* [gentoo-commits] proj/sci:master commit in: sci-biology/graf-bin/
@ 2016-07-28 17:09 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2016-07-28 17:09 UTC (permalink / raw
To: gentoo-commits
commit: b32b535a799fb9bb775d41e3beb00a66b8154cdd
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 28 17:09:03 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jul 28 17:09:03 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b32b535a
sci-biology/graf-bin: new binary package
Package-Manager: portage-2.2.28
sci-biology/graf-bin/graf-bin-20151102.ebuild | 31 +++++++++++++++++++++++++++
sci-biology/graf-bin/metadata.xml | 12 +++++++++++
2 files changed, 43 insertions(+)
diff --git a/sci-biology/graf-bin/graf-bin-20151102.ebuild b/sci-biology/graf-bin/graf-bin-20151102.ebuild
new file mode 100644
index 0000000..87c852d
--- /dev/null
+++ b/sci-biology/graf-bin/graf-bin-20151102.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Find closely related subjects using SNP genotype data, validate pedigree file"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi"
+SRC_URI="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetZip.cgi?zip_name=GRAF_files.zip -> ${P}.zip"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64" # 64bit exe only
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_install(){
+ dobin graf PlotGraf.pl
+ dodoc GRAF_ReadMe.docx
+ insinto /usr/share/"${PN}"
+ doins SsToRs.txt
+}
+
+pkg_postinst(){
+ einfo "Probably you will use this program with sci-biology/plink and"
+ einfo "sci-biology/plinkseq outputs"
+}
diff --git a/sci-biology/graf-bin/metadata.xml b/sci-biology/graf-bin/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/graf-bin/metadata.xml
@@ -0,0 +1,12 @@
+<?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>
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/graf-bin/
@ 2016-07-31 11:44 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2016-07-31 11:44 UTC (permalink / raw
To: gentoo-commits
commit: 7817458227965491d57626e3102af409f3c8af95
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jul 31 11:44:22 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jul 31 11:44:22 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=78174582
sci-biology/graf-bin: fix shebang line, inherit perl-module
Package-Manager: portage-2.3.0
sci-biology/graf-bin/graf-bin-20151102.ebuild | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/sci-biology/graf-bin/graf-bin-20151102.ebuild b/sci-biology/graf-bin/graf-bin-20151102.ebuild
index 87c852d..61664c9 100644
--- a/sci-biology/graf-bin/graf-bin-20151102.ebuild
+++ b/sci-biology/graf-bin/graf-bin-20151102.ebuild
@@ -4,6 +4,8 @@
EAPI=5
+inherit perl-module
+
DESCRIPTION="Find closely related subjects using SNP genotype data, validate pedigree file"
HOMEPAGE="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi"
SRC_URI="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetZip.cgi?zip_name=GRAF_files.zip -> ${P}.zip"
@@ -18,6 +20,10 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}"
+src_prepare(){
+ sed -e 's#/usr/local/bin/perl#/usr/bin/perl#' -i PlotGraf.pl || die # there is not perl_fix_shebang
+}
+
src_install(){
dobin graf PlotGraf.pl
dodoc GRAF_ReadMe.docx
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/graf-bin/
@ 2018-01-19 15:02 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-19 15:02 UTC (permalink / raw
To: gentoo-commits
commit: 2e3808167bc60baafd5873b023e2d1066a26750d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 19 15:02:24 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 19 15:02:24 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e380816
sci-biology/graf-bin: version bump
Usptream does not version release tarballs, and the
zip file is actually a .tar.gz.
Package-Manager: Portage-2.3.19, Repoman-2.3.6
.../{graf-bin-20151102.ebuild => graf-bin-20171212.ebuild} | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/sci-biology/graf-bin/graf-bin-20151102.ebuild b/sci-biology/graf-bin/graf-bin-20171212.ebuild
similarity index 76%
rename from sci-biology/graf-bin/graf-bin-20151102.ebuild
rename to sci-biology/graf-bin/graf-bin-20171212.ebuild
index 99c4b56d8..d8ddb6aa1 100644
--- a/sci-biology/graf-bin/graf-bin-20151102.ebuild
+++ b/sci-biology/graf-bin/graf-bin-20171212.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -7,7 +7,8 @@ inherit perl-module
DESCRIPTION="Find closely related subjects using SNP genotype data, validate pedigree file"
HOMEPAGE="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi"
-SRC_URI="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetZip.cgi?zip_name=GRAF_files.zip -> ${P}.zip"
+SRC_URI="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetZip.cgi?zip_name=GRAF_files.zip -> ${P}.tar.gz"
+# the .zip is indeed .tar.gz
LICENSE="public-domain"
SLOT="0"
@@ -24,10 +25,10 @@ src_prepare(){
}
src_install(){
- dobin graf PlotGraf.pl
- dodoc GRAF_ReadMe.docx
+ dobin graf graf_dups *.pl
+ dodoc GRAF_ReadMe_.docx GRAF-popDocumentation*.docx
insinto /usr/share/"${PN}"
- doins SsToRs.txt
+ doins *.txt *.bed *.bim *.fam
}
pkg_postinst(){
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/graf-bin/
@ 2018-01-19 15:11 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-19 15:11 UTC (permalink / raw
To: gentoo-commits
commit: 746e2088e9ff4af1c13e0febeae1cc39bbe465a5
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 19 15:11:50 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 19 15:11:50 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=746e2088
sci-biology/graf-bin: fix typo
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/graf-bin/graf-bin-20171212.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/graf-bin/graf-bin-20171212.ebuild b/sci-biology/graf-bin/graf-bin-20171212.ebuild
index d8ddb6aa1..7187ad7a6 100644
--- a/sci-biology/graf-bin/graf-bin-20171212.ebuild
+++ b/sci-biology/graf-bin/graf-bin-20171212.ebuild
@@ -26,7 +26,7 @@ src_prepare(){
src_install(){
dobin graf graf_dups *.pl
- dodoc GRAF_ReadMe_.docx GRAF-popDocumentation*.docx
+ dodoc GRAF_ReadMe_*.docx GRAF-popDocumentation*.docx
insinto /usr/share/"${PN}"
doins *.txt *.bed *.bim *.fam
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/graf-bin/
@ 2018-01-19 15:17 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-19 15:17 UTC (permalink / raw
To: gentoo-commits
commit: 48c5e6c53fcaf69305f4d449889eb1fb0a358402
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 19 15:17:43 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 19 15:17:43 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=48c5e6c5
sci-biology/graf-bin: fix shebang line
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/graf-bin/graf-bin-20171212.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/graf-bin/graf-bin-20171212.ebuild b/sci-biology/graf-bin/graf-bin-20171212.ebuild
index 7187ad7a6..93d554892 100644
--- a/sci-biology/graf-bin/graf-bin-20171212.ebuild
+++ b/sci-biology/graf-bin/graf-bin-20171212.ebuild
@@ -21,7 +21,7 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}"
src_prepare(){
- sed -e 's#/usr/local/bin/perl#/usr/bin/perl#' -i PlotGraf.pl || die # there is not perl_fix_shebang
+ sed -e 's#/usr/local/bin/perl#/usr/bin/env perl#' -i *.pl || die # there is not perl_fix_shebang
}
src_install(){
^ permalink raw reply related [flat|nested] 5+ messages in thread
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