* [gentoo-commits] proj/sci:master commit in: sci-biology/pbbam/
@ 2019-01-17 12:24 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2019-01-17 12:24 UTC (permalink / raw
To: gentoo-commits
commit: a9b6ba591d4477409c689f8612051d5be85364fa
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 17 12:23:55 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 17 12:23:55 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a9b6ba59
sci-biology/pbbam: new package needed by sci-biology/blasr
Builds and install for me, make cmake/clang deps could be
improved.
https://github.com/PacificBiosciences/pbbam/issues/25
Package-Manager: Portage-2.3.55, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/pbbam/metadata.xml | 12 +++++++++
sci-biology/pbbam/pbbam-9999.ebuild | 49 +++++++++++++++++++++++++++++++++++++
2 files changed, 61 insertions(+)
diff --git a/sci-biology/pbbam/metadata.xml b/sci-biology/pbbam/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/pbbam/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/pbbam/pbbam-9999.ebuild b/sci-biology/pbbam/pbbam-9999.ebuild
new file mode 100644
index 000000000..5593b4072
--- /dev/null
+++ b/sci-biology/pbbam/pbbam-9999.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit git-r3 multilib
+
+DESCRIPTION="PacBio modified BAM file format"
+HOMEPAGE="https://pbbam.readthedocs.io/en/latest/index.html"
+EGIT_REPO_URI="https://github.com/PacificBiosciences/pbbam.git"
+
+LICENSE="blasr"
+SLOT="0"
+IUSE="hdf5 doc"
+KEYWORDS=""
+# https://github.com/PacificBiosciences/pbbam/issues/25
+
+CDEPEND="
+ dev-util/meson
+ dev-util/ninja
+ dev-util/pkgconfig
+ >=dev-cpp/gtest-1.8.1
+ >=dev-lang/swig-3.0.5
+ doc? ( app-doc/doxygen )"
+DEPEND="
+ >=sci-libs/htslib-1.3.1:=
+ >=dev-libs/boost-1.55:=[threads]
+ hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
+RDEPEND=""
+
+#S="${WORKDIR}/${PN}"
+
+src_compile(){
+ mkdir -p build || die
+ cd build || die
+ meson --prefix "${ED}/usr" || die
+ ninja || die
+ use doc && ( ninja doc )
+}
+
+src_install() {
+ cd build || die
+ ninja install || die
+ #dobin bin/*
+ #insinto /usr/include
+ #doins include/*
+ #insinto /usr/$(get_libdir)/${P}
+ #doins lib/*
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pbbam/
@ 2021-01-10 13:37 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-01-10 13:37 UTC (permalink / raw
To: gentoo-commits
commit: c9b9e54c8a322ac7d623f844c7edab0f3187965e
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 13:37:38 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 13:37:38 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c9b9e54c
sci-biology/pbbam: add 1.6.0 version
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/pbbam/pbbam-1.6.0.ebuild | 26 +++++++++++++++++++++++
sci-biology/pbbam/pbbam-9999.ebuild | 41 ++++++++----------------------------
2 files changed, 35 insertions(+), 32 deletions(-)
diff --git a/sci-biology/pbbam/pbbam-1.6.0.ebuild b/sci-biology/pbbam/pbbam-1.6.0.ebuild
new file mode 100644
index 000000000..98f0089e3
--- /dev/null
+++ b/sci-biology/pbbam/pbbam-1.6.0.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit meson
+
+DESCRIPTION="PacBio modified BAM file format"
+HOMEPAGE="https://pbbam.readthedocs.io/en/latest/index.html"
+SRC_URI="https://github.com/PacificBiosciences/pbbam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="blasr"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+BDEPEND="
+ virtual/pkgconfig
+ >=dev-cpp/gtest-1.8.1
+ >=dev-lang/swig-3.0.5
+"
+DEPEND="
+ sci-biology/pbcopper
+ >=sci-libs/htslib-1.3.1:=
+ >=dev-libs/boost-1.55:=[threads]
+"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/pbbam/pbbam-9999.ebuild b/sci-biology/pbbam/pbbam-9999.ebuild
index 5593b4072..1f03ab1a9 100644
--- a/sci-biology/pbbam/pbbam-9999.ebuild
+++ b/sci-biology/pbbam/pbbam-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-inherit git-r3 multilib
+inherit git-r3 meson
DESCRIPTION="PacBio modified BAM file format"
HOMEPAGE="https://pbbam.readthedocs.io/en/latest/index.html"
@@ -11,39 +11,16 @@ EGIT_REPO_URI="https://github.com/PacificBiosciences/pbbam.git"
LICENSE="blasr"
SLOT="0"
-IUSE="hdf5 doc"
KEYWORDS=""
-# https://github.com/PacificBiosciences/pbbam/issues/25
-CDEPEND="
- dev-util/meson
- dev-util/ninja
- dev-util/pkgconfig
+BDEPEND="
+ virtual/pkgconfig
>=dev-cpp/gtest-1.8.1
>=dev-lang/swig-3.0.5
- doc? ( app-doc/doxygen )"
+"
DEPEND="
+ sci-biology/pbcopper
>=sci-libs/htslib-1.3.1:=
>=dev-libs/boost-1.55:=[threads]
- hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
-RDEPEND=""
-
-#S="${WORKDIR}/${PN}"
-
-src_compile(){
- mkdir -p build || die
- cd build || die
- meson --prefix "${ED}/usr" || die
- ninja || die
- use doc && ( ninja doc )
-}
-
-src_install() {
- cd build || die
- ninja install || die
- #dobin bin/*
- #insinto /usr/include
- #doins include/*
- #insinto /usr/$(get_libdir)/${P}
- #doins lib/*
-}
+"
+RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pbbam/
@ 2022-01-15 14:14 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2022-01-15 14:14 UTC (permalink / raw
To: gentoo-commits
commit: 451387c7b33bf9d4d62a8eef7c8817031689a7a0
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 14:13:38 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 14:13:38 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=451387c7
sci-biology/pbbam: drop unavailable flag
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/pbbam/pbbam-1.6.0.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/pbbam/pbbam-1.6.0.ebuild b/sci-biology/pbbam/pbbam-1.6.0.ebuild
index 98f0089e3..076b04e81 100644
--- a/sci-biology/pbbam/pbbam-1.6.0.ebuild
+++ b/sci-biology/pbbam/pbbam-1.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -21,6 +21,6 @@ BDEPEND="
DEPEND="
sci-biology/pbcopper
>=sci-libs/htslib-1.3.1:=
- >=dev-libs/boost-1.55:=[threads]
+ >=dev-libs/boost-1.55:=
"
RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pbbam/
@ 2022-01-23 13:32 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2022-01-23 13:32 UTC (permalink / raw
To: gentoo-commits
commit: 9432356c9debf8c1815b663d7149af04682990c5
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 23 13:14:44 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Jan 23 13:14:44 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9432356c
sci-biology/pbbam: drop live
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/pbbam/pbbam-9999.ebuild | 26 --------------------------
1 file changed, 26 deletions(-)
diff --git a/sci-biology/pbbam/pbbam-9999.ebuild b/sci-biology/pbbam/pbbam-9999.ebuild
deleted file mode 100644
index 1f03ab1a9..000000000
--- a/sci-biology/pbbam/pbbam-9999.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit git-r3 meson
-
-DESCRIPTION="PacBio modified BAM file format"
-HOMEPAGE="https://pbbam.readthedocs.io/en/latest/index.html"
-EGIT_REPO_URI="https://github.com/PacificBiosciences/pbbam.git"
-
-LICENSE="blasr"
-SLOT="0"
-KEYWORDS=""
-
-BDEPEND="
- virtual/pkgconfig
- >=dev-cpp/gtest-1.8.1
- >=dev-lang/swig-3.0.5
-"
-DEPEND="
- sci-biology/pbcopper
- >=sci-libs/htslib-1.3.1:=
- >=dev-libs/boost-1.55:=[threads]
-"
-RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pbbam/
@ 2022-01-23 13:32 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2022-01-23 13:32 UTC (permalink / raw
To: gentoo-commits
commit: 96a3248a3de53830040c8195b89bbf53db49adb2
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 23 13:25:54 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Jan 23 13:25:54 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=96a3248a
sci-biology/pbbam: bump to 1.8.1
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/pbbam/{pbbam-1.6.0.ebuild => pbbam-1.8.1.ebuild} | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/pbbam/pbbam-1.6.0.ebuild b/sci-biology/pbbam/pbbam-1.8.1.ebuild
similarity index 94%
rename from sci-biology/pbbam/pbbam-1.6.0.ebuild
rename to sci-biology/pbbam/pbbam-1.8.1.ebuild
index 076b04e81..a114da0fc 100644
--- a/sci-biology/pbbam/pbbam-1.6.0.ebuild
+++ b/sci-biology/pbbam/pbbam-1.8.1.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit meson
@@ -20,6 +20,7 @@ BDEPEND="
"
DEPEND="
sci-biology/pbcopper
+ sci-biology/samtools:0
>=sci-libs/htslib-1.3.1:=
>=dev-libs/boost-1.55:=
"
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pbbam/
@ 2023-04-21 5:55 Horea Christian
0 siblings, 0 replies; 7+ messages in thread
From: Horea Christian @ 2023-04-21 5:55 UTC (permalink / raw
To: gentoo-commits
commit: 843df392d47604eb0b95ae7c9670c58ad52ecce8
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Apr 21 05:55:20 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Apr 21 05:55:20 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=843df392
sci-biology/pbbam: add 2.1.0, drop 1.8.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/pbbam/{pbbam-1.8.1.ebuild => pbbam-2.1.0.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/pbbam/pbbam-1.8.1.ebuild b/sci-biology/pbbam/pbbam-2.1.0.ebuild
similarity index 100%
rename from sci-biology/pbbam/pbbam-1.8.1.ebuild
rename to sci-biology/pbbam/pbbam-2.1.0.ebuild
^ permalink raw reply [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pbbam/
@ 2023-04-21 5:55 Horea Christian
0 siblings, 0 replies; 7+ messages in thread
From: Horea Christian @ 2023-04-21 5:55 UTC (permalink / raw
To: gentoo-commits
commit: 7a2bf5e471ab0340b8dcf2fc0350d7e3f7773168
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Apr 21 05:55:41 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Apr 21 05:55:41 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7a2bf5e4
sci-biology/pbbam: add github upstream metadata
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/pbbam/metadata.xml | 3 +++
1 file changed, 3 insertions(+)
diff --git a/sci-biology/pbbam/metadata.xml b/sci-biology/pbbam/metadata.xml
index 138cb7705..e12f3579e 100644
--- a/sci-biology/pbbam/metadata.xml
+++ b/sci-biology/pbbam/metadata.xml
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">PacificBiosciences/pbbam</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 7+ messages in thread
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