[gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
commit: 74bee558a76964dd78bcd11e37b42d97382183b0
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Jan 5 18:58:20 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Jan 5 18:58:20 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=74bee558
sci-chemistry/cs-rossetta: dep was removed
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
.../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild | 103 -
sci-chemistry/cs-rosetta/metadata.xml | 8 --
2 files changed, 111 deletions(-)
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
deleted file mode 100644
index 74cf932d8..0
--- a/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild
+++ /dev/null
@@ -1,103 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit flag-o-matic fortran-2 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 ->
${P}-changelog"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS=""
-IUSE="custom-cflags"
-
-RDEPEND="
- dev-lang/perl
- || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )
- sci-biology/profphd
- sci-biology/psipred
- sci-biology/samtools
- ~sci-libs/cs-rosetta-db-${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=2"
-
- 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,pdbrms/pdbrms,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
deleted file mode 100644
index da36ecbfc..0
--- a/sci-chemistry/cs-rosetta/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- sci-chemis...@gentoo.org
- Gentoo Chemistry Project
-
-
[gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
commit: 0956c347f052c43bf6df2ed94b6be08f54be728e Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Mon Nov 17 09:06:16 2014 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Mon Nov 17 09:06:16 2014 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0956c347 sci-chemistry/cs-rosetta: Drop all keywords Package-Manager: portage-2.2.14 --- sci-chemistry/cs-rosetta/ChangeLog | 4 sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/sci-chemistry/cs-rosetta/ChangeLog b/sci-chemistry/cs-rosetta/ChangeLog index ba57b80..651329e 100644 --- a/sci-chemistry/cs-rosetta/ChangeLog +++ b/sci-chemistry/cs-rosetta/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Nov 2014; Justin Lecher j...@gentoo.org + cs-rosetta-1.01.2009.1109.11.ebuild: + Drop all keywords + 16 Sep 2014; Christoph Junghans ott...@gentoo.org cs-rosetta-1.01.2009.1109.11.ebuild: dropped ~amd64 as sci-chemistry/nmrpipe doesn't have ~amd64 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 index ce0bbc6..8d42a2b 100644 --- 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 @@ -15,7 +15,7 @@ SRC_URI= SLOT=0 LICENSE=all-rights-reserved -KEYWORDS=~x86 ~amd64-linux ~x86-linux +KEYWORDS= IUSE=custom-cflags RDEPEND=
[gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
commit: 54305102018185bd00b9a735d45916e03d9dcb8b Author: Christoph Junghans ottxor AT gentoo DOT org AuthorDate: Tue Sep 16 03:14:09 2014 + Commit: Christoph Junghans ottxor AT gentoo DOT org CommitDate: Tue Sep 16 03:14:09 2014 + URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=54305102 dropped ~amd64 as sci-chemistry/nmrpipe doesn't have ~amd64 Package-Manager: portage-2.2.8-r1 --- sci-chemistry/cs-rosetta/ChangeLog | 5 - sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/sci-chemistry/cs-rosetta/ChangeLog b/sci-chemistry/cs-rosetta/ChangeLog index 61fc16a..ba57b80 100644 --- a/sci-chemistry/cs-rosetta/ChangeLog +++ b/sci-chemistry/cs-rosetta/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Sep 2014; Christoph Junghans ott...@gentoo.org + cs-rosetta-1.01.2009.1109.11.ebuild: + dropped ~amd64 as sci-chemistry/nmrpipe doesn't have ~amd64 + 19 May 2014; Justin Lecher j...@gentoo.org cs-rosetta-1.01.2009.1109.11.ebuild: Add optional dep on sci-biology/update-blastdb @@ -19,4 +23,3 @@ 20 Mar 2013; Justin Lecher j...@gentoo.org +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 index f3981fb..ce0bbc6 100644 --- 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 @@ -15,7 +15,7 @@ SRC_URI= SLOT=0 LICENSE=all-rights-reserved -KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux +KEYWORDS=~x86 ~amd64-linux ~x86-linux IUSE=custom-cflags RDEPEND=
[gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
commit: ca2b6d3956df8d5afa087f69d192a6e9febb630a Author: Justin Lecher jlec AT gentoo DOT org AuthorDate: Mon May 19 12:26:51 2014 + Commit: Justin Lecher jlec AT gentoo DOT org CommitDate: Mon May 19 12:28:47 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ca2b6d39 sci-chemistry/cs-rosetta: Add optional dep on sci-biology/update-blastdb Package-Manager: portage-2.2.10 --- sci-chemistry/cs-rosetta/ChangeLog | 6 +- sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/sci-chemistry/cs-rosetta/ChangeLog b/sci-chemistry/cs-rosetta/ChangeLog index bc0a70e..61fc16a 100644 --- a/sci-chemistry/cs-rosetta/ChangeLog +++ b/sci-chemistry/cs-rosetta/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/cs-rosetta -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 19 May 2014; Justin Lecher j...@gentoo.org + cs-rosetta-1.01.2009.1109.11.ebuild: + Add optional dep on sci-biology/update-blastdb + 22 Mar 2013; Justin Lecher j...@gentoo.org cs-rosetta-1.01.2009.1109.11.ebuild: Missing exec bit for pdbrms 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 index 9ee4f6e..f3981fb 100644 --- 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 @@ -20,7 +20,7 @@ IUSE=custom-cflags RDEPEND= dev-lang/perl - sci-biology/ncbi-tools++ + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) sci-biology/profphd sci-biology/psipred sci-biology/samtools
