d0098ccb62c40694bec SHA256 3f57bccd12539303e492110cc4fc69601eac86647dce6dbae5d87e5771018ebd
-DIST rosetta3_fragments.tgz 443866583 RMD160 8fde0b53898a9c8fad0fa4326529ad4dcb8447f8 SHA1 33edeb4339cdd01533543c77ffb4671039ca4356 SHA256 fb446f70efe1cf8cfd3ec9173357a12937d17415853d02be0b8f82070f84ccb7
-EBUILD rosetta-fragments-3.0.ebuild 1303 RMD160 26ef9997ea9a5dd9d059534e2eec971afeaf5046 SHA1 cfc1a0eef4a96cad4151d3ac4e3e0d674da26b21 SHA256 90b8db9d424a7c08829c38f353cc8200630d8c5ed5bc8d7d87e30df4a620f0c7
-MISC ChangeLog 351 RMD160 b2b29aac3eac7aa536dd6d2730870dd0b9faf6b0 SHA1 ee118bcad9c231812189ef0ae92f915eb2406b4a SHA256 eebf1ae0c54988668ba7cfb2189ffe779a32b9d8cee424192026821ddfa9dcdb
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-libs/rosetta-fragments/files/3.0-chemshift.patch b/sci-libs/rosetta-fragments/files/3.0-chemshift.patch
deleted file mode 100644
index 6ea69b210..000000000
--- a/sci-libs/rosetta-fragments/files/3.0-chemshift.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- chemshift/makefile	2009-01-09 16:08:00.000000000 +0100
-+++ chemshift/makefile.new	2009-04-09 11:30:34.179824057 +0200
-@@ -64,7 +64,7 @@
- # rule to compile executable
- compile: $(BASE_NAME).$(COMPILER)
- $(BASE_NAME).$(COMPILER) : print ${OBJS}
--	$(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
-+	$(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
- 
- # rule to compile object files:
- .$(COMPILER).%.o: %.f
---- chemshift/make.system	2009-01-09 16:08:00.000000000 +0100
-+++ chemshift/make.system.new	2009-04-09 11:35:16.126466293 +0200
-@@ -61,16 +61,14 @@
- 
- # defaults
- F77=f77
--FFLAGS=
- FOPTIMFLAGS=-O
- FDEBUGFLAGS=-g
- FPROFILEFLAGS=-P
- 
- ifeq ($(COMPILER),gnu)
--	F77 = g77
--	FFLAGS = -finline-functions -funroll-loops -W  -ffixed-line-length-132 -Wimplicit
--	FOPTIMFLAGS = -O -ffast-math -malign-double
--	FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W
-+	F77 = $(FORTRANC)
-+	FOPTIMFLAGS = 
-+	FDEBUGFLAGS = 
- 	FPROFILEFLAGS = -pg
- endif
- 
diff --git a/sci-libs/rosetta-fragments/files/3.0-nnmake.patch b/sci-libs/rosetta-fragments/files/3.0-nnmake.patch
deleted file mode 100644
index 35568bb9f..000000000
--- a/sci-libs/rosetta-fragments/files/3.0-nnmake.patch
+++ /dev/null
@@ -1,107 +0,0 @@
---- nnmake/make.system	2009-01-09 16:07:59.000000000 +0100
-+++ nnmake/make.system.new	2009-04-09 10:54:50.000000000 +0200
-@@ -62,10 +62,9 @@
- FPROFILEFLAGS=-P
- 
- ifeq ($(COMPILER),gnu)
--	F77 = g77
--	FFLAGS = -finline-functions -funroll-loops -W  -ffixed-line-length-132 -Wimplicit
--	FOPTIMFLAGS = -O -ffast-math -malign-double
--	FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W
-+	F77 = $(FORTRANC)
-+	FOPTIMFLAGS = 
-+	FDEBUGFLAGS = 
- 	FPROFILEFLAGS = -pg
- endif
- 
---- nnmake/dipolar_nn.f	2009-01-09 16:08:00.000000000 +0100
-+++ nnmake/dipolar_nn.f.new	2009-04-09 11:06:24.923302302 +0200
-@@ -1396,7 +1396,7 @@
-             write(0,*)'rejected' 
-             write(0,*)x(1,iset),x(2,iset),x(3,iset),x(4,iset),x(5,iset)
-             do i=1,maplength(iset)
--               write(0,'(i,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5),
-+               write(0,'(i6,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5),
-      #              b(i)
-             enddo
-             goto 300
---- nnmake/make.system	2009-04-09 11:10:34.399945087 +0200
-+++ nnmake/make.system.new	2009-04-09 11:19:41.287390259 +0200
-@@ -55,7 +55,6 @@
- 
- # defaults
- F77=f77
--FFLAGS=
- FOPTIMFLAGS=-O
- FDEBUGFLAGS=-g
- FPROFILEFLAGS=-P
---- nnmake/makefile	2009-01-09 16:08:00.000000000 +0100
-+++ nnmake/makefile.new	2009-04-09 11:22:43.454037887 +0200
-@@ -102,7 +102,7 @@
- # rule to compile executable
- compile: print $(BASE_NAME).$(COMPILER)
- $(BASE_NAME).$(COMPILER) :  ${OBJS}
--	$(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
-+	$(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
- 
- coord_compile: print $(COORD_BASE_NAME).$(COMPILER)
- $(COORD_BASE_NAME).$(COMPILER) :  ${COORD_OBJS}
---- nnmake/make_fragments.pl	2009-01-09 15:53:33.000000000 +0100
-+++ nnmake/make_fragments.pl.new	2009-04-09 13:01:52.987174602 +0200
-@@ -19,38 +19,38 @@
- 
- my $TAIL = "_v1_3";
- 
--$src_dir = '/work/chu/rosetta/rosetta_C++/rosetta-2.2.0/rosetta_fragments';
--$shareware_dir = '/work/chu/src/shareware';
--$scratch = "/scratch/shared";
-+$src_dir = '/';
-+$shareware_dir = '$src_dir/usr/share';
-+$scratch = "$src_dir/scratch/shared";
- 
- # psi-blast
- #my $BLAST_BIN_DIR = "$shareware_dir/new_blast/blast-2.2.12/bin";
--my $PSIBLAST = "$shareware_dir/blast/bin/blastpgp";     # PSI-BLAST (duh.)
--my $NR = "/$scratch/genomes/nr";                # nr blast database filename
--my $VALL_BLAST_DB = "/$scratch/nnmake_database/vall.blast.2006-05-05";        # vall blast database filename (cvs respository 'nnmake_database')
--my $BLOSUM = "$scratch/nnmake_database/";      # BLOSUM score matrices directory (cvs repository 'nnmake_database')
-+my $PSIBLAST = "$src_dir/usr/bin/blastpgp";     # PSI-BLAST (duh.)
-+my $NR = "$shareware_dir/blast-db/nr";                # nr blast database filename
-+my $VALL_BLAST_DB = "$shareware_dir/rosetta-fragments/nnmake_database/vall.blast.2006-05-05";        # vall blast database filename (cvs respository 'nnmake_database')
-+my $BLOSUM = "$shareware_dir/rosetta-fragments/nnmake_database/";      # BLOSUM score matrices directory (cvs repository 'nnmake_database')
- 
- # psipred
--my $FILTNR = "$scratch/genomes/filtnr";        # filtnr blast database filename
--my $MAKEMAT = "$shareware_dir/blast/bin/makemat";       # makemat utility (part of NCBI tools)
--my $PSIPRED = "$shareware_dir/psipred/bin/psipred";       # psipred
--my $PSIPASS2 = "$shareware_dir/psipred/bin/psipass2";     # psipass2 (part of psipred pkg)
-+my $FILTNR = "$src_dir/tmp/filtnr";        # filtnr blast database filename
-+my $MAKEMAT = "$src_dir/usr/bin/makemat";       # makemat utility (part of NCBI tools)
-+my $PSIPRED = "$src_dir/usr/bin/psipred";       # psipred
-+my $PSIPASS2 = "$src_dir/usr/bin/psipass2";     # psipass2 (part of psipred pkg)
- my $PSIPRED_DATA = "$shareware_dir/psipred/data";         # dir containing psipred data files.
- 
- # prof
- #my $PROF = "$shareware_dir/prof/run_prof.py";
--my $PROF = "$src_dir/nnmake/run_prof.py"; # remember to change prof executable location in run_prof.py
-+my $PROF = "$src_dir/usr/bin/run_prof.py"; # remember to change prof executable location in run_prof.py
- 
- # nnmake
--my $VALL = "$scratch/nnmake_database";          # dir containing vall database (cvs repository 'nnmake_database')
--my $VALL2 = "$scratch/nnmake_database";             # alt dir containing vall database (cvs repository 'nnmake_database')
-+my $VALL = "$shareware_dir/rosetta-fragments/nnmake_database";          # dir containing vall database (cvs repository 'nnmake_database')
-+my $VALL2 = "$shareware_dir/rosetta-fragments/nnmake_database";             # alt dir containing vall database (cvs repository 'nnmake_database')
- my $VALL_NAME = "vall.dat.2006-05-05";                 # filename of vall (vall.dat.<id> and vall_cst_coord.dat.<id> must exist)
--my $NNMAKE = "$src_dir/nnmake/pNNMAKE.gnu";                         # nnmake binary  (cvs respository 'nnmake')
--my $TRIMLOOPS = "$src_dir/nnmake/trimLoopLibrary.pl";                  # trimLoopLibrary.pl (cvs respository 'nnmake')
-+my $NNMAKE = "$src_dir/usr/bin/pNNMAKE";                         # nnmake binary  (cvs respository 'nnmake')
-+my $TRIMLOOPS = "$src_dir/usr/bin/trimLoopLibrary.pl";                  # trimLoopLibrary.pl (cvs respository 'nnmake')
- 
- # chemshift
--my $CHEMSHIFT = "$src_dir/chemshift/pCHEMSHIFT.gnu";     # chemshift binary (cvs repository 'chemshift')
--my $TALOS_DB = "$scratch/chemshift_database";                          # TALOS databases directory (cvs respository 'chemshift_database')
-+my $CHEMSHIFT = "$src_dir/usr/bin/pCHEMSHIFT";     # chemshift binary (cvs repository 'chemshift')
-+my $TALOS_DB = "$shareware_dir/rosetta-fragments/chemshift_database";                          # TALOS databases directory (cvs respository 'chemshift_database')
- 
- # jufo (secondary structure prediction software)
- my $JUFO = "$shareware_dir/jufo/molecule.exe";                              # jufo executable
diff --git a/sci-libs/rosetta-fragments/metadata.xml b/sci-libs/rosetta-fragments/metadata.xml
deleted file mode 100644
index efb490d78..000000000
--- a/sci-libs/rosetta-fragments/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.0.ebuild b/sci-libs/rosetta-fragments/rosetta-fragments-3.0.ebuild
deleted file mode 100644
index 55d00ff0e..000000000
--- a/sci-libs/rosetta-fragments/rosetta-fragments-3.0.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit fortran flag-o-matic
-
-DESCRIPTION="Fragment library for rosetta"
-HOMEPAGE="www.rosettacommons.org"
-SRC_URI="rosetta3_fragments.tgz"
-
-LICENSE="|| ( rosetta-academic rosetta-commercial )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RESTRICT="fetch"
-
-RDEPEND="sci-biology/ncbi-tools
-	sci-biology/blast-db
-	sci-biology/psipred"
-
-S="${WORKDIR}"/${PN/-/_}
-
-FORTRAN="g77 gfortran ifc"
-
-pkg_nofetch() {
-	einfo "Go to ${HOMEPAGE} and get ${PN}.tgz and rename it to ${A}"
-	einfo "which must be placed in ${DISTDIR}"
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-nnmake.patch
-	epatch "${FILESDIR}"/${PV}-chemshift.patch
-}
-
-src_compile() {
-	append-fflags -ffixed-line-length-132
-
-	cd "${S}"/nnmake && \
-	emake || die
-
-	cd "${S}"/chemshift && \
-	emake || die
-}
-
-src_install() {
-	find . -type d -name ".svn" -exec rm -rf '{}' \; 2> /dev/null
-
-	newbin nnmake/pNNMAKE.gnu pNNMAKE && \
-	newbin chemshift/pCHEMSHIFT.gnu pCHEMSHIFT || \
-	die "failed to install the bins"
-
-	dobin nnmake/*.pl || die "no additional perl scripts"
-
-	insinto /usr/share/${PN}
-	doins -r *_database || die
-	dodoc fragments.README nnmake/{nnmake.README,vall/*.pl} chemshift/chemshift.README || die "no docs"
-}