* [gentoo-commits] proj/sci:master commit in: sci-biology/pvmsx/
@ 2015-01-07 22:12 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-01-07 22:12 UTC (permalink / raw
To: gentoo-commits
commit: 3010ecf4051cb4cbab7d5adfceca5bccf1e312df
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 22:11:27 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 22:11:27 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3010ecf4
Initial ebuild
---
sci-biology/pvmsx/metadata.xml | 9 ++++++++
sci-biology/pvmsx/pvmsx-0.1.ebuild | 46 ++++++++++++++++++++++++++++++++++++++
2 files changed, 55 insertions(+)
diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/pvmsx/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild
new file mode 100644
index 0000000..b194f08
--- /dev/null
+++ b/sci-biology/pvmsx/pvmsx-0.1.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="parallel multi-FASTA file processing tool using PVM from TIGR Gene Indices project tools, an alternative to psx"
+HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
+ ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sys-cluster/pvm"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}
+
+src_unpack(){
+ mkdir ${PN} || die
+ cd ${PN} || die "Failed to chdir"
+ unpack ${PN}.tar.gz || die
+}
+
+src_prepare() {
+ # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h
+ sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed"
+ sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die
+ sed -i "s#-I-#-iquote#" ${S}/${PN}/Makefile
+ cd ${PN} || die
+ ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
+}
+
+src_compile() {
+ cd ${PN} || die
+ emake || die "emake failed in "${S}"/${PN}"
+}
+
+src_install() {
+ cd ${PN} || die
+ dobin ${PN} || die "Failed to install ${PN} binary"
+ newdoc README README.${PN}
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pvmsx/
@ 2015-01-10 14:37 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-01-10 14:37 UTC (permalink / raw
To: gentoo-commits
commit: 1addc38c5ff55f17bdb2da77ecf3463f76463f50
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:22:49 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:22:49 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1addc38c
sci-biology/pvmsx: Soma QA and polishing
Package-Manager: portage-2.2.15
---
sci-biology/pvmsx/ChangeLog | 7 +++++++
sci-biology/pvmsx/metadata.xml | 10 +++++-----
sci-biology/pvmsx/pvmsx-0.1.ebuild | 36 +++++++++++++++++-------------------
3 files changed, 29 insertions(+), 24 deletions(-)
diff --git a/sci-biology/pvmsx/ChangeLog b/sci-biology/pvmsx/ChangeLog
new file mode 100644
index 0000000..506319d
--- /dev/null
+++ b/sci-biology/pvmsx/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/pvmsx
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 10 Jan 2015; Justin Lecher <jlec@gentoo.org> pvmsx-0.1.ebuild, metadata.xml:
+ Soma QA and polishing
+
diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/pvmsx/metadata.xml
+++ b/sci-biology/pvmsx/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
- <maintainer>
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild
index b194f08..feac0d2 100644
--- a/sci-biology/pvmsx/pvmsx-0.1.ebuild
+++ b/sci-biology/pvmsx/pvmsx-0.1.ebuild
@@ -4,43 +4,41 @@
EAPI=5
-DESCRIPTION="parallel multi-FASTA file processing tool using PVM from TIGR Gene Indices project tools, an alternative to psx"
+DESCRIPTION="Parallel multi-FASTA file processing tool"
HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
- ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
+SRC_URI="
+ ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
+ ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND="sys-cluster/pvm"
-RDEPEND="${DEPEND}"
+#DEPEND="sys-cluster/pvm"
+#RDEPEND="${DEPEND}"
S=${WORKDIR}
-src_unpack(){
- mkdir ${PN} || die
- cd ${PN} || die "Failed to chdir"
- unpack ${PN}.tar.gz || die
-}
-
src_prepare() {
# we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h
- sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed"
- sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die
- sed -i "s#-I-#-iquote#" ${S}/${PN}/Makefile
- cd ${PN} || die
+ sed \
+ -e 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \
+ -i "${S}"/Makefile || die "Failed to run sed"
+ sed \
+ -e 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' \
+ -i "${S}"/Makefile || die
+ sed \
+ -e "s#-I-#-iquote#" \
+ -i "${S}"/Makefile || die
ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
}
src_compile() {
- cd ${PN} || die
- emake || die "emake failed in "${S}"/${PN}"
+ emake
}
src_install() {
- cd ${PN} || die
- dobin ${PN} || die "Failed to install ${PN} binary"
+ dobin ${PN}
newdoc README README.${PN}
}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pvmsx/
@ 2021-01-18 21:39 Aisha Tammy
0 siblings, 0 replies; 3+ messages in thread
From: Aisha Tammy @ 2021-01-18 21:39 UTC (permalink / raw
To: gentoo-commits
commit: d08f55efd3ed478e2ebf4a68bc83ee36e875c33c
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Mon Jan 18 21:38:14 2021 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Mon Jan 18 21:38:44 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d08f55ef
sci-biology/pvmsx: drop dead package
upstream has not updated in 14 years
Closes: https://bugs.gentoo.org/755830
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>
sci-biology/pvmsx/metadata.xml | 12 -----------
sci-biology/pvmsx/pvmsx-0.1.ebuild | 43 --------------------------------------
2 files changed, 55 deletions(-)
diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/pvmsx/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild
deleted file mode 100644
index b88863a45..000000000
--- a/sci-biology/pvmsx/pvmsx-0.1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Parallel multi-FASTA file processing tool"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="
- ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
- ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-#DEPEND="sys-cluster/pvm"
-#RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-src_prepare() {
- # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h
- sed \
- -e 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \
- -i "${S}"/Makefile || die "Failed to run sed"
- sed \
- -e 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' \
- -i "${S}"/Makefile || die
- sed \
- -e "s#-I-#-iquote#" \
- -i "${S}"/Makefile || die
- ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
-}
-
-src_compile() {
- default
-}
-
-src_install() {
- dobin ${PN}
- newdoc README README.${PN}
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
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