* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs_tools/
@ 2016-07-12 14:51 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-07-12 14:51 UTC (permalink / raw
To: gentoo-commits
commit: 6b020466331bf69a623d04b7f30b7a6b3f78fd50
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 14:51:39 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 14:51:39 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6b020466
sci-biology/wgs_tools: add taxonomy-related info to NCBI SRA and BLAST+
Package-Manager: portage-2.2.28
sci-biology/wgs_tools/metadata.xml | 12 ++++++++++
sci-biology/wgs_tools/wgs_tools-9999.ebuild | 36 +++++++++++++++++++++++++++++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/wgs_tools/metadata.xml b/sci-biology/wgs_tools/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/wgs_tools/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>
diff --git a/sci-biology/wgs_tools/wgs_tools-9999.ebuild b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
new file mode 100644
index 0000000..d3c7656
--- /dev/null
+++ b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Scripts for ncbi-tools++ and SRA postprocessing using taxonomy"
+HOMEPAGE="ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS
+ http://www.ncbi.nlm.nih.gov/books/NBK279690/
+ http://www.ncbi.nlm.nih.gov/genbank/wgs"
+SRC_URI="ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/taxid2tsa.pl
+ ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/taxid2wgs.pl"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ dev-lang/perl"
+
+src_install(){
+ dobin *.pl
+ dodoc README*
+}
+
+pkg_postinst(){
+ einfo "These scripts are helpful for VDB-enabled blast+ applications"
+ einfo "and for tools from SRA toolkit sci-biology/sra_sdk or"
+ einfo "sci-biology/sra_toolkit-bin. They are not added to DEPENDENCIES"
+ einfo "yet until the packages are stable. Probably you want to download"
+ einfo "Please read http://www.ncbi.nlm.nih.gov/books/NBK158899/"
+ einfo "and unpack one of the prebuilt binaries from:"
+ einfo "https://github.com/ncbi/sra-tools/wiki/Downloads"
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs_tools/
@ 2017-02-18 6:32 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2017-02-18 6:32 UTC (permalink / raw
To: gentoo-commits
commit: 9abfd42fb22d481a3ce589897e26461939f3d4b2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 18 06:32:39 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 18 06:32:39 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9abfd42f
sci-biology/wgs_tools: fix install procedure
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/wgs_tools/wgs_tools-9999.ebuild | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/wgs_tools/wgs_tools-9999.ebuild b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
index d3c7656d3..115aa2509 100644
--- a/sci-biology/wgs_tools/wgs_tools-9999.ebuild
+++ b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -20,9 +20,11 @@ DEPEND=""
RDEPEND="${DEPEND}
dev-lang/perl"
+S="${W}/"
+
src_install(){
+ cd "${DISTDIR}" || die
dobin *.pl
- dodoc README*
}
pkg_postinst(){
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs_tools/
@ 2021-01-18 12:26 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2021-01-18 12:26 UTC (permalink / raw
To: gentoo-commits
commit: 7d31e6b17e47b0c0012c527aba7ac0d963e96e10
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 12:25:42 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 12:25:42 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d31e6b1
sci-biology/wgs_tools: regen manifest
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/wgs_tools/wgs_tools-9999.ebuild | 11 ++++-------
1 file changed, 4 insertions(+), 7 deletions(-)
diff --git a/sci-biology/wgs_tools/wgs_tools-9999.ebuild b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
index 94a2d9648..9048d106a 100644
--- a/sci-biology/wgs_tools/wgs_tools-9999.ebuild
+++ b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
DESCRIPTION="Scripts for ncbi-tools++ and SRA postprocessing using taxonomy"
HOMEPAGE="ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS
@@ -13,13 +13,10 @@ SRC_URI="ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/taxid2tsa.pl
LICENSE="all-rights-reserved"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
-DEPEND=""
-RDEPEND="${DEPEND}
- dev-lang/perl"
+RDEPEND="dev-lang/perl"
-S="${W}/"
+S="${WORKDIR}"
src_install(){
cd "${DISTDIR}" || die
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wgs_tools/
@ 2021-03-03 15:51 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2021-03-03 15:51 UTC (permalink / raw
To: gentoo-commits
commit: 95437c6322b182202af3d79d673042c7e9477325
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Mar 3 15:50:02 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Mar 3 15:50:02 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=95437c63
sci-biology/wgs_tools: use https
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/wgs_tools/wgs_tools-9999.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/wgs_tools/wgs_tools-9999.ebuild b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
index 9048d106a..8ea3959ea 100644
--- a/sci-biology/wgs_tools/wgs_tools-9999.ebuild
+++ b/sci-biology/wgs_tools/wgs_tools-9999.ebuild
@@ -5,8 +5,8 @@ EAPI=7
DESCRIPTION="Scripts for ncbi-tools++ and SRA postprocessing using taxonomy"
HOMEPAGE="ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS
- http://www.ncbi.nlm.nih.gov/books/NBK279690/
- http://www.ncbi.nlm.nih.gov/genbank/wgs"
+ https://www.ncbi.nlm.nih.gov/books/NBK279690/
+ https://www.ncbi.nlm.nih.gov/genbank/wgs"
SRC_URI="ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/taxid2tsa.pl
ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS/taxid2wgs.pl"
^ permalink raw reply related [flat|nested] 4+ messages in thread
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