Initial addition, #250415

(Portage version: 2.2_rc67/cvs/Linux x86_64)

5 files changed, 218 insertions, 0 deletions

diff --git a/sci-libs/rosetta-fragments/ChangeLog b/sci-libs/rosetta-fragments/ChangeLog
new file mode 100644
index 000000000000..56bd00106466
--- /dev/null
+++ b/sci-libs/rosetta-fragments/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-libs/rosetta-fragments
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/rosetta-fragments/ChangeLog,v 1.1 2010/05/18 20:40:03 jlec Exp $
+
+*rosetta-fragments-3.1 (18 May 2010)
+
+  18 May 2010; Justin Lecher <jlec@gentoo.org> +files/3.1-chemshift.patch,
+  +files/3.1-nnmake.patch, +rosetta-fragments-3.1.ebuild, +metadata.xml:
+  Initial addition, #250415
+
diff --git a/sci-libs/rosetta-fragments/files/3.1-chemshift.patch b/sci-libs/rosetta-fragments/files/3.1-chemshift.patch
new file mode 100644
index 000000000000..6ea69b210e82
--- /dev/null
+++ b/sci-libs/rosetta-fragments/files/3.1-chemshift.patch
@@ -0,0 +1,33 @@
+--- 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 = $(FORTRANC)
++	FOPTIMFLAGS = 
++	FDEBUGFLAGS = 
+ 	FPROFILEFLAGS = -pg
+ endif
+ 
diff --git a/sci-libs/rosetta-fragments/files/3.1-nnmake.patch b/sci-libs/rosetta-fragments/files/3.1-nnmake.patch
new file mode 100644
index 000000000000..35568bb9f805
--- /dev/null
+++ b/sci-libs/rosetta-fragments/files/3.1-nnmake.patch
@@ -0,0 +1,107 @@
+--- nnmake/make.system	2009-01-09 16:07:59.000000000 +0100
++++ nnmake/make.system.new	2009-04-09 10:54:50.000000000 +0200
+@@ -62,10 +62,9 @@
+ FPROFILEFLAGS=-P
+ 
+ ifeq ($(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
new file mode 100644
index 000000000000..d691b2482707
--- /dev/null
+++ b/sci-libs/rosetta-fragments/metadata.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+<maintainer>
+  <email>jlec@gentoo.org</email>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.1.ebuild b/sci-libs/rosetta-fragments/rosetta-fragments-3.1.ebuild
new file mode 100644
index 000000000000..65ef698a2138
--- /dev/null
+++ b/sci-libs/rosetta-fragments/rosetta-fragments-3.1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/rosetta-fragments/rosetta-fragments-3.1.ebuild,v 1.1 2010/05/18 20:40:03 jlec Exp $
+
+EAPI="2"
+
+inherit flag-o-matic fortran
+
+DESCRIPTION="Fragment library for rosetta"
+HOMEPAGE="www.rosettacommons.org"
+SRC_URI="rosetta3.1_fragments.tgz"
+
+LICENSE="rosetta"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RESTRICT="fetch"
+
+RDEPEND="
+	sci-biology/ncbi-tools
+	sci-biology/ncbi-tools++
+	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"
+}