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

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

[Martin Mokrejs]

commit:     f093654801e9bb7ad831c30a592f1da016ed9aca
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 17 12:38:17 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 17 12:38:17 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f0936548

sci-biology/blasr: partial improvements of the ebuild

Package-Manager: Portage-2.3.55, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/blasr/blasr-9999.ebuild | 30 ++++++++++++++++++++++--------
 1 file changed, 22 insertions(+), 8 deletions(-)

diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
index 2b1716bdd..3fe868450 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -16,17 +16,31 @@ SLOT="0"
 IUSE="hdf5"
 KEYWORDS=""
 
-DEPEND="hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
+CDEPEND="
+	dev-util/meson
+	dev-util/ninja
+	dev-util/cmake
+	dev-util/pkgconfig"
+# needs libblasr
+DEPEND="
+	sci-biology/pbbam
+	dev-libs/boost:=[threads]
+	hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
 RDEPEND=""
 
 S="${WORKDIR}/blasr-9999"
 
-src_configure(){
-	if use hdf5; then \
-		python ./configure.py --shared --sub --no-pbbam HDF5_INCLUDE="${EPREFIX}"/usr/include HDF5_LIB="${EPREFIX}"/usr/lib64 || die
-	else
-		python ./configure.py --shared --sub --no-pbbam || die
-	fi
+#src_configure(){
+#	if use hdf5; then \
+#		python ./configure.py --shared --sub --no-pbbam HDF5_INCLUDE="${EPREFIX}"/usr/include HDF5_LIB="${EPREFIX}"/usr/lib64 || die
+#	else
+#		python ./configure.py --shared --sub --no-pbbam || die
+#	fi
+#}
+
+src_compile(){
+	bash scripts/ci/build.sh || die
+	# BUG: meson.build:54:0: ERROR:  Dependency "pbbam" not found, tried pkgconfig and cmake
 }
 
 src_install() {

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

[Horea Christian]

commit:     0be70757d0c75bf2465dfec009bca25a6baf2286
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Feb 17 20:58:28 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Feb 17 20:58:31 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0be70757

sci-biology/blasr: treeclean (missing sources could not find any)

Apparently this project was pulled by upstream and is no longer mentioned on the
HOMEPAGE (which redirects to https://www.pacb.com/support/documentation/ ).
There seems to be a copy on GitHub https://github.com/BioinformaticsArchive/blasr
but it has no releases and it seems severely up to date.

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

 sci-biology/blasr/blasr-5.3.5.ebuild | 24 ------------------------
 sci-biology/blasr/metadata.xml       |  8 --------
 2 files changed, 32 deletions(-)

diff --git a/sci-biology/blasr/blasr-5.3.5.ebuild b/sci-biology/blasr/blasr-5.3.5.ebuild
deleted file mode 100644
index 85e4ea66d..000000000
--- a/sci-biology/blasr/blasr-5.3.5.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit meson
-
-DESCRIPTION="The PacBio long read aligner"
-HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-SRC_URI="https://github.com/PacificBiosciences/blasr/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="blasr"
-SLOT="0"
-KEYWORDS="~amd64"
-
-BDEPEND="
-	dev-util/cmake
-	virtual/pkgconfig
-"
-DEPEND="
-	sci-biology/libblasr
-	dev-libs/boost:=
-"
-RDEPEND="${DEPEND}"

diff --git a/sci-biology/blasr/metadata.xml b/sci-biology/blasr/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/blasr/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<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/blasr/

[Andrew Ammerlaan]

commit:     a2228f613414291c239ed579cd29920ace2aa2e8
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 15:30:46 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 15:30:46 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a2228f61

sci-biology/blasr: fix ObsoleteUri

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/blasr/blasr-5.3.5.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/blasr/blasr-5.3.5.ebuild b/sci-biology/blasr/blasr-5.3.5.ebuild
index 8552bff9e..85e4ea66d 100644
--- a/sci-biology/blasr/blasr-5.3.5.ebuild
+++ b/sci-biology/blasr/blasr-5.3.5.ebuild
@@ -7,7 +7,7 @@ inherit meson
 
 DESCRIPTION="The PacBio long read aligner"
 HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
+SRC_URI="https://github.com/PacificBiosciences/blasr/archive/${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="blasr"
 SLOT="0"

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

[Andrew Ammerlaan]

commit:     ccc86e1e9fe7b3fca58f75d094e1d49edb667e88
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 23 13:32:45 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Jan 23 13:32:45 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ccc86e1e

sci-biology/blasr: bump to 5.3.5

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 .../blasr/{blasr-9999.ebuild => blasr-5.3.5.ebuild}        | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-5.3.5.ebuild
similarity index 53%
rename from sci-biology/blasr/blasr-9999.ebuild
rename to sci-biology/blasr/blasr-5.3.5.ebuild
index cbd012727..8552bff9e 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-5.3.5.ebuild
@@ -1,26 +1,24 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-inherit meson git-r3
+inherit meson
 
 DESCRIPTION="The PacBio long read aligner"
 HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
-#SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
+SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
 
 LICENSE="blasr"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 
 BDEPEND="
 	dev-util/cmake
 	virtual/pkgconfig
 "
 DEPEND="
-	sci-biology/pbbam
 	sci-biology/libblasr
-	dev-libs/boost:=[threads(-)]
+	dev-libs/boost:=
 "
 RDEPEND="${DEPEND}"

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

[Andrew Ammerlaan]

commit:     547cdc94f404ad7bf0f4c700a5aeb48015435f88
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 31 09:35:24 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 31 09:35:24 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=547cdc94

sci-biology/blasr: add MissingUseDepDefault

Package-Manager: Portage-3.0.22, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/blasr/blasr-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
index 6f5d10b16..cbd012727 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -21,6 +21,6 @@ BDEPEND="
 DEPEND="
 	sci-biology/pbbam
 	sci-biology/libblasr
-	dev-libs/boost:=[threads]
+	dev-libs/boost:=[threads(-)]
 "
 RDEPEND="${DEPEND}"

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

[Andrew Ammerlaan]

commit:     f7b9dacac004dc76d69a9b619f77963a5f83ca17
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 13 20:17:55 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 13 20:17:55 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7b9daca

sci-biology/blasr: add dep on libblasr

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

 sci-biology/blasr/blasr-9999.ebuild | 43 +++++++++----------------------------
 1 file changed, 10 insertions(+), 33 deletions(-)

diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
index 3fe868450..6f5d10b16 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -1,49 +1,26 @@
-# 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
+inherit meson git-r3
 
 DESCRIPTION="The PacBio long read aligner"
 HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-#SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
-SRC_URI=""
 EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
+#SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
 
 LICENSE="blasr"
 SLOT="0"
-IUSE="hdf5"
 KEYWORDS=""
 
-CDEPEND="
-	dev-util/meson
-	dev-util/ninja
+BDEPEND="
 	dev-util/cmake
-	dev-util/pkgconfig"
-# needs libblasr
+	virtual/pkgconfig
+"
 DEPEND="
 	sci-biology/pbbam
+	sci-biology/libblasr
 	dev-libs/boost:=[threads]
-	hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
-RDEPEND=""
-
-S="${WORKDIR}/blasr-9999"
-
-#src_configure(){
-#	if use hdf5; then \
-#		python ./configure.py --shared --sub --no-pbbam HDF5_INCLUDE="${EPREFIX}"/usr/include HDF5_LIB="${EPREFIX}"/usr/lib64 || die
-#	else
-#		python ./configure.py --shared --sub --no-pbbam || die
-#	fi
-#}
-
-src_compile(){
-	bash scripts/ci/build.sh || die
-	# BUG: meson.build:54:0: ERROR:  Dependency "pbbam" not found, tried pkgconfig and cmake
-}
-
-src_install() {
-	dodir /usr/bin
-	emake install ASSEMBLY_HOME="${ED}/usr"
-}
+"
+RDEPEND="${DEPEND}"

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

[Martin Mokrejs]

commit:     dcaef9198998b857285e72ea009b7df8d4a1c175
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 15:45:42 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 15:45:42 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dcaef919

sci-biology/blasr: improved ebuild a bit, waiting for bug #586816 now

Package-Manager: portage-2.2.28

 sci-biology/blasr/blasr-9999.ebuild | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
index ca4ff28..e651b6e 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
 EAPI=5
 
-MY_HASH=885c33a
-
 inherit git-r3
 
 DESCRIPTION="The PacBio long read aligner"
@@ -16,13 +14,21 @@ EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
 
 LICENSE="blasr"
 SLOT="0"
-IUSE=""
+IUSE="hdf5"
 KEYWORDS=""
 
-DEPEND="sci-libs/hdf5[cxx]"
+DEPEND="hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
 RDEPEND=""
 
-S="${WORKDIR}/blasr-${MY_HASH}"
+S="${WORKDIR}/blasr-9999"
+
+src_configure(){
+	if use hdf5; then \
+		python ./configure.py --shared --sub --no-pbbam HDF5_INCLUDE="${EPREFIX}"/usr/include HDF5_LIB="${EPREFIX}"/usr/lib64 || die
+	else
+		python ./configure.py --shared --sub --no-pbbam || die
+	fi
+}
 
 src_install() {
 	dodir /usr/bin

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

[Justin Lecher]

commit:     0f86f7079dec64da1b2a0318cac230dd862e1a07
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan  6 18:59:13 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  6 18:59:13 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0f86f707

sci-biology/blasr: Switch from git-2 to git-r3

Package-Manager: portage-2.2.8

---
 sci-biology/blasr/ChangeLog         | 5 ++++-
 sci-biology/blasr/blasr-9999.ebuild | 6 ++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/sci-biology/blasr/ChangeLog b/sci-biology/blasr/ChangeLog
index 7a26c1b..6176561 100644
--- a/sci-biology/blasr/ChangeLog
+++ b/sci-biology/blasr/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/blasr
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> blasr-9999.ebuild:
+  Switch from git-2 to git-r3
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> blasr-9999.ebuild:
   correct license
 

diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
index 9d620ba..634535f 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-9999.ebuild,v 1.1 2011/10/31 21:18:17 weaver Exp $
 
@@ -6,7 +6,7 @@ EAPI=5
 
 MY_HASH=885c33a
 
-inherit git-2
+inherit git-r3
 
 DESCRIPTION="The PacBio long read aligner"
 HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
@@ -24,8 +24,6 @@ RDEPEND=""
 
 S="${WORKDIR}/blasr-${MY_HASH}"
 
-ASSEMBLY_HOME="${D}/usr"
-
 src_install() {
 	dodir /usr/bin
 	emake install ASSEMBLY_HOME="${ED}/usr" || die

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

[Andrey Kislyuk]

commit:     773f59b25f75fd5e9b2492e3bd5c318c520d4866
Author:     Andrey Kislyuk <kislyuk <AT> gmail <DOT> com>
AuthorDate: Thu Mar 22 20:43:46 2012 +0000
Commit:     Andrey Kislyuk <weaver <AT> gentoo <DOT> org>
CommitDate: Thu Mar 22 20:43:46 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=773f59b2

New package, ebuild written by me

---
 sci-biology/blasr/ChangeLog         |   10 ++++++++++
 sci-biology/blasr/blasr-9999.ebuild |   33 +++++++++++++++++++++++++++++++++
 sci-biology/blasr/metadata.xml      |    9 +++++++++
 3 files changed, 52 insertions(+), 0 deletions(-)

diff --git a/sci-biology/blasr/ChangeLog b/sci-biology/blasr/ChangeLog
new file mode 100644
index 0000000..f10ba22
--- /dev/null
+++ b/sci-biology/blasr/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/blasr
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*blasr-9999 (22 Mar 2012)
+
+  22 Mar 2012; Andrey Kislyuk <weaver@gentoo.org> +blasr-9999.ebuild,
+  +metadata.xml:
+  New package, ebuild written by me
+

diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
new file mode 100644
index 0000000..94e874f
--- /dev/null
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-9999.ebuild,v 1.1 2011/10/31 21:18:17 weaver Exp $
+
+EAPI=4
+
+MY_HASH=885c33a
+
+EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
+
+inherit git
+
+DESCRIPTION="The PacBio long read aligner"
+HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
+#SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
+SRC_URI=""
+
+LICENSE="as-is"
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+DEPEND="sci-libs/hdf5[cxx]"
+RDEPEND=""
+
+S="${WORKDIR}/blasr-${MY_HASH}"
+
+ASSEMBLY_HOME="${D}/usr"
+
+src_install() {
+	dodir /usr/bin
+	make install ASSEMBLY_HOME="${D}/usr" || die
+}

diff --git a/sci-biology/blasr/metadata.xml b/sci-biology/blasr/metadata.xml
new file mode 100644
index 0000000..3302123
--- /dev/null
+++ b/sci-biology/blasr/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>