[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/
commit: 17688a432b33d4ce2ecb5fe1cbc25e7e36efe288
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 02:05:41 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 02:05:41 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=17688a43
sci-biology/deeptools: dropped ~x86, added PEP517
Signed-off-by: Horea Christian chymera.eu>
sci-biology/deeptools/deeptools-3.5.0.ebuild | 5 +++--
sci-biology/deeptools/deeptools-3.5.1.ebuild | 5 +++--
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild
b/sci-biology/deeptools/deeptools-3.5.0.ebuild
index a76bf6690..7c2eaa739 100644
--- a/sci-biology/deeptools/deeptools-3.5.0.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild
@@ -3,7 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -13,7 +14,7 @@
SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# TODO: fix this
RESTRICT="test"
diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild
b/sci-biology/deeptools/deeptools-3.5.1.ebuild
index a76bf6690..7c2eaa739 100644
--- a/sci-biology/deeptools/deeptools-3.5.1.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild
@@ -3,7 +3,8 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..10} )
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
@@ -13,7 +14,7 @@
SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# TODO: fix this
RESTRICT="test"
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools-intervals/
commit: 28e13faae5552df828a4a1bfba3781c4052f7266 Author: Horea Christian chymera eu> AuthorDate: Mon Mar 6 04:23:44 2023 + Commit: Horea Christian gmail com> CommitDate: Mon Mar 6 04:23:44 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=28e13faa sci-biology/deeptools-intervals: update upstream metadata Signed-off-by: Horea Christian chymera.eu> sci-biology/deeptools-intervals/metadata.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/deeptools-intervals/metadata.xml b/sci-biology/deeptools-intervals/metadata.xml index 08881e6e4..853bd539c 100644 --- a/sci-biology/deeptools-intervals/metadata.xml +++ b/sci-biology/deeptools-intervals/metadata.xml @@ -6,6 +6,6 @@ Gentoo Biology Project - fidelram/deepTools_intervals + deeptools/deeptools_intervals
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/, sci-biology/ruffus/
commit: d48974481a1dda0471421ee005826b8be5457d2f
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 16 07:42:48 2023 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 16 07:42:48 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d4897448
sci-biology/*: updated doc package name
Signed-off-by: Horea Christian chymera.eu>
sci-biology/deeptools/deeptools-3.5.0.ebuild | 2 +-
sci-biology/deeptools/deeptools-3.5.1.ebuild | 2 +-
sci-biology/ruffus/ruffus-2.8.4.ebuild | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild
b/sci-biology/deeptools/deeptools-3.5.0.ebuild
index fc48e2224..a76bf6690 100644
--- a/sci-biology/deeptools/deeptools-3.5.0.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild
@@ -32,5 +32,5 @@ RDEPEND="
S="${WORKDIR}/deepTools-${PV}"
-distutils_enable_sphinx docs dev-python/sphinx_rtd_theme
dev-python/sphinx-argparse
+distutils_enable_sphinx docs dev-python/sphinx-rtd-theme
dev-python/sphinx-argparse
#distutils_enable_tests nose
diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild
b/sci-biology/deeptools/deeptools-3.5.1.ebuild
index fc48e2224..a76bf6690 100644
--- a/sci-biology/deeptools/deeptools-3.5.1.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild
@@ -32,5 +32,5 @@ RDEPEND="
S="${WORKDIR}/deepTools-${PV}"
-distutils_enable_sphinx docs dev-python/sphinx_rtd_theme
dev-python/sphinx-argparse
+distutils_enable_sphinx docs dev-python/sphinx-rtd-theme
dev-python/sphinx-argparse
#distutils_enable_tests nose
diff --git a/sci-biology/ruffus/ruffus-2.8.4.ebuild
b/sci-biology/ruffus/ruffus-2.8.4.ebuild
index beda7db9a..28a03c4e6 100644
--- a/sci-biology/ruffus/ruffus-2.8.4.ebuild
+++ b/sci-biology/ruffus/ruffus-2.8.4.ebuild
@@ -22,5 +22,5 @@ RDEPEND="
media-gfx/graphviz
"
-distutils_enable_sphinx doc dev-python/sphinx_rtd_theme
+distutils_enable_sphinx doc dev-python/sphinx-rtd-theme
distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/
commit: e77cdd7196f6fe5a0c488260fd37a76bd9ea7f8c
Author: Horea Christian chymera eu>
AuthorDate: Fri Jan 13 08:53:46 2023 +
Commit: Horea Christian gmail com>
CommitDate: Fri Jan 13 08:53:46 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e77cdd71
sci-biology/deeptools: deprecating tests
Signed-off-by: Horea Christian chymera.eu>
sci-biology/deeptools/deeptools-3.5.0.ebuild | 2 +-
sci-biology/deeptools/deeptools-3.5.1.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild
b/sci-biology/deeptools/deeptools-3.5.0.ebuild
index 5dbf6dc55..fc48e2224 100644
--- a/sci-biology/deeptools/deeptools-3.5.0.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild
@@ -33,4 +33,4 @@ RDEPEND="
S="${WORKDIR}/deepTools-${PV}"
distutils_enable_sphinx docs dev-python/sphinx_rtd_theme
dev-python/sphinx-argparse
-distutils_enable_tests nose
+#distutils_enable_tests nose
diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild
b/sci-biology/deeptools/deeptools-3.5.1.ebuild
index 5dbf6dc55..fc48e2224 100644
--- a/sci-biology/deeptools/deeptools-3.5.1.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild
@@ -33,4 +33,4 @@ RDEPEND="
S="${WORKDIR}/deepTools-${PV}"
distutils_enable_sphinx docs dev-python/sphinx_rtd_theme
dev-python/sphinx-argparse
-distutils_enable_tests nose
+#distutils_enable_tests nose
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/
commit: 701845a53aaac429eca917f44a0de89e5a7b4024
Author: Horea Christian chymera eu>
AuthorDate: Fri Jan 13 08:53:00 2023 +
Commit: Horea Christian gmail com>
CommitDate: Fri Jan 13 08:53:00 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=701845a5
sci-biology/deeptools: add 3.5.1
Signed-off-by: Horea Christian chymera.eu>
sci-biology/deeptools/deeptools-3.5.1.ebuild | 36
1 file changed, 36 insertions(+)
diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild
b/sci-biology/deeptools/deeptools-3.5.1.ebuild
new file mode 100644
index 0..5dbf6dc55
--- /dev/null
+++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
+HOMEPAGE="https://github.com/deeptools/deepTools;
+SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz ->
${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# TODO: fix this
+RESTRICT="test"
+
+RDEPEND="
+ >=sci-biology/deeptools-intervals-0.1.8[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.9.0[${PYTHON_USEDEP}]
+ >=dev-python/numpydoc-0.5[${PYTHON_USEDEP}]
+ >=dev-python/scipy-0.17.0[${PYTHON_USEDEP}]
+ dev-python/plotly[${PYTHON_USEDEP}]
+ >=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}]
+ >=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}]
+ >=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-3.1.0[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/deepTools-${PV}"
+
+distutils_enable_sphinx docs dev-python/sphinx_rtd_theme
dev-python/sphinx-argparse
+distutils_enable_tests nose
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/
commit: 7d409d7497bc831fda6854cb3b511986001e3d86
Author: Horea Christian chymera eu>
AuthorDate: Fri Jan 13 08:50:33 2023 +
Commit: Horea Christian gmail com>
CommitDate: Fri Jan 13 08:50:33 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d409d74
sci-biology/deeptools: update EAPI 7 -> 8
Signed-off-by: Horea Christian chymera.eu>
sci-biology/deeptools/deeptools-3.5.0.ebuild | 8
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild
b/sci-biology/deeptools/deeptools-3.5.0.ebuild
index f53a19bcb..5dbf6dc55 100644
--- a/sci-biology/deeptools/deeptools-3.5.0.ebuild
+++ b/sci-biology/deeptools/deeptools-3.5.0.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=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..10} )
inherit distutils-r1
@@ -23,7 +23,7 @@ RDEPEND="
>=dev-python/numpy-1.9.0[${PYTHON_USEDEP}]
>=dev-python/numpydoc-0.5[${PYTHON_USEDEP}]
>=dev-python/scipy-0.17.0[${PYTHON_USEDEP}]
- >=dev-python/plotly-2.0.0[${PYTHON_USEDEP}]
+ dev-python/plotly[${PYTHON_USEDEP}]
>=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}]
>=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}]
>=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools-intervals/
commit: 1a6a11935660571034093947f1f2a7aa979f34ef
Author: Horea Christian chymera eu>
AuthorDate: Fri Jan 13 07:55:29 2023 +
Commit: Horea Christian gmail com>
CommitDate: Fri Jan 13 07:55:29 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a6a1193
sci-biology/deeptools-intervals: update EAPI 7 -> 8
Signed-off-by: Horea Christian chymera.eu>
sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
index 1eecdd1b9..38f9aea0f 100644
--- a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
+++ b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.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=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/
commit: 76926ef29fca81c7d72833654c27f9dccc09358c
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Jan 2 13:35:22 2021 +
Commit: Horea Christian gmail com>
CommitDate: Sun Jan 3 06:25:30 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=76926ef2
sci-biology/deeptools: version bump, bump py targets, enable sphinx
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
Signed-off-by: Horea Christian chymera.eu>
sci-biology/deeptools/deeptools-2.5.0.ebuild | 30 ---
sci-biology/deeptools/deeptools-3.5.0.ebuild | 36
sci-biology/deeptools/deeptools-.ebuild | 29 --
3 files changed, 36 insertions(+), 59 deletions(-)
diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild
b/sci-biology/deeptools/deeptools-2.5.0.ebuild
deleted file mode 100644
index e57fe3313..0
--- a/sci-biology/deeptools/deeptools-2.5.0.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-[[ "$PV" == "" ]] && inherit git-r3
-
-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
-HOMEPAGE="https://github.com/fidelram/deepTools;
-if [[ "$PV" == "" ]]; then
- EGIT_REPO_URI="https://github.com/fidelram/deepTools;
-else
- SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz ->
${P}.tar.gz"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND=">=dev-python/numpy-1.8.0
- >=dev-python/scipy-0.17.0
- >=dev-python/py2bit-0.1.0
- >=dev-python/pyBigWig-0.2.1
- >=sci-biology/pysam-0.8
- >=dev-python/matplotlib-1.4.0"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild
b/sci-biology/deeptools/deeptools-3.5.0.ebuild
new file mode 100644
index 0..f53a19bcb
--- /dev/null
+++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
+HOMEPAGE="https://github.com/deeptools/deepTools;
+SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz ->
${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# TODO: fix this
+RESTRICT="test"
+
+RDEPEND="
+ >=sci-biology/deeptools-intervals-0.1.8[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.9.0[${PYTHON_USEDEP}]
+ >=dev-python/numpydoc-0.5[${PYTHON_USEDEP}]
+ >=dev-python/scipy-0.17.0[${PYTHON_USEDEP}]
+ >=dev-python/plotly-2.0.0[${PYTHON_USEDEP}]
+ >=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}]
+ >=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}]
+ >=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-3.1.0[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/deepTools-${PV}"
+
+distutils_enable_sphinx docs dev-python/sphinx_rtd_theme
dev-python/sphinx-argparse
+distutils_enable_tests nose
diff --git a/sci-biology/deeptools/deeptools-.ebuild
b/sci-biology/deeptools/deeptools-.ebuild
deleted file mode 100644
index 89a8bf763..0
--- a/sci-biology/deeptools/deeptools-.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-[[ "$PV" == "" ]] && inherit git-r3
-
-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
-HOMEPAGE="https://github.com/fidelram/deepTools;
-if [[ "$PV" == "" ]]; then
- EGIT_REPO_URI="https://github.com/fidelram/deepTools;
-else
- SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz ->
${P}.tar.gz"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-
-DEPEND=">=dev-python/numpy-1.8.0
- >=dev-python/scipy-0.17.0
- >=dev-python/py2bit-0.1.0
- >=dev-python/pyBigWig-0.2.1
- >=sci-biology/pysam-0.8
- >=dev-python/matplotlib-1.4.0"
-RDEPEND="${DEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools-intervals/
commit: e4dbbb39070f7a427379fbbc8bcab4bb24394df9
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Jan 2 13:22:41 2021 +
Commit: Horea Christian gmail com>
CommitDate: Sun Jan 3 06:25:30 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e4dbbb39
sci-biology/deeptools-intervals: new dep
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
Signed-off-by: Horea Christian chymera.eu>
.../deeptools-intervals-0.1.9.ebuild | 18 ++
sci-biology/deeptools-intervals/metadata.xml | 11 +++
2 files changed, 29 insertions(+)
diff --git a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
new file mode 100644
index 0..1eecdd1b9
--- /dev/null
+++ b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Constructing interval trees with associated exon/annotation
information"
+HOMEPAGE="https://github.com/deeptools/deeptools_intervals;
+SRC_URI="https://github.com/deeptools/deeptools_intervals/archive/${PV}.tar.gz
-> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${PN//-/_}-${PV}"
diff --git a/sci-biology/deeptools-intervals/metadata.xml
b/sci-biology/deeptools-intervals/metadata.xml
new file mode 100644
index 0..08881e6e4
--- /dev/null
+++ b/sci-biology/deeptools-intervals/metadata.xml
@@ -0,0 +1,11 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
+ fidelram/deepTools_intervals
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/
commit: 021ac334c980bba7a50590d2dd6c7345a3c67e39
Author: Horea Christian chymera eu>
AuthorDate: Sun Sep 13 21:10:22 2020 +
Commit: Horea Christian gmail com>
CommitDate: Sun Sep 13 21:10:22 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=021ac334
sci-biology/deeptools: QA fix: KEYWORDS and conditional definition
Package-Manager: Portage-3.0.6, Repoman-3.0.1
Signed-off-by: Horea Christian chymera.eu>
sci-biology/deeptools/deeptools-2.5.0.ebuild | 8 +++-
sci-biology/deeptools/deeptools-.ebuild | 7 ++-
2 files changed, 5 insertions(+), 10 deletions(-)
diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild
b/sci-biology/deeptools/deeptools-2.5.0.ebuild
index a0d1d47cd..eb9d530dd 100644
--- a/sci-biology/deeptools/deeptools-2.5.0.ebuild
+++ b/sci-biology/deeptools/deeptools-2.5.0.ebuild
@@ -7,21 +7,19 @@ PYTHON_COMPAT=( python2_7 python3_5 )
inherit distutils-r1
-[ "$PV" == "" ] && inherit git-2
+[[ "$PV" == "" ]] && inherit git-r3
DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
HOMEPAGE="https://github.com/fidelram/deepTools;
-if [ "$PV" == "" ]; then
+if [[ "$PV" == "" ]]; then
EGIT_REPO_URI="https://github.com/fidelram/deepTools;
- KEYWORDS=""
else
SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz ->
${P}.tar.gz"
- KEYWORDS="~amd64"
fi
LICENSE="GPL-3"
SLOT="0"
-IUSE=""
+KEYWORDS="~amd64"
DEPEND=">=dev-python/numpy-1.8.0
>=sci-libs/scipy-0.17.0
diff --git a/sci-biology/deeptools/deeptools-.ebuild
b/sci-biology/deeptools/deeptools-.ebuild
index 3e73bdec5..7c3896433 100644
--- a/sci-biology/deeptools/deeptools-.ebuild
+++ b/sci-biology/deeptools/deeptools-.ebuild
@@ -7,21 +7,18 @@ PYTHON_COMPAT=( python2_7 python3_5 )
inherit distutils-r1
-[ "$PV" == "" ] && inherit git-r3
+[[ "$PV" == "" ]] && inherit git-r3
DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
HOMEPAGE="https://github.com/fidelram/deepTools;
-if [ "$PV" == "" ]; then
+if [[ "$PV" == "" ]]; then
EGIT_REPO_URI="https://github.com/fidelram/deepTools;
- KEYWORDS=""
else
SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz ->
${P}.tar.gz"
- KEYWORDS="~amd64"
fi
LICENSE="GPL-3"
SLOT="0"
-IUSE=""
DEPEND=">=dev-python/numpy-1.8.0
>=sci-libs/scipy-0.17.0
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/
commit: 7427cd98637c28d8ca30cc61094c980034113dfb Author: Horea Christian chymera eu> AuthorDate: Sun Sep 13 20:39:57 2020 + Commit: Horea Christian gmail com> CommitDate: Sun Sep 13 20:39:57 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7427cd98 sci-biology/deeptools: QA fix: EAPI 7, git-r3 eclass, copyright bump Package-Manager: Portage-3.0.6, Repoman-3.0.1 Signed-off-by: Horea Christian chymera.eu> sci-biology/deeptools/deeptools-2.5.0.ebuild | 4 ++-- sci-biology/deeptools/deeptools-.ebuild | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild b/sci-biology/deeptools/deeptools-2.5.0.ebuild index e69672942..a0d1d47cd 100644 --- a/sci-biology/deeptools/deeptools-2.5.0.ebuild +++ b/sci-biology/deeptools/deeptools-2.5.0.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 PYTHON_COMPAT=( python2_7 python3_5 ) diff --git a/sci-biology/deeptools/deeptools-.ebuild b/sci-biology/deeptools/deeptools-.ebuild index a2c1fcfb9..3e73bdec5 100644 --- a/sci-biology/deeptools/deeptools-.ebuild +++ b/sci-biology/deeptools/deeptools-.ebuild @@ -1,13 +1,13 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 PYTHON_COMPAT=( python2_7 python3_5 ) inherit distutils-r1 -[ "$PV" == "" ] && inherit git-2 +[ "$PV" == "" ] && inherit git-r3 DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig" HOMEPAGE="https://github.com/fidelram/deepTools;
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/
commit: b0176e52f19303e32d2797d6b41273a70dfb2b2c
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Mar 31 21:10:09 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Mar 31 21:10:09 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b0176e52
sci-biology/deeptools: add new package
Package-Manager: Portage-2.3.5, Repoman-2.3.1
sci-biology/deeptools/deeptools-2.5.0.ebuild | 32
sci-biology/deeptools/deeptools-.ebuild | 32
sci-biology/deeptools/metadata.xml | 12 +++
3 files changed, 76 insertions(+)
diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild
b/sci-biology/deeptools/deeptools-2.5.0.ebuild
new file mode 100644
index 0..e69672942
--- /dev/null
+++ b/sci-biology/deeptools/deeptools-2.5.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_5 )
+
+inherit distutils-r1
+
+[ "$PV" == "" ] && inherit git-2
+
+DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
+HOMEPAGE="https://github.com/fidelram/deepTools;
+if [ "$PV" == "" ]; then
+ EGIT_REPO_URI="https://github.com/fidelram/deepTools;
+ KEYWORDS=""
+else
+ SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz ->
${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=">=dev-python/numpy-1.8.0
+ >=sci-libs/scipy-0.17.0
+ >=dev-python/py2bit-0.1.0
+ >=dev-python/pyBigWig-0.2.1
+ >=sci-biology/pysam-0.8
+ >=dev-python/matplotlib-1.4.0"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/deeptools/deeptools-.ebuild
b/sci-biology/deeptools/deeptools-.ebuild
new file mode 100644
index 0..a2c1fcfb9
--- /dev/null
+++ b/sci-biology/deeptools/deeptools-.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_5 )
+
+inherit distutils-r1
+
+[ "$PV" == "" ] && inherit git-2
+
+DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
+HOMEPAGE="https://github.com/fidelram/deepTools;
+if [ "$PV" == "" ]; then
+ EGIT_REPO_URI="https://github.com/fidelram/deepTools;
+ KEYWORDS=""
+else
+ SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz ->
${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=">=dev-python/numpy-1.8.0
+ >=sci-libs/scipy-0.17.0
+ >=dev-python/py2bit-0.1.0
+ >=dev-python/pyBigWig-0.2.1
+ >=sci-biology/pysam-0.8
+ >=dev-python/matplotlib-1.4.0"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/deeptools/metadata.xml
b/sci-biology/deeptools/metadata.xml
new file mode 100644
index 0..f68a1b6fa
--- /dev/null
+++ b/sci-biology/deeptools/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/deeptools/, dev-python/pyBigWig/, sci-biology/plinkseq/, ...
commit: 4647f40e12c546cd0b18b1966acd944fc8a21641
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Mar 31 21:00:05 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Mar 31 21:00:05 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4647f40e
Revert "sci-biology/deeptools: add a new package"
This reverts commit 81a1355ea065924e0c6426772af7c16d90432ccd.
dev-python/pyBigWig/metadata.xml | 12
dev-python/pyBigWig/pyBigWig-0.3.4.ebuild| 16 -
dev-python/pyBigWig/pyBigWig-.ebuild | 18 --
sci-biology/deeptools/deeptools-2.5.0.ebuild | 33 --
sci-biology/deeptools/deeptools-.ebuild | 34 --
sci-biology/deeptools/metadata.xml | 12
sci-biology/mira/mira-4.9.6.ebuild | 93
sci-biology/plinkseq/plinkseq-.ebuild| 13 ++--
8 files changed, 5 insertions(+), 226 deletions(-)
diff --git a/dev-python/pyBigWig/metadata.xml b/dev-python/pyBigWig/metadata.xml
deleted file mode 100644
index f68a1b6fa..0
--- a/dev-python/pyBigWig/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
-mmokr...@fold.natur.cuni.cz
-Martin Mokrejs
-
-
-sci-biol...@gentoo.org
-Gentoo Biology Project
-
-
diff --git a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
b/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
deleted file mode 100644
index 33664c388..0
--- a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Python extension written in C for quick access to and creation of
bigWig files"
-HOMEPAGE="https://github.com/dpryan79/pyBigWig;
-SRC_URI="https://github.com/dpryan79/pyBigWig/archive/0.3.4.tar.gz ->
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-biology/libBigWig"
-RDEPEND="${DEPEND}"
diff --git a/dev-python/pyBigWig/pyBigWig-.ebuild
b/dev-python/pyBigWig/pyBigWig-.ebuild
deleted file mode 100644
index 0e2cd40c8..0
--- a/dev-python/pyBigWig/pyBigWig-.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3
-
-DESCRIPTION="Python extension written in C for quick access to and creation of
bigWig files"
-HOMEPAGE="https://github.com/dpryan79/pyBigWig;
-EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig.git;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sci-biology/libBigWig"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild
b/sci-biology/deeptools/deeptools-2.5.0.ebuild
deleted file mode 100644
index 6f9a41d54..0
--- a/sci-biology/deeptools/deeptools-2.5.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-[ "$PV" == "" ] && inherit git-2
-
-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
-HOMEPAGE="https://github.com/fidelram/deepTools;
-if [ "$PV" == "" ]; then
- EGIT_REPO_URI="https://github.com/fidelram/deepTools;
- KEYWORDS=""
-else
- SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz ->
${P}.tar.gz"
- KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND=">=dev-python/numpy-1.8.0
- >=sci-libs/scipy-0.17.0
- >=dev-python/py2bit-0.1.0
- >=dev-python/pyBigWig-0.2.1
- >=sci-biology/pysam-0.8
- >=dev-python/matplotlib-1.4.0"
-RDEPEND="${DEPEND}"
-
diff --git a/sci-biology/deeptools/deeptools-.ebuild
b/sci-biology/deeptools/deeptools-.ebuild
deleted file mode 100644
index 4d6d2fa77..0
--- a/sci-biology/deeptools/deeptools-.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-[ "$PV" == "" ] && inherit git-2
-
-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert
BAM to bigWig"
-HOMEPAGE="https://github.com/fidelram/deepTools;
-if [ "$PV" == "" ]; then
- EGIT_REPO_URI="https://github.com/fidelram/deepTools;
- KEYWORDS=""
-else
- SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz ->
${P}.tar.gz"
- KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND=">=dev-python/numpy-1.8.0
- >=sci-libs/scipy-0.17.0
- >=dev-python/py2bit-0.1.0
- >=dev-python/pyBigWig-0.2.1
- >=sci-biology/pysam-0.8
-
