[gentoo-commits] proj/sci:master commit in: sci-biology/act-bin/

[gentoo-commits] proj/sci:master commit in: sci-biology/act-bin/

[Martin Mokrejs]

commit:     aeb330b5d14397ab0a558befd4ff1434a6835e91
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 14:18:44 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 14:18:44 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=aeb330b5

sci-biology/act-bin: new java package with upstream binaries

Package-Manager: portage-2.2.28

 sci-biology/act-bin/act-bin-13.0.0.ebuild | 50 +++++++++++++++++++++++++++++++
 sci-biology/act-bin/metadata.xml          | 12 ++++++++
 2 files changed, 62 insertions(+)

diff --git a/sci-biology/act-bin/act-bin-13.0.0.ebuild b/sci-biology/act-bin/act-bin-13.0.0.ebuild
new file mode 100644
index 0000000..debf770
--- /dev/null
+++ b/sci-biology/act-bin/act-bin-13.0.0.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit java-pkg-2
+
+DESCRIPTION="DNA contig sequence comparison tool supplementing Artemis"
+HOMEPAGE="http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/sact_v13.jar
+	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_v13.jar
+	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_manual_complete.pdf -> ${P}.manual.pdf
+	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_html_build.zip -> ${P}.html_build.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+	!sci-biology/artemis"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.6:*"
+
+S="${WORKDIR}"
+
+src_unpack(){
+	unzip "${DISTDIR}"/${P}.html_build.zip || die
+}
+
+src_prepare(){
+	default
+	cd act_html_build || die
+	rm -f .DS_Store HTML.index HTML.manifest || die
+}
+
+src_install(){
+	java-pkg_dojar "${DISTDIR}"/*.jar
+	dodoc "${DISTDIR}"/${P}.manual.pdf
+	insinto /usr/share/doc/"${PN}"/html
+	doins act_html_build/*
+}
+
+pkg_postinst(){
+	einfo "For BAM file support please install sci-biology/BamView"
+	einfo "You may find interesting the additional web resources:"
+	einfo "http://www.webact.org/WebACT"
+	einfo "http://www.hpa-bioinfotools.org.uk/pise/double_act.html"
+}

diff --git a/sci-biology/act-bin/metadata.xml b/sci-biology/act-bin/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/act-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>

[gentoo-commits] proj/sci:master commit in: sci-biology/act-bin/

[Martin Mokrejs]

commit:     f7b79ae7f74d85694989bb51d362dc885ae955f4
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 09:51:30 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 09:51:30 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7b79ae7

sci-biology/act-bin: version bump

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 .../act-bin/{act-bin-13.0.0.ebuild => act-bin-17.0.1.ebuild}  | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/sci-biology/act-bin/act-bin-13.0.0.ebuild b/sci-biology/act-bin/act-bin-17.0.1.ebuild
similarity index 73%
rename from sci-biology/act-bin/act-bin-13.0.0.ebuild
rename to sci-biology/act-bin/act-bin-17.0.1.ebuild
index caddeab7e..8d69910ad 100644
--- a/sci-biology/act-bin/act-bin-13.0.0.ebuild
+++ b/sci-biology/act-bin/act-bin-17.0.1.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=6
@@ -7,10 +7,11 @@ inherit java-pkg-2
 
 DESCRIPTION="DNA contig sequence comparison tool supplementing Artemis"
 HOMEPAGE="http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/sact_v13.jar
-	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_v13.jar
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/act/v17/v${PV}/sact-v${PV}.jar
+	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v17/v${PV}/act-v${PV}.jar
 	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_manual_complete.pdf -> ${P}.manual.pdf
-	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_html_build.zip -> ${P}.html_build.zip"
+	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_html_build.zip -> ${P}.html_build.zip
+	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v17/v${PV}/release_notes.txt"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -36,7 +37,7 @@ src_prepare(){
 
 src_install(){
 	java-pkg_dojar "${DISTDIR}"/*.jar
-	dodoc "${DISTDIR}"/${P}.manual.pdf
+	dodoc "${DISTDIR}"/${P}.manual.pdf "${DISTDIR}"/release_notes.txt
 	insinto /usr/share/doc/"${PN}"/html
 	doins act_html_build/*
 }

[gentoo-commits] proj/sci:master commit in: sci-biology/act-bin/

[Martin Mokrejs]

commit:     ecfa19a5441839b113280dd4905078178fa346a3
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 11:26:37 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 11:26:37 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ecfa19a5

sci-biology/act-bin: raise require java version

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 sci-biology/act-bin/act-bin-17.0.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/act-bin/act-bin-17.0.1.ebuild b/sci-biology/act-bin/act-bin-17.0.1.ebuild
index 8d69910ad..c61df75f3 100644
--- a/sci-biology/act-bin/act-bin-17.0.1.ebuild
+++ b/sci-biology/act-bin/act-bin-17.0.1.ebuild
@@ -21,7 +21,7 @@ IUSE=""
 DEPEND="
 	!sci-biology/artemis"
 RDEPEND="${DEPEND}
-	>=virtual/jre-1.6:*"
+	>=virtual/jre-1.8:*"
 
 S="${WORKDIR}"
 

[gentoo-commits] proj/sci:master commit in: sci-biology/act-bin/

[Andrew Ammerlaan]

commit:     ac7f647b0e067e80e50813b99c26ab9a46330631
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:13:41 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:13:41 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ac7f647b

sci-biology/act-bin: depend on unzip

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/act-bin/act-bin-17.0.1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/act-bin/act-bin-17.0.1.ebuild b/sci-biology/act-bin/act-bin-17.0.1.ebuild
index c61df75f3..1311e1e24 100644
--- a/sci-biology/act-bin/act-bin-17.0.1.ebuild
+++ b/sci-biology/act-bin/act-bin-17.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -18,7 +18,7 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND="
+DEPEND="app-arch/unzip
 	!sci-biology/artemis"
 RDEPEND="${DEPEND}
 	>=virtual/jre-1.8:*"

[gentoo-commits] proj/sci:master commit in: sci-biology/act-bin/

[Andrew Ammerlaan]

commit:     556cca191809d49bd435235f3f4887ec46a108ac
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Feb  5 11:48:36 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Feb  5 11:48:36 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=556cca19

sci-biology/act-bin: use https

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/act-bin/act-bin-17.0.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/act-bin/act-bin-17.0.1.ebuild b/sci-biology/act-bin/act-bin-17.0.1.ebuild
index 1311e1e24..6e68ba25a 100644
--- a/sci-biology/act-bin/act-bin-17.0.1.ebuild
+++ b/sci-biology/act-bin/act-bin-17.0.1.ebuild
@@ -6,7 +6,7 @@ EAPI=6
 inherit java-pkg-2
 
 DESCRIPTION="DNA contig sequence comparison tool supplementing Artemis"
-HOMEPAGE="http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
+HOMEPAGE="https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
 SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/act/v17/v${PV}/sact-v${PV}.jar
 	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v17/v${PV}/act-v${PV}.jar
 	ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_manual_complete.pdf -> ${P}.manual.pdf

[gentoo-commits] proj/sci:master commit in: sci-biology/act-bin/

[Andrew Ammerlaan]

commit:     28d6f30cf9dbcdd6e3ee32831d180ecc04b327bb
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar  4 20:32:22 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar  4 20:32:22 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=28d6f30c

sci-biology/act-bin: remove nonexistent blocker

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/act-bin/act-bin-17.0.1.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-biology/act-bin/act-bin-17.0.1.ebuild b/sci-biology/act-bin/act-bin-17.0.1.ebuild
index 6e68ba25a..a124d5ab1 100644
--- a/sci-biology/act-bin/act-bin-17.0.1.ebuild
+++ b/sci-biology/act-bin/act-bin-17.0.1.ebuild
@@ -18,8 +18,7 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND="app-arch/unzip
-	!sci-biology/artemis"
+DEPEND="app-arch/unzip"
 RDEPEND="${DEPEND}
 	>=virtual/jre-1.8:*"
 

[gentoo-commits] proj/sci:master commit in: sci-biology/act-bin/

[Andrew Ammerlaan]

commit:     33b7a421d24ccb77f9632e5699270448a880576f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar  5 21:23:41 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar  5 21:23:41 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=33b7a421

sci-biology/act-bin: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/act-bin/act-bin-17.0.1.ebuild | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/sci-biology/act-bin/act-bin-17.0.1.ebuild b/sci-biology/act-bin/act-bin-17.0.1.ebuild
index a124d5ab1..31bad30bb 100644
--- a/sci-biology/act-bin/act-bin-17.0.1.ebuild
+++ b/sci-biology/act-bin/act-bin-17.0.1.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit java-pkg-2
 
@@ -16,9 +16,8 @@ SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/act/v17/v${PV}/sact-v${PV
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
-DEPEND="app-arch/unzip"
+BDEPEND="app-arch/unzip"
 RDEPEND="${DEPEND}
 	>=virtual/jre-1.8:*"
 
@@ -37,8 +36,8 @@ src_prepare(){
 src_install(){
 	java-pkg_dojar "${DISTDIR}"/*.jar
 	dodoc "${DISTDIR}"/${P}.manual.pdf "${DISTDIR}"/release_notes.txt
-	insinto /usr/share/doc/"${PN}"/html
-	doins act_html_build/*
+	docinto html
+	dodoc act_html_build/*
 }
 
 pkg_postinst(){