diff options
Diffstat (limited to 'sci-libs/rosetta-fragments')
5 files changed, 286 insertions, 0 deletions
diff --git a/sci-libs/rosetta-fragments/Manifest b/sci-libs/rosetta-fragments/Manifest new file mode 100644 index 000000000000..a4b4008cb433 --- /dev/null +++ b/sci-libs/rosetta-fragments/Manifest @@ -0,0 +1,7 @@ +AUX rosetta-fragments-3.1-chemshift.patch 1721 SHA256 02ab89d1d762c65653c6582481f5ece77c57d79c79bc6b16609c522ceafcbb49 SHA512 3475a4fd7a433d4d380ccd5ab11cf32f326fafc828d1bead0dbb0e03f5e53c613bf57c7950e090d8a2eb34c4ba93ecf25b25afcc9f251ff5f943e6b7e3112bb1 WHIRLPOOL d86a5147f7be585bcae825f0ab03eac84ab173aa781351ac4414cfd9ddc0329815097609beb2fc54a88636e3cb277894fe1ad73d5bda77d6d6cb528365fd594a +AUX rosetta-fragments-3.1-nnmake.patch 7030 SHA256 cfb08b00ee66e4342afda54129c735358b3fbd6a70ef88647b9ca18d96ce33b1 SHA512 de6d41f68911a5beddc8a15c9ce33013b03462642229aaf3b09ae4123c281260fa725bbd55593eea305b05d2ed21e1d17394686ee4e42bda20825d71d9367501 WHIRLPOOL 8ae1e9b64c3842e2091bc0cac434673f40ca8e0512ee417a78eeb4ea11c2c48368aa1bf1547843cb26e41c2c5f1e49e6ce3e4487d1b53e248f496db2a07ef5ed +DIST rosetta3.1_fragments.tgz 221931894 SHA256 2211cab76e4848d80d6fd311e97535de220a865d8afc72d8ca12f90b7d4641bf SHA512 a2b2646c916ea1b98e2c7267c1eadb1fd6cb76d015c24bd4e8318ce127cb5d96ca56bfdd76821e1dd884e03d59631f544e221b9f541ad4063a99e96dbb029da1 WHIRLPOOL 32d0758e6782da8088178e11af5bfe23b457e98a3ab9a8cbb583d4e4aa48e5d1ef9005825ff62944c5c755a0ac99b3ff88fb7c1d1b249940110287969ff0118a +EBUILD rosetta-fragments-3.1-r1.ebuild 1133 SHA256 2447cade451d79957ac718d4abff4c7e266949c2866d3a1506f538e21df30750 SHA512 7d424dcfeed1d073c27c2ba5a86d75877c597bfea95f40ab7acff767d41786b66576dbedb0a626e84d00ca63cd0f9131227d3ff200c35ad6b4d33ff485be5ab7 WHIRLPOOL 1c9b9e8eae47c7bab86c8264b438b3050f0542658eb4dcaeeed2fc09fe303f00f26bc52cf7581836332cf347a8d321676593fe4970494730c1a08f4375f21d19 +MISC ChangeLog 2747 SHA256 f27e11f976b2e5f1e144b14a1cdcd603c97d21ea27919a1a99ab7125dfe499b1 SHA512 62a4ec9d7aa0a05a074083ebf74295be4d608317cd86c66b0b46b7932da02388b1fa095b03472e04432d2993670c8e6e602bea31ecd90ed20037621d328e9172 WHIRLPOOL a57ed1ba5934098532e525b2071bdbf1b9e4c66c0d0099acbfe3dcee4909e0331d75838909e2b4c1f95f9dd5ff4b7f932ba2c43cad708c5931f1acf3612fad7b +MISC ChangeLog-2015 1336 SHA256 83a5ea22bb3a9e8e19728f9c48c63adca8912fd367264f98f1c8ad258b674c92 SHA512 74f65c0d5dd99e7fa1d5b0c569917f7d4b66f169f1dbacbaaf91d3151f46b3befc1d75bbe79f26a1f58f370daedc25f337482c6405f6a4ed77e1708478467a3a WHIRLPOOL 9ab4b9cc9d0246d7433d73b864cfd11536d76543f46fa53cf5c2393e386e1c731c670631cd6491d4ef8d686357bb66c812736f811341c5b37892c9aa32165569 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch new file mode 100644 index 000000000000..cb8fd9197d1b --- /dev/null +++ b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch @@ -0,0 +1,62 @@ + chemshift/make.system | 24 ++++++++++++------------ + chemshift/makefile | 2 +- + 2 files changed, 13 insertions(+), 13 deletions(-) + +diff --git a/chemshift/make.system b/chemshift/make.system +index 53bbd38..d105802 100644 +--- a/chemshift/make.system ++++ b/chemshift/make.system +@@ -60,18 +60,18 @@ endif + ########## once COMPILER is set, here are the options + + # defaults +-F77=f77 +-FFLAGS= +-FOPTIMFLAGS=-O +-FDEBUGFLAGS=-g ++F77?=f77 ++FFLAGS?= ++FOPTIMFLAGS?= ++FDEBUGFLAGS?= + FPROFILEFLAGS=-P + + ifeq ($(COMPILER),gnu) +- F77 = g77 +- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit +- FOPTIMFLAGS = -O -ffast-math -malign-double +- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W +- FPROFILEFLAGS = -pg ++ F77 ?= g77 ++ FFLAGS += -W -ffixed-line-length-132 -Wimplicit ++ FOPTIMFLAGS += -malign-double ++ FDEBUGFLAGS += -Wall -Wimplicit -Wsurprising -Wformat -W ++ FPROFILEFLAGS = + endif + + ifeq ($(COMPILER),pgi) # on mary, good bounds checking +@@ -108,9 +108,9 @@ endif + + # Suse ppc gnu + ifeq ($(COMPILER),ppc) +- F77 = g77 +- FFLAGS = -Wall -finline-functions -funroll-loops -W -ffixed-line-length-132 +- FDEBUGFLAGS = -g -C -Mbounds ++ F77 ?= g77 ++ FFLAGS += -Wall -W -ffixed-line-length-132 ++ FDEBUGFLAGS += -C -Mbounds + FOPTIMFLAGS = + endif + +diff --git a/chemshift/makefile b/chemshift/makefile +index 712e98f..05d3b64 100644 +--- a/chemshift/makefile ++++ b/chemshift/makefile +@@ -64,7 +64,7 @@ regular: compile + # 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 diff --git a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch new file mode 100644 index 000000000000..91da48017eff --- /dev/null +++ b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch @@ -0,0 +1,153 @@ + nnmake/dipolar_nn.f | 2 +- + nnmake/make.system | 33 ++++++++++++++++----------------- + nnmake/make_fragments.pl | 36 ++++++++++++++++++------------------ + nnmake/makefile | 2 +- + 4 files changed, 36 insertions(+), 37 deletions(-) + +diff --git a/nnmake/dipolar_nn.f b/nnmake/dipolar_nn.f +index c159888..4412a20 100644 +--- a/nnmake/dipolar_nn.f ++++ b/nnmake/dipolar_nn.f +@@ -1396,7 +1396,7 @@ car pairDipolar(1,i) .le. pairDipolar(1,i+1) + 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 +diff --git a/nnmake/make.system b/nnmake/make.system +index 34bea8f..2fbfabf 100644 +--- a/nnmake/make.system ++++ b/nnmake/make.system +@@ -55,18 +55,17 @@ endif + ########## once COMPILER is set, here are the options + + # defaults +-F77=f77 +-FFLAGS= +-FOPTIMFLAGS=-O +-FDEBUGFLAGS=-g +-FPROFILEFLAGS=-P ++F77?=f77 ++FOPTIMFLAGS= ++FDEBUGFLAGS= ++FPROFILEFLAGS= + + ifeq ($(COMPILER),gnu) +- F77 = g77 +- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit +- FOPTIMFLAGS = -O -ffast-math -malign-double +- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W +- FPROFILEFLAGS = -pg ++ F77 ?= g77 ++ FFLAGS += -W -ffixed-line-length-132 -Wimplicit ++ FOPTIMFLAGS += -malign-double ++ FDEBUGFLAGS += -Wall -Wimplicit -Wsurprising -Wformat -W ++ FPROFILEFLAGS = + endif + + ifeq ($(COMPILER),pgi) # on mary, good bounds checking +@@ -82,9 +81,9 @@ ifeq ($(COMPILER),pgi) # on mary, good bounds checking + endif + + ifeq ($(COMPILER),absoft) # on mary, fast +- F77 = f77 +- FFLAGS = -N109 -s -W +- LINKFLAGS = -lU77 ++ F77 ?= f77 ++ FFLAGS ?= -N109 -s -W ++ LINKFLAGS += -lU77 + FDEBUGFLAGS = -C -g + FOPTIMFLAGS = -O -N18 + FPROFILEFLAGS = -P -O +@@ -103,10 +102,10 @@ endif + + # Suse ppc gnu + ifeq ($(COMPILER),ppc) +- F77 = g77 +- FFLAGS = -Wall -finline-functions -funroll-loops -W -ffixed-line-length-132 +- FDEBUGFLAGS = -g -C -Mbounds +- FOPTIMFLAGS = ++ F77 ?= g77 ++ FFLAGS += -Wall -W -ffixed-line-length-132 ++ FDEBUGFLAGS += -C -Mbounds ++ FOPTIMFLAGS += + endif + + # alpha flags +diff --git a/nnmake/make_fragments.pl b/nnmake/make_fragments.pl +index 5273685..29619a2 100755 +--- a/nnmake/make_fragments.pl ++++ b/nnmake/make_fragments.pl +@@ -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"; ++$src_dir = '@GENTOO_PORTAGE_EPREFIX@/'; ++$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/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/nnmake/makefile b/nnmake/makefile +index c09ac1c..ebfde68 100644 +--- a/nnmake/makefile ++++ b/nnmake/makefile +@@ -102,7 +102,7 @@ VallCoord: coord_compile + # 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) : ${COORD_OBJS} diff --git a/sci-libs/rosetta-fragments/metadata.xml b/sci-libs/rosetta-fragments/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/rosetta-fragments/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild new file mode 100644 index 000000000000..055c225edf1d --- /dev/null +++ b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic prefix toolchain-funcs + +DESCRIPTION="Fragment library for rosetta" +HOMEPAGE="http://www.rosettacommons.org" +SRC_URI="rosetta3.1_fragments.tgz" + +LICENSE="rosetta" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="" +RDEPEND=" + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) + sci-biology/psipred" + +RESTRICT="fetch" + +S="${WORKDIR}"/${PN/-/_} + +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}"/${P}-nnmake.patch \ + "${FILESDIR}"/${P}-chemshift.patch + tc-export F77 + eprefixify nnmake/*.pl +} + +src_compile() { + emake -C nnmake + emake -C chemshift +} + +src_install() { + esvn_clean . + + newbin nnmake/pNNMAKE.gnu pNNMAKE + newbin chemshift/pCHEMSHIFT.gnu pCHEMSHIFT + + dobin nnmake/*.pl + + insinto /usr/share/${PN} + doins -r *_database + dodoc fragments.README nnmake/{nnmake.README,vall/*.pl} chemshift/chemshift.README +} |