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

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

[Martin Mokrejs]

commit:     9b2792faf3aac9829d3c30dc8ea5c5ec92fc9a8f
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 11:39:30 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 11:39:30 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9b2792fa

sci-biology/tigmint: new package

It is not yet enabled because an install procedure is missing.

Bug: https://github.com/bcgsc/tigmint/issues/10
Package-Manager: Portage-2.3.28, Repoman-2.3.9

 sci-biology/tigmint/metadata.xml         | 12 ++++++++++++
 sci-biology/tigmint/tigmint-1.1.0.ebuild | 31 +++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+)

diff --git a/sci-biology/tigmint/metadata.xml b/sci-biology/tigmint/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/tigmint/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/tigmint/tigmint-1.1.0.ebuild b/sci-biology/tigmint/tigmint-1.1.0.ebuild
new file mode 100644
index 000000000..66a1f3460
--- /dev/null
+++ b/sci-biology/tigmint/tigmint-1.1.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="Correct misassemblies using linked reads from 10x Genomics Chromium"
+HOMEPAGE="https://github.com/bcgsc/tigmint"
+SRC_URI="https://github.com/bcgsc/tigmint/archive/1.1.0.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+	dev-python/intervaltree
+	sci-biology/pybedtools
+	sci-biology/pysam
+	dev-python/statistics"
+RDEPEND="${DEPEND}
+	sci-biology/bwa
+	sci-biology/bedtools
+	sci-biology/samtools:0
+	sci-biology/seqtools
+	dev-util/makefile2graph
+	media-gfx/graphviz
+	dev-vcs/git
+	dev-libs/libxslt
+	net-misc/curl"
+# for full features also sci-biology/abyss should be installed but it addition here
+# would create circular dependency

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

[Martin Mokrejs]

commit:     61199804d047b3bb60a69643a79263d4d9f9ff6c
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Fri Jan 10 16:13:53 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 10 16:13:58 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=61199804

sci-biology/tigmint: fix package name

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/tigmint/tigmint-1.1.0.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/tigmint/tigmint-1.1.0.ebuild b/sci-biology/tigmint/tigmint-1.1.0.ebuild
index 66a1f3460..7e2d6d143 100644
--- a/sci-biology/tigmint/tigmint-1.1.0.ebuild
+++ b/sci-biology/tigmint/tigmint-1.1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -21,7 +21,7 @@ RDEPEND="${DEPEND}
 	sci-biology/bwa
 	sci-biology/bedtools
 	sci-biology/samtools:0
-	sci-biology/seqtools
+	sci-biology/seqtk
 	dev-util/makefile2graph
 	media-gfx/graphviz
 	dev-vcs/git

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

[Horea Christian]

commit:     34fb671e52382f1d6c2196917dc43014d413ddde
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan  4 13:11:07 2021 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jan  5 06:08:00 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=34fb671e

sci-biology/tigmint: version bump, bump py targets, add keywords

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/tigmint/tigmint-1.1.0.ebuild | 31 -------------------------------
 sci-biology/tigmint/tigmint-1.2.1.ebuild | 29 +++++++++++++++++++++++++++++
 2 files changed, 29 insertions(+), 31 deletions(-)

diff --git a/sci-biology/tigmint/tigmint-1.1.0.ebuild b/sci-biology/tigmint/tigmint-1.1.0.ebuild
deleted file mode 100644
index 7e2d6d143..000000000
--- a/sci-biology/tigmint/tigmint-1.1.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Correct misassemblies using linked reads from 10x Genomics Chromium"
-HOMEPAGE="https://github.com/bcgsc/tigmint"
-SRC_URI="https://github.com/bcgsc/tigmint/archive/1.1.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-python/intervaltree
-	sci-biology/pybedtools
-	sci-biology/pysam
-	dev-python/statistics"
-RDEPEND="${DEPEND}
-	sci-biology/bwa
-	sci-biology/bedtools
-	sci-biology/samtools:0
-	sci-biology/seqtk
-	dev-util/makefile2graph
-	media-gfx/graphviz
-	dev-vcs/git
-	dev-libs/libxslt
-	net-misc/curl"
-# for full features also sci-biology/abyss should be installed but it addition here
-# would create circular dependency

diff --git a/sci-biology/tigmint/tigmint-1.2.1.ebuild b/sci-biology/tigmint/tigmint-1.2.1.ebuild
new file mode 100644
index 000000000..e2a9c626a
--- /dev/null
+++ b/sci-biology/tigmint/tigmint-1.2.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8} )
+
+inherit distutils-r1
+
+DESCRIPTION="Correct misassemblies using linked reads from 10x Genomics Chromium"
+HOMEPAGE="https://github.com/bcgsc/tigmint https://bcgsc.github.io/tigmint/"
+SRC_URI="https://github.com/bcgsc/tigmint/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# TODO: fix this
+# FileNotFoundError: [Errno 2] No such file or directory
+# happens even with --install
+RESTRICT="test"
+
+RDEPEND="
+	dev-python/intervaltree[${PYTHON_USEDEP}]
+	sci-biology/pybedtools[${PYTHON_USEDEP}]
+	sci-biology/pysam[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest

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

[Martin Mokrejs]

commit:     12a8a79abb8942a51cd8e15db9668bd0683221d3
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Sun Oct 17 12:08:06 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Oct 17 12:08:06 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=12a8a79a

sci-biology/tigmint: version bump, update SRC_URI

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/tigmint/{tigmint-1.2.1.ebuild => tigmint-1.2.4.ebuild} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/tigmint/tigmint-1.2.1.ebuild b/sci-biology/tigmint/tigmint-1.2.4.ebuild
similarity index 89%
rename from sci-biology/tigmint/tigmint-1.2.1.ebuild
rename to sci-biology/tigmint/tigmint-1.2.4.ebuild
index e2a9c626a..12a32bc2b 100644
--- a/sci-biology/tigmint/tigmint-1.2.1.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4.ebuild
@@ -9,7 +9,7 @@ inherit distutils-r1
 
 DESCRIPTION="Correct misassemblies using linked reads from 10x Genomics Chromium"
 HOMEPAGE="https://github.com/bcgsc/tigmint https://bcgsc.github.io/tigmint/"
-SRC_URI="https://github.com/bcgsc/tigmint/archive/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/bcgsc/tigmint/releases/download/v${PV}/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"

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

[Martin Mokrejs]

commit:     63dcb460ddbccacd2c2b7deb9a66bdd5705eb7ec
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Sun Oct 17 16:21:54 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Oct 17 16:21:54 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=63dcb460

sci-biology/tigmint: any python3 is supported

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/tigmint/tigmint-1.2.4.ebuild | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/sci-biology/tigmint/tigmint-1.2.4.ebuild b/sci-biology/tigmint/tigmint-1.2.4.ebuild
index 12a32bc2b..627aba19b 100644
--- a/sci-biology/tigmint/tigmint-1.2.4.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{7,8,9} )
 
 inherit distutils-r1
 
@@ -15,9 +15,6 @@ LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-# TODO: fix this
-# FileNotFoundError: [Errno 2] No such file or directory
-# happens even with --install
 RESTRICT="test"
 
 RDEPEND="

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

[Martin Mokrejs]

commit:     60b98c5ebef8040cd4d47494fc8e6ee5aa3e26b0
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Tue Oct 19 14:24:00 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct 19 14:24:00 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=60b98c5e

sci-biology/tigmint: add missing dependencies not listed by upstream

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/tigmint/tigmint-1.2.4.ebuild | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/sci-biology/tigmint/tigmint-1.2.4.ebuild b/sci-biology/tigmint/tigmint-1.2.4.ebuild
index 627aba19b..89d73318d 100644
--- a/sci-biology/tigmint/tigmint-1.2.4.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4.ebuild
@@ -21,6 +21,10 @@ RDEPEND="
 	dev-python/intervaltree[${PYTHON_USEDEP}]
 	sci-biology/pybedtools[${PYTHON_USEDEP}]
 	sci-biology/pysam[${PYTHON_USEDEP}]
+	app-arch/pigz
+	sci-biology/samtools
+	sci-biology/minimap2
+	sci-biology/seqtk
 "
 
 distutils_enable_tests pytest

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

[Martin Mokrejs]

commit:     6c45174a480dae72e147dbf764bda33b72404a56
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Tue Oct 19 15:06:25 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct 19 15:06:25 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6c45174a

sci-biology/tigmint: drop KEYWORDS until python install path is fixed

The 'from read_fasta import read_fasta' is supposed to work but Makefile
places the file into $prefix.

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/tigmint/tigmint-1.2.4.ebuild | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/sci-biology/tigmint/tigmint-1.2.4.ebuild b/sci-biology/tigmint/tigmint-1.2.4.ebuild
index 89d73318d..1b181ea44 100644
--- a/sci-biology/tigmint/tigmint-1.2.4.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4.ebuild
@@ -13,7 +13,7 @@ SRC_URI="https://github.com/bcgsc/tigmint/releases/download/v${PV}/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
 
 RESTRICT="test"
 
@@ -28,3 +28,28 @@ RDEPEND="
 "
 
 distutils_enable_tests pytest
+
+# install the executable into /usr/bin
+# BUG: the read_fasta.py should be installed into python modules
+#   so it can be imported into python
+src_prepare(){
+	sed -i Makefile -e 's#prefix=/usr/local#prefix=/usr#'
+	default
+}
+
+src_configure(){
+	python_setup
+	default
+}
+
+# do not run src_compile step as it runs git, makefile2graph, gsed, tred
+
+src_install(){
+	default
+	distutils-r1_src_install
+}
+
+src_test(){
+	default
+	python_foreach_impl python_test
+}

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

[Andrew Ammerlaan]

commit:     9a13af8737903d7bb70f8667fa53e6056fd3d429
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 20 13:12:14 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Oct 20 13:12:14 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9a13af87

sci-biology/tigmint: properly install python things

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 ...igmint-1.2.4.ebuild => tigmint-1.2.4-r1.ebuild} | 33 +++++++++++++++-------
 1 file changed, 23 insertions(+), 10 deletions(-)

diff --git a/sci-biology/tigmint/tigmint-1.2.4.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
similarity index 57%
rename from sci-biology/tigmint/tigmint-1.2.4.ebuild
rename to sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
index 1b181ea44..6900ea7aa 100644
--- a/sci-biology/tigmint/tigmint-1.2.4.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
@@ -1,9 +1,10 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_USE_SETUPTOOLS=no
 
 inherit distutils-r1
 
@@ -13,9 +14,10 @@ SRC_URI="https://github.com/bcgsc/tigmint/releases/download/v${PV}/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 
 RESTRICT="test"
+PROPERTIES="test_network"
 
 RDEPEND="
 	dev-python/intervaltree[${PYTHON_USEDEP}]
@@ -29,10 +31,8 @@ RDEPEND="
 
 distutils_enable_tests pytest
 
-# install the executable into /usr/bin
-# BUG: the read_fasta.py should be installed into python modules
-#   so it can be imported into python
 src_prepare(){
+	# install the executable into /usr/bin
 	sed -i Makefile -e 's#prefix=/usr/local#prefix=/usr#'
 	default
 }
@@ -44,12 +44,25 @@ src_configure(){
 
 # do not run src_compile step as it runs git, makefile2graph, gsed, tred
 
-src_install(){
-	default
-	distutils-r1_src_install
+python_install() {
+	# This is a bit unorthodox, but it allows us to get both a symlink from
+	# /usr/bin to our script using the correct python implementation
+	# *and* to import it from the python shell
+	python_domodule bin/*.py
+	python_domodule bin/tigmint-arcs-tsv
+	python_domodule bin/tigmint-cut
+
+	python_doscript bin/*.py
+	python_doscript bin/tigmint-arcs-tsv
+	python_doscript bin/tigmint-cut
+}
+
+python_install_all() {
+	dobin bin/tigmint
+	dobin bin/tigmint-make
 }
 
 src_test(){
 	default
-	python_foreach_impl python_test
+	distutils-r1_src_test
 }

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

[Martin Mokrejs]

commit:     7b40dd3b9eb83ed33a243cbc61baca5d6c5b3ac1
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Thu Oct 21 08:59:06 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Oct 21 08:59:06 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7b40dd3b

sci-biology/tigmint: add undocumented DEPENDency on zsh

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/tigmint/tigmint-1.2.4-r1.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
index 6900ea7aa..84b582151 100644
--- a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
@@ -24,6 +24,7 @@ RDEPEND="
 	sci-biology/pybedtools[${PYTHON_USEDEP}]
 	sci-biology/pysam[${PYTHON_USEDEP}]
 	app-arch/pigz
+	app-shells/zsh
 	sci-biology/samtools
 	sci-biology/minimap2
 	sci-biology/seqtk

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

[Horea Christian]

commit:     68cf951482f7c6cfc4e238b28f4f4c2dd7844128
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 07:42:22 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 07:42:22 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=68cf9514

sci-biology/tigmint: enable py3.10 and disable py3.8, py3.9

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/tigmint/tigmint-1.2.4-r1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
index 84b582151..c5f630a96 100644
--- a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{10..10} )
 DISTUTILS_USE_SETUPTOOLS=no
 
 inherit distutils-r1