* [gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
@ 2013-03-21 6:54 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2013-03-21 6:54 UTC (permalink / raw
To: gentoo-commits
commit: 06503ff3f3ec649b49060508ee184d6f0d34c03e
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 20 15:04:06 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> 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 <jlec@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
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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
@ 2013-03-21 16:11 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2013-03-21 16:11 UTC (permalink / raw
To: gentoo-commits
commit: dacf07b5176ba91a236bb202e957eab01bd9c094
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 21 09:22:21 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 21 09:22:21 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dacf07b5
sci-chemistry/cs-rosetta: Use Fortran eclass
Package-Manager: portage-2.2.0_alpha166
---
sci-chemistry/cs-rosetta/ChangeLog | 4 ++++
.../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletions(-)
diff --git a/sci-chemistry/cs-rosetta/ChangeLog b/sci-chemistry/cs-rosetta/ChangeLog
index f98c85b..9152840 100644
--- a/sci-chemistry/cs-rosetta/ChangeLog
+++ b/sci-chemistry/cs-rosetta/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 21 Mar 2013; Justin Lecher <jlec@gentoo.org>
+ cs-rosetta-1.01.2009.1109.11.ebuild:
+ Use Fortran eclass
+
*cs-rosetta-1.01.2009.1109.11 (20 Mar 2013)
20 Mar 2013; Justin Lecher <jlec@gentoo.org>
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 9c33f7d..edc6772 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
@@ -4,7 +4,7 @@
EAPI=5
-inherit flag-o-matic toolchain-funcs
+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/"
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
@ 2013-03-22 8:31 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2013-03-22 8:31 UTC (permalink / raw
To: gentoo-commits
commit: c0705aea6069b07e24263858de5174571463520e
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 22 08:31:01 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Mar 22 08:31:01 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c0705aea
sci-chemistry/cs-rosetta: Missing exec bit for pdbrms
Package-Manager: portage-2.2.0_alpha166
---
sci-chemistry/cs-rosetta/ChangeLog | 4 ++++
.../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletions(-)
diff --git a/sci-chemistry/cs-rosetta/ChangeLog b/sci-chemistry/cs-rosetta/ChangeLog
index 9152840..bc0a70e 100644
--- a/sci-chemistry/cs-rosetta/ChangeLog
+++ b/sci-chemistry/cs-rosetta/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 22 Mar 2013; Justin Lecher <jlec@gentoo.org>
+ cs-rosetta-1.01.2009.1109.11.ebuild:
+ Missing exec bit for pdbrms
+
21 Mar 2013; Justin Lecher <jlec@gentoo.org>
cs-rosetta-1.01.2009.1109.11.ebuild:
Use Fortran eclass
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 edc6772..1f294c3 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
@@ -95,7 +95,7 @@ src_install() {
doins -r *
chmod 755 \
"${ED}"/opt/${PN}/com/* \
- "${ED}"/opt/${PN}/src/{mfr2rosetta/mfr2rosetta,SPARTA/src/SPARTA,TALOS/TALOS,rosettaFrag2csFrag/rosettaFrag2csFrag,nnmake/pNNMAKE} \
+ "${ED}"/opt/${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
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
@ 2014-05-19 12:28 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2014-05-19 12:28 UTC (permalink / raw
To: gentoo-commits
commit: ca2b6d3956df8d5afa087f69d192a6e9febb630a
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May 19 12:26:51 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon May 19 12:28:47 2014 +0000
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 <jlec@gentoo.org>
+ cs-rosetta-1.01.2009.1109.11.ebuild:
+ Add optional dep on sci-biology/update-blastdb
+
22 Mar 2013; Justin Lecher <jlec@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
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
@ 2014-09-16 4:07 Christoph Junghans
0 siblings, 0 replies; 7+ messages in thread
From: Christoph Junghans @ 2014-09-16 4:07 UTC (permalink / raw
To: gentoo-commits
commit: 54305102018185bd00b9a735d45916e03d9dcb8b
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 03:14:09 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 03:14:09 2014 +0000
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 <ottxor@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 <jlec@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 <jlec@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="
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
@ 2014-11-17 9:20 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2014-11-17 9:20 UTC (permalink / raw
To: gentoo-commits
commit: 0956c347f052c43bf6df2ed94b6be08f54be728e
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 17 09:06:16 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 17 09:06:16 2014 +0000
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 <jlec@gentoo.org>
+ cs-rosetta-1.01.2009.1109.11.ebuild:
+ Drop all keywords
+
16 Sep 2014; Christoph Junghans <ottxor@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="
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/
@ 2021-01-05 18:59 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-01-05 18:59 UTC (permalink / raw
To: gentoo-commits
commit: 74bee558a76964dd78bcd11e37b42d97382183b0
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 5 18:58:20 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 5 18:58:20 2021 +0000
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 <andrewammerlaan <AT> 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..000000000
--- 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=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,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..000000000
--- a/sci-chemistry/cs-rosetta/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?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>
^ permalink raw reply related [flat|nested] 7+ messages in thread
end of thread, other threads:[~2021-01-05 18:59 UTC | newest]
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2014-05-19 12:28 [gentoo-commits] proj/sci:master commit in: sci-chemistry/cs-rosetta/ Justin Lecher
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2014-11-17 9:20 Justin Lecher
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