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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
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committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-chemistry/pdb-tools | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
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
Diffstat (limited to 'sci-chemistry/pdb-tools')
-rw-r--r-- | sci-chemistry/pdb-tools/Manifest | 1 | ||||
-rw-r--r-- | sci-chemistry/pdb-tools/metadata.xml | 11 | ||||
-rw-r--r-- | sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild | 80 | ||||
-rw-r--r-- | sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild | 84 |
4 files changed, 176 insertions, 0 deletions
diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest new file mode 100644 index 000000000000..bf2e4bfa7dce --- /dev/null +++ b/sci-chemistry/pdb-tools/Manifest @@ -0,0 +1 @@ +DIST pdbTools_0.2.1.tar.gz 103835 SHA256 317a5246e806a2b3d0425d080d679646fc77388e3e855412527603f945fa37ae SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 WHIRLPOOL 36d8cf71ba9f9b28e3ad59828539f4e94bbb8bc4514f050ddcbec63857b154ecdc7c32c2945c0d15f4d718c4fe5ab3adcb2e62a4368bfd819b80e9641a9dfd88 diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml new file mode 100644 index 000000000000..13e9a3c93979 --- /dev/null +++ b/sci-chemistry/pdb-tools/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> + <upstream> + <remote-id type="google-code">pdb-tools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild new file mode 100644 index 000000000000..ad4ab1dec397 --- /dev/null +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 pypy ) + +inherit fortran-2 python-single-r1 toolchain-funcs + +MY_PN="pdbTools" + +DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files" +HOMEPAGE="http://code.google.com/p/pdb-tools/" +SRC_URI="http://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_PN}_${PV} + +pkg_setup() { + python-single-r1_pkg_setup + fortran-2_pkg_setup +} + +src_prepare() { + sed \ + -e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \ + -i pdb_sasa.py || die + sed \ + -e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \ + -i pdb_satk.py || die + sed \ + -e 's:> %:>%:g' \ + -i pdb_seq.py || die +} + +src_compile() { + mkdir bin + cd satk + for i in *.f; do + einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}" + $(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die + $(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die + sed \ + -e "s:${i/.f}.out:${i/.f}:g" \ + -i ../pdb_satk.py || die + done +} + +src_install() { + local script + insinto /usr/share/${PN} + doins -r pdb_data/peptides + rm -rf pdb_data/peptides || die + + python_domodule helper pdb_data + + python_moduleinto ${PN/-/_} + python_domodule *.py + + for i in pdb_*.py; do + cat > ${i/.py} <<- EOF + #!${EPREFIX}/bin/bash + ${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@ + EOF + dobin ${i/.py} + done + + dobin bin/* + dodoc README +} diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild new file mode 100644 index 000000000000..e56798f3c95b --- /dev/null +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit fortran-2 python-single-r1 toolchain-funcs + +MY_PN="pdbTools" + +DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files" +HOMEPAGE="http://code.google.com/p/pdb-tools/" +SRC_URI="http://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_PN}_${PV} + +pkg_setup() { + python-single-r1_pkg_setup + fortran-2_pkg_setup +} + +src_prepare() { + sed \ + -e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \ + -i pdb_sasa.py || die + sed \ + -e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \ + -i pdb_satk.py || die + sed \ + -e 's:> %:>%:g' \ + -i pdb_seq.py || die + + sed \ + -e "/import/s:helper:${PN/-/_}.helper:g" \ + -i *.py || die +} + +src_compile() { + mkdir bin + cd satk + for i in *.f; do + einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}" + $(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die + $(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die + sed \ + -e "s:${i/.f}.out:${i/.f}:g" \ + -i ../pdb_satk.py || die + done +} + +src_install() { + local script + insinto /usr/share/${PN} + doins -r pdb_data/peptides + rm -rf pdb_data/peptides || die + + python_domodule pdb_data + + python_moduleinto ${PN/-/_} + python_domodule helper *.py + + for i in pdb_*.py; do + cat > ${i/.py} <<- EOF + #!${EPREFIX}/bin/bash + ${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@ + EOF + dobin ${i/.py} + done + + dobin bin/* + dodoc README +} |