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

2023-05-13 Thread Horea Christian 
commit: ee9c9c90028dfb8995247065ee89895f85195fe2
Author: Horea Christian  chymera  eu>
AuthorDate: Sun May 14 04:34:23 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Sun May 14 04:34:23 2023 +
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  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

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

2023-05-13 Thread Horea Christian 
commit: 0a46961dd5d3492c1b98b8ae8f4163ed5a12fdff
Author: Horea Christian  chymera  eu>
AuthorDate: Sun May 14 04:25:44 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Sun May 14 04:25:44 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a46961d

sci-biology/MaSuRCA: update HOMEPAGE

Signed-off-by: Horea Christian  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 @@
sci-biol...@gentoo.org
Gentoo Biology Project

+   
+   alekseyzimin/masurca
+

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

2021-01-31 Thread Andrew Ammerlaan 
commit: 295c07c0f1dc210afcb0131f0451f86b3c83b1b3
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Mon Feb  1 07:41:14 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Mon Feb  1 07:41:14 2021 +
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  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/

2017-07-28 Thread Martin Mokrejs 
commit: ca3c78a25e5a5bd13aa159c7e762b3e0ad223896
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Fri Jul 28 19:13:16 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jul 28 20:05:19 2017 +
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/

2017-05-15 Thread Martin Mokrejs 
commit: c1d81c6bb160f87609eb3005d0ac9457649aeda2
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Mon May 15 23:27:17 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon May 15 23:27:17 2017 +
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..0
--- 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 0..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/

2015-04-30 Thread Martin Mokrejs 
commit: fbb39ffdcd8232fb3e7346355f4d7b50eb429dc1
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Thu Apr 30 21:16:20 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Thu Apr 30 21:16:20 2015 +
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 mmokr...@fold.natur.cuni.cz
+  +MaSuRCA-2.3.2b.ebuild, -MaSuRCA-2.1.0.ebuild:
+  sci-biology/MaSuRCA: version bump
+
   16 Sep 2014; Christoph Junghans ott...@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..01b 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/

2014-09-15 Thread Christoph Junghans 
commit: b82e51e0a6a261027ed1744dc437d9fc47e61e41
Author: Christoph Junghans ottxor AT gentoo DOT org
AuthorDate: Tue Sep 16 02:52:51 2014 +
Commit: Christoph Junghans ottxor AT gentoo DOT org
CommitDate: Tue Sep 16 02:52:51 2014 +
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 ott...@gentoo.org MaSuRCA-2.1.0.ebuild:
+  added license
+
   23 Mar 2014; Martin Mokrejs mmokr...@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/

2014-07-04 Thread Martin Mokrejs 
commit: ef77fde804f2bef3d832e8b4758d5e47498e69c3
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Fri Jul  4 21:27:01 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Fri Jul  4 21:27:01 2014 +
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/

2014-03-23 Thread Martin Mokrejs 
commit: 53929302ae532c55728634317cc5487698803a61
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Sun Mar 23 20:53:38 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Sun Mar 23 20:53:38 2014 +
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 000..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 mmokr...@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/

2014-03-23 Thread Martin Mokrejs 
commit: a788b3a56fa7e60683c10ae8c8e73490d1575e0f
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Sun Mar 23 20:52:30 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Sun Mar 23 20:52:30 2014 +
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 000..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 000..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
+  herdsci-biology/herd
+  maintainer
+emailmmokr...@fold.natur.cuni.cz/email
+nameMartin Mokrejs/name
+  /maintainer
+/pkgmetadata