[gentoo-commits] proj/sci:master commit in: sci-biology/trans-abyss/

[gentoo-commits] proj/sci:master commit in: sci-biology/trans-abyss/

[Martin Mokrejs]

commit:     3348aa6294b4e7ef88327026db0f601c646c95b0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan  7 22:42:20 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan  7 22:42:20 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3348aa62

Initial ebuild

---
 sci-biology/trans-abyss/ChangeLog                | 10 ++++++++++
 sci-biology/trans-abyss/metadata.xml             |  9 +++++++++
 sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild | 24 ++++++++++++++++++++++++
 3 files changed, 43 insertions(+)

diff --git a/sci-biology/trans-abyss/ChangeLog b/sci-biology/trans-abyss/ChangeLog
new file mode 100644
index 0000000..47ce379
--- /dev/null
+++ b/sci-biology/trans-abyss/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/trans-abyss
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*trans-abyss-1.4.8 (07 Jan 2015)
+
+  07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +trans-abyss-1.4.8.ebuild, +metadata.xml:
+  initial ebuild
+

diff --git a/sci-biology/trans-abyss/metadata.xml b/sci-biology/trans-abyss/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/trans-abyss/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/trans-abyss/trans-abyss-1.4.8.ebuild b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
new file mode 100644
index 0000000..c8538cb
--- /dev/null
+++ b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Analyze and combine multiple assemblies from abyss"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss"
+SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/"${PV}"/trans-ABySS-v"${PV}"_20130916.tar.gz"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# perl and python
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/trans-ABySS-v"${PV}"
+
+# TODO
+#src_install(){
+#}

[gentoo-commits] proj/sci:master commit in: sci-biology/trans-abyss/

[Justin Lecher]

commit:     df448be0623dea0474f8943cb2de92e6774a6ea3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:41:16 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:41:16 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=df448be0

sci-biology/trans-abyss: Soma polishing

Package-Manager: portage-2.2.15

---
 sci-biology/trans-abyss/ChangeLog                | 3 +++
 sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/trans-abyss/ChangeLog b/sci-biology/trans-abyss/ChangeLog
index 47ce379..5268abe 100644
--- a/sci-biology/trans-abyss/ChangeLog
+++ b/sci-biology/trans-abyss/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Jan 2015; Justin Lecher <jlec@gentoo.org> trans-abyss-1.4.8.ebuild:
+  Soma polishing
+
 *trans-abyss-1.4.8 (07 Jan 2015)
 
   07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
index 9d6a250..76bb799 100644
--- a/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
+++ b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 DESCRIPTION="Analyze and combine multiple assemblies from abyss"
 HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss"
-SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/"${PV}"/trans-ABySS-v"${PV}"_20130916.tar.gz"
+SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/${PV}/trans-ABySS-v${PV}_20130916.tar.gz"
 
 # http://www.bcgsc.ca/platform/bioinfo/license/bcca_2010
 LICENSE="bcca_2010"

[gentoo-commits] proj/sci:master commit in: sci-biology/trans-abyss/

[Andrew Ammerlaan]

commit:     bc37c11b916f4db2d7135345be34e02ff828eb38
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 15:36:41 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 15:36:41 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bc37c11b

sci-biology/trans-abyss: update, fix install, EAPI bump

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

 sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild | 24 ----------------
 sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild | 35 ++++++++++++++++++++++++
 2 files changed, 35 insertions(+), 24 deletions(-)

diff --git a/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild b/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
deleted file mode 100644
index dbb2d668f..000000000
--- a/sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Analyze and combine multiple assemblies from abyss"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss"
-SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/${PV}/trans-ABySS-v${PV}_20130916.tar.gz"
-
-# http://www.bcgsc.ca/platform/bioinfo/license/bcca_2010
-LICENSE="bcca_2010"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# perl and python
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/trans-ABySS-v"${PV}"
-
-# TODO
-#src_install(){
-#}

diff --git a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild b/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild
new file mode 100644
index 000000000..859783cc0
--- /dev/null
+++ b/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_7 )
+
+inherit python-r1
+
+DESCRIPTION="Analyze and combine multiple assemblies from abyss"
+HOMEPAGE="https://www.bcgsc.ca/resources/software/trans-abyss"
+SRC_URI="https://github.com/bcgsc/transabyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+	dev-lang/perl
+	dev-python/python-igraph[${PYTHON_USEDEP}]
+	sci-biology/abyss
+	sci-biology/blat
+"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/transabyss-${PV}"
+
+src_install() {
+	einstalldocs
+	python_foreach_impl python_domodule utilities
+	dobin transabyss
+	dobin transabyss-merge
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/trans-abyss/

[Andrew Ammerlaan]

commit:     a3cd1f5c1c74e3d870c2e547715b6fb3083ac791
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Apr 18 09:22:16 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Apr 18 09:22:38 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a3cd1f5c

sci-biology/trans-abyss: bump python compat

not completely tested, because there is not test suite

Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild b/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild
index 859783cc0..cf10dd3b9 100644
--- a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild
+++ b/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
 
 inherit python-r1