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

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

[Martin Mokrejs]

commit:     a788b3a56fa7e60683c10ae8c8e73490d1575e0f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 20:52:30 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 20:52:30 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a788b3a5

sci-biology/MaSuRCA: new package but with a missing LICENSE and needs tweak to get all configure's running

---
 sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild | 63 ++++++++++++++++++++++++++++++++
 sci-biology/MaSuRCA/metadata.xml         |  9 +++++
 2 files changed, 72 insertions(+)

diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
new file mode 100644
index 0000000..28934c3
--- /dev/null
+++ b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Assembler to combine Sanger, Roche 454 and Illumina Solexa reads"
+HOMEPAGE="http://www.genome.umd.edu/masurca.html"
+SRC_URI="ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-"${PV}".tar.gz
+		ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/perl
+		app-arch/bzip2"
+RDEPEND="${DEPEND}"
+
+# the ebuild mimics "${S}"/install.sh
+src_configure(){
+	cd jellyfish-1.1.11 || die
+	econf
+
+	cd ../jellyfish-2.0.0rc1 || die
+	econf --program-suffix=-2.0
+
+	cd ../CA/kmer || die
+	sh ./configure.sh
+	econf
+
+	cd ../../SuperReads-0.3.2 || die
+	econf
+
+	cd ../quorum-0.3.2 || die
+	econf --enable-relative-paths --with-relative-jf-path
+}
+
+src_compile(){
+	cd jellyfish-1.1.11 || die
+	emake
+
+	cd ../jellyfish-2.0.0rc1 || die
+	emake
+
+	cd ../CA/kmer || die
+	emake
+
+	cd ../../CA/src || die
+	emake
+
+	cd ../SuperReads-0.3.2 || die
+	emake
+
+	cd ../quorum-0.3.2 || die
+	emake
+}
+
+src_install(){
+	dobin masurca
+	dodoc sr_config_example.txt
+}

diff --git a/sci-biology/MaSuRCA/metadata.xml b/sci-biology/MaSuRCA/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/MaSuRCA/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>

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

[Martin Mokrejs]

commit:     53929302ae532c55728634317cc5487698803a61
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 20:53:38 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 20:53:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=53929302

sci-biology/MaSuRCA: new package but with a missing LICENSE and needs tweak to get all configure's running

---
 sci-biology/MaSuRCA/ChangeLog | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/sci-biology/MaSuRCA/ChangeLog b/sci-biology/MaSuRCA/ChangeLog
new file mode 100644
index 0000000..865ee42
--- /dev/null
+++ b/sci-biology/MaSuRCA/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/MaSuRCA
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ChangeLog:
+  new package but with a missing LICENSE and needs tweak to get all configure's
+  running
+

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

[Martin Mokrejs]

commit:     ef77fde804f2bef3d832e8b4758d5e47498e69c3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul  4 21:27:01 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul  4 21:27:01 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ef77fde8

sci-biology/MaSuRCA: add dependency on sci-biology/quorum

---
 sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
index 28934c3..5b8f9fb 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
@@ -16,7 +16,8 @@ IUSE=""
 
 DEPEND="dev-lang/perl
 		app-arch/bzip2"
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+	sci-biology/quorum"
 
 # the ebuild mimics "${S}"/install.sh
 src_configure(){

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

[Christoph Junghans]

commit:     b82e51e0a6a261027ed1744dc437d9fc47e61e41
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 02:52:51 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 02:52:51 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b82e51e0

added license

Package-Manager: portage-2.2.8-r1

---
 sci-biology/MaSuRCA/ChangeLog            | 4 +++-
 sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild | 8 ++++----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/sci-biology/MaSuRCA/ChangeLog b/sci-biology/MaSuRCA/ChangeLog
index 865ee42..e9d6a2c 100644
--- a/sci-biology/MaSuRCA/ChangeLog
+++ b/sci-biology/MaSuRCA/ChangeLog
@@ -2,7 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MaSuRCA-2.1.0.ebuild:
+  added license
+
   23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ChangeLog:
   new package but with a missing LICENSE and needs tweak to get all configure's
   running
-

diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
index 5b8f9fb..04e8172 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.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: $
 
@@ -9,15 +9,15 @@ HOMEPAGE="http://www.genome.umd.edu/masurca.html"
 SRC_URI="ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-"${PV}".tar.gz
 		ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
 
-LICENSE=""
+LICENSE="BSD GPL-2 GPL-3"
 SLOT="0"
 KEYWORDS=""
 IUSE=""
 
 DEPEND="dev-lang/perl
 		app-arch/bzip2"
-RDEPEND="${DEPEND}
-	sci-biology/quorum"
+RDEPEND="${DEPEND}"
+	#sci-biology/quorum"
 
 # the ebuild mimics "${S}"/install.sh
 src_configure(){

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

[Martin Mokrejs]

commit:     fbb39ffdcd8232fb3e7346355f4d7b50eb429dc1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 21:16:20 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 21:16:20 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fbb39ffd

sci-biology/MaSuRCA: version bump

Package-Manager: portage-2.2.18

 sci-biology/MaSuRCA/ChangeLog                      |  8 ++++++-
 ...{MaSuRCA-2.1.0.ebuild => MaSuRCA-2.3.2b.ebuild} | 26 +++++++++-------------
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/sci-biology/MaSuRCA/ChangeLog b/sci-biology/MaSuRCA/ChangeLog
index e9d6a2c..4014eea 100644
--- a/sci-biology/MaSuRCA/ChangeLog
+++ b/sci-biology/MaSuRCA/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-biology/MaSuRCA
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*MaSuRCA-2.3.2b (30 Apr 2015)
+
+  30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +MaSuRCA-2.3.2b.ebuild, -MaSuRCA-2.1.0.ebuild:
+  sci-biology/MaSuRCA: version bump
+
   16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MaSuRCA-2.1.0.ebuild:
   added license
 

diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
similarity index 67%
rename from sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
rename to sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
index 04e8172..01eeeeb 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -16,33 +16,27 @@ IUSE=""
 
 DEPEND="dev-lang/perl
 		app-arch/bzip2"
-RDEPEND="${DEPEND}"
-	#sci-biology/quorum"
+RDEPEND="${DEPEND}
+	>=sci-biology/quorum-0.2.1
+	>=sci-biology/jellyfish-1.1.11"
 
 # the ebuild mimics "${S}"/install.sh
 src_configure(){
-	cd jellyfish-1.1.11 || die
+	cd jellyfish || die
 	econf
 
-	cd ../jellyfish-2.0.0rc1 || die
-	econf --program-suffix=-2.0
-
 	cd ../CA/kmer || die
-	sh ./configure.sh
 	econf
 
-	cd ../../SuperReads-0.3.2 || die
+	cd ../../SuperReads || die
 	econf
 
-	cd ../quorum-0.3.2 || die
+	cd ../quorum || die
 	econf --enable-relative-paths --with-relative-jf-path
 }
 
 src_compile(){
-	cd jellyfish-1.1.11 || die
-	emake
-
-	cd ../jellyfish-2.0.0rc1 || die
+	cd jellyfish || die
 	emake
 
 	cd ../CA/kmer || die
@@ -51,10 +45,10 @@ src_compile(){
 	cd ../../CA/src || die
 	emake
 
-	cd ../SuperReads-0.3.2 || die
+	cd ../SuperReads || die
 	emake
 
-	cd ../quorum-0.3.2 || die
+	cd ../quorum || die
 	emake
 }
 

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

[Martin Mokrejs]

commit:     c1d81c6bb160f87609eb3005d0ac9457649aeda2
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 15 23:27:17 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 15 23:27:17 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c1d81c6b

sci-biology/MaSuRCA: version bump

The package is actually a bundle of many, including SOAPdenovo2 somewhat patched so that it
compiles (unlike vanilla 2.04-r240).

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild | 57 -------------------------------
 sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild  | 34 ++++++++++++++++++
 2 files changed, 34 insertions(+), 57 deletions(-)

diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
deleted file mode 100644
index 38a3d703e..000000000
--- a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Assembler to combine Sanger, Roche 454 and Illumina Solexa reads"
-HOMEPAGE="http://www.genome.umd.edu/masurca.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-"${PV}".tar.gz
-		ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
-
-LICENSE="BSD GPL-2 GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/perl
-		app-arch/bzip2"
-RDEPEND="${DEPEND}
-	>=sci-biology/quorum-0.2.1
-	>=sci-biology/jellyfish-1.1.11"
-
-# the ebuild mimics "${S}"/install.sh
-src_configure(){
-	cd jellyfish || die
-	econf
-
-	cd ../CA/kmer || die
-	econf
-
-	cd ../../SuperReads || die
-	econf
-
-	cd ../quorum || die
-	econf --enable-relative-paths --with-relative-jf-path
-}
-
-src_compile(){
-	cd jellyfish || die
-	default
-
-	cd ../CA/kmer || die
-	default
-
-	cd ../../CA/src || die
-	default
-
-	cd ../SuperReads || die
-	default
-
-	cd ../quorum || die
-	default
-}
-
-src_install(){
-	dobin masurca
-	dodoc sr_config_example.txt
-}

diff --git a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
new file mode 100644
index 000000000..d9e667792
--- /dev/null
+++ b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
+HOMEPAGE="http://www.genome.umd.edu/masurca.html"
+SRC_URI="${P}.tar.gz
+	ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
+
+LICENSE="BSD GPL-2 GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=">=dev-lang/perl-5.8
+		app-arch/bzip2"
+RDEPEND="${DEPEND}"
+
+RESTRICT="fetch"
+
+# the ebuild mimics "${S}"/install.sh
+src_configure(){
+	./install.sh || die
+}
+
+src_compile(){
+	./install.sh || die
+}
+
+src_install(){
+	dobin masurca
+	dodoc sr_config_example.txt
+}

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

[Martin Mokrejs]

commit:     ca3c78a25e5a5bd13aa159c7e762b3e0ad223896
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 28 19:13:16 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:05:19 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca3c78a2

sci-biology/MaSuRCA: add more URLs to HOMEPAGE

Package-Manager: Portage-2.3.6, Repoman-2.3.3

 sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
index d9e667792..2f2f9ddbd 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
@@ -4,7 +4,9 @@
 EAPI=6
 
 DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
-HOMEPAGE="http://www.genome.umd.edu/masurca.html"
+HOMEPAGE="http://www.genome.umd.edu/masurca.html
+	http://bioinformatics.oxfordjournals.org/content/29/21/2669
+	http://biorxiv.org/content/biorxiv/early/2016/07/26/066100.full.pdf"
 SRC_URI="${P}.tar.gz
 	ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
 
@@ -19,7 +21,6 @@ RDEPEND="${DEPEND}"
 
 RESTRICT="fetch"
 
-# the ebuild mimics "${S}"/install.sh
 src_configure(){
 	./install.sh || die
 }

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

[Andrew Ammerlaan]

commit:     295c07c0f1dc210afcb0131f0451f86b3c83b1b3
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb  1 07:41:14 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb  1 07:41:14 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=295c07c0

sci-biology/MaSuRCA: version bump 4.0.1

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../{MaSuRCA-3.2.2.ebuild => MaSuRCA-4.0.1.ebuild} | 26 ++++++++--------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
similarity index 52%
rename from sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
rename to sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
index 2f2f9ddbd..8e6d2925e 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
@@ -1,35 +1,27 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
 HOMEPAGE="http://www.genome.umd.edu/masurca.html
 	http://bioinformatics.oxfordjournals.org/content/29/21/2669
-	http://biorxiv.org/content/biorxiv/early/2016/07/26/066100.full.pdf"
-SRC_URI="${P}.tar.gz
-	ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
+	https://biorxiv.org/content/biorxiv/early/2016/07/26/066100.full.pdf"
+SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz"
 
 LICENSE="BSD GPL-2 GPL-3"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
-DEPEND=">=dev-lang/perl-5.8
-		app-arch/bzip2"
+DEPEND="
+	>=dev-lang/perl-5.8
+	app-arch/bzip2
+"
 RDEPEND="${DEPEND}"
 
-RESTRICT="fetch"
-
-src_configure(){
-	./install.sh || die
-}
-
 src_compile(){
 	./install.sh || die
 }
-
 src_install(){
 	dobin masurca
-	dodoc sr_config_example.txt
 }

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

[Horea Christian]

commit:     0a46961dd5d3492c1b98b8ae8f4163ed5a12fdff
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun May 14 04:25:44 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun May 14 04:25:44 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a46961d

sci-biology/MaSuRCA: update HOMEPAGE

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

 sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild | 2 +-
 sci-biology/MaSuRCA/metadata.xml         | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
index 8e6d2925e..71d0fbf0a 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
@@ -6,7 +6,7 @@ EAPI=7
 DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
 HOMEPAGE="http://www.genome.umd.edu/masurca.html
 	http://bioinformatics.oxfordjournals.org/content/29/21/2669
-	https://biorxiv.org/content/biorxiv/early/2016/07/26/066100.full.pdf"
+	https://github.com/alekseyzimin/masurca"
 SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz"
 
 LICENSE="BSD GPL-2 GPL-3"

diff --git a/sci-biology/MaSuRCA/metadata.xml b/sci-biology/MaSuRCA/metadata.xml
index 138cb7705..8a631d677 100644
--- a/sci-biology/MaSuRCA/metadata.xml
+++ b/sci-biology/MaSuRCA/metadata.xml
@@ -9,4 +9,7 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">alekseyzimin/masurca</remote-id>
+	</upstream>
 </pkgmetadata>

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

[Horea Christian]

commit:     ee9c9c90028dfb8995247065ee89895f85195fe2
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun May 14 04:34:23 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun May 14 04:34:23 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ee9c9c90

sci-biology/MaSuRCA: version bump and hard mask until issues are fixed

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

 sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild                          | 8 +++++---
 .../MaSuRCA/{MaSuRCA-4.0.1.ebuild => MaSuRCA-4.1.0.ebuild}        | 8 +++++---
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
index 71d0fbf0a..7b070e595 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
@@ -1,7 +1,7 @@
-# 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
 
 DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
 HOMEPAGE="http://www.genome.umd.edu/masurca.html
@@ -11,7 +11,9 @@ SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.t
 
 LICENSE="BSD GPL-2 GPL-3"
 SLOT="0"
-KEYWORDS="~amd64"
+# Known to produce build failure:
+# https://github.com/alekseyzimin/masurca/issues/323
+KEYWORDS=""
 
 DEPEND="
 	>=dev-lang/perl-5.8

diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild
similarity index 80%
copy from sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
copy to sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild
index 71d0fbf0a..7b070e595 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild
@@ -1,7 +1,7 @@
-# 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
 
 DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
 HOMEPAGE="http://www.genome.umd.edu/masurca.html
@@ -11,7 +11,9 @@ SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.t
 
 LICENSE="BSD GPL-2 GPL-3"
 SLOT="0"
-KEYWORDS="~amd64"
+# Known to produce build failure:
+# https://github.com/alekseyzimin/masurca/issues/323
+KEYWORDS=""
 
 DEPEND="
 	>=dev-lang/perl-5.8