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Thu, 21 Mar 2013 06:54:42 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1363791846.06503ff3f3ec649b49060508ee184d6f0d34c03e.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/cs-rosetta/ChangeLog sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild sci-chemistry/cs-rosetta/metadata.xml X-VCS-Directories: sci-chemistry/cs-rosetta/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 06503ff3f3ec649b49060508ee184d6f0d34c03e X-VCS-Branch: master Date: Thu, 21 Mar 2013 06:54:42 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 6ba697e9-24c6-4319-8ab2-51ae2e221220 X-Archives-Hash: db14f4929c8d05b72ca954aee4829f75 commit: 06503ff3f3ec649b49060508ee184d6f0d34c03e Author: Justin Lecher gentoo org> AuthorDate: Wed Mar 20 15:04:06 2013 +0000 Commit: Justin Lecher gentoo org> CommitDate: Wed Mar 20 15:04:06 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=06503ff3 sci-chemistry/cs-rosetta: New addition Package-Manager: portage-2.2.0_alpha166 --- sci-chemistry/cs-rosetta/ChangeLog | 10 ++ .../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild | 104 ++++++++++++++++++++ sci-chemistry/cs-rosetta/metadata.xml | 5 + 3 files changed, 119 insertions(+), 0 deletions(-) diff --git a/sci-chemistry/cs-rosetta/ChangeLog b/sci-chemistry/cs-rosetta/ChangeLog new file mode 100644 index 0000000..f98c85b --- /dev/null +++ b/sci-chemistry/cs-rosetta/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-chemistry/cs-rosetta +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*cs-rosetta-1.01.2009.1109.11 (20 Mar 2013) + + 20 Mar 2013; Justin Lecher + +cs-rosetta-1.01.2009.1109.11.ebuild, +metadata.xml: + New addition + diff --git a/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild b/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild new file mode 100644 index 0000000..9c33f7d --- /dev/null +++ b/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild @@ -0,0 +1,104 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="System for chemical shifts based protein structure prediction using ROSETTA" +HOMEPAGE="http://spin.niddk.nih.gov/bax/software/CSROSETTA/" +SRC_URI=" + http://spin.niddk.nih.gov/bax/software/CSROSETTA/install.com -> ${P}-install.com + http://spin.niddk.nih.gov/bax/software/CSROSETTA/CSRosetta.tar.Z -> ${P}.tar.Z + http://spin.niddk.nih.gov/bax/software/CSROSETTA/changeLog -> ${P}-changelog" + +SLOT="0" +LICENSE="all-rights-reserved" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="custom-cflags" + +RDEPEND=" + dev-lang/perl + sci-biology/ncbi-tools++ + sci-biology/profphd + sci-biology/psipred + sci-biology/samtools + ~sci-libs/cs-rosetta-db-${PV} + sci-chemistry/nmrpipe + sci-chemistry/rosetta" +DEPEND="" + +S="${WORKDIR}" + +src_unpack() { + unpack ${P}.tar.Z +} + +src_prepare() { + cat >> "${T}"/39${PN} <<- EOF + rosetta3="${EPREFIX}/usr/bin/AbinitioRelax" + rosetta3_extpdbs="${EPREFIX}/usr/bin/extract_pdbs" + rosetta3DB="${EPREFIX}/usr/share/rosetta-db" + csrosettaDir="${EPREFIX}/opt/${PN}" + csrosettaCom="${EPREFIX}/opt/${PN}/com" + PATH="${EPREFIX}/opt/${PN}/com" + MFR="${EPREFIX}/opt/${PN}/com/mfr.tcl" + EOF + + # needs more love + sed \ + -e "s:CSROSETTA_DIR/src/nnmake/pNNMAKE.gnu:${EPREFIX}/opt/${PN}/src/nnmake/pNNMAKE:g" \ + -i com/make_fragments_2000.pl || die + + append-fflags -ffixed-line-length-132 +} + +src_compile() { + use custom-cflags || CXXFLAGS="-pipe -ffor-scope -fno-exceptions -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000" + + compilation() { + if [[ -f dipolar_nn.f ]]; then + sed \ + -e '/write/s:(i,6f6.3):(i3,6(1x,f6.3)):g' \ + -i dipolar_nn.f || die + fi + + sed \ + -e '/LDFLAGS/s: = : ?= :g' \ + -e '/CCFLAGS/s: = : += :g' \ + -e 's:$(OBJECT) $(LDFLAGS):$(LDFLAGS) $(OBJECT) -lm -o:g' \ + -e 's:$(FFLAGS) -o:$(FFLAGS) $(LDFLAGS) -o:g' \ + -e '/make.system/d' \ + -i *akefile || die + emake \ + CC=$(tc-getCXX) \ + CCFLAGS="${CXXFLAGS}" + + if [[ -f pNNMAKE. ]]; then + mv pNNMAKE{.,} || die + emake almostsuperclean + else + emake clean + fi + } + + for i in src/{mfr2rosetta,SPARTA/src,pdbrms,TALOS,rosettaFrag2csFrag,nnmake}; do + pushd ${i} > /dev/null + compilation + popd > /dev/null + done +} + +src_install() { + insinto /opt/${PN}/ + doins -r * + chmod 755 \ + "${ED}"/opt/${PN}/com/* \ + "${ED}"/opt/${PN}/src/{mfr2rosetta/mfr2rosetta,SPARTA/src/SPARTA,TALOS/TALOS,rosettaFrag2csFrag/rosettaFrag2csFrag,nnmake/pNNMAKE} \ + || die + + dosym make_fragments_2000.pl /opt/${PN}/com/make_fragment_2000.pl + + doenvd "${T}"/39${PN} +} diff --git a/sci-chemistry/cs-rosetta/metadata.xml b/sci-chemistry/cs-rosetta/metadata.xml new file mode 100644 index 0000000..897aa2e --- /dev/null +++ b/sci-chemistry/cs-rosetta/metadata.xml @@ -0,0 +1,5 @@ + + + + sci +