[gentoo-commits] proj/sci:master commit in: sci-biology/proovread/
commit: f60510efb81dbeeb9474bb50071a0b0ed59a5964
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue May 2 12:10:37 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue May 2 12:15:16 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f60510ef
sci-biology/proovread: treeclean
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/proovread/metadata.xml| 12 ---
sci-biology/proovread/proovread-2.14.1.ebuild | 51 ---
sci-biology/proovread/proovread-.ebuild | 51 ---
3 files changed, 114 deletions(-)
diff --git a/sci-biology/proovread/metadata.xml
b/sci-biology/proovread/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/proovread/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/sci-biology/proovread/proovread-2.14.1.ebuild
b/sci-biology/proovread/proovread-2.14.1.ebuild
deleted file mode 100644
index be1d610b0..0
--- a/sci-biology/proovread/proovread-2.14.1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="Error correct PacBio subreads using Illumina reads"
-HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread;
-if [ "$PV" == "" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread;
-else
-
SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz;
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Artistic-2 GPL-3 blasr"
-SLOT="0"
-
-# TODO: package shrimp and update blasr
-# blasr requires new dep libblasr, which
-# I cannot get to compile successfully
-RDEPEND="
- >=dev-lang/perl-5.10
- dev-perl/Log-Log4perl
- dev-perl/File-Which
- >=sci-biology/ncbi-tools++-2.2.24
- >=sci-biology/samtools-1.1
-"
-DEPEND="${RDEPEND}"
-
-src_install(){
- cd bin || die
- dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera
samfilter sam2cns proovread-flex proovread
- cd ../util/bwa || die
- dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1
- cd ../../util/SeqFilter || die
- dobin bin/SeqFilter
- cd ../../util/SeqChunker || die
- dobin bin/*
- cd ../../lib || die
- perl_domodule -r -C ${PN} *
- cd ../util/blasr-1.3.1 || die
- dobin blasr
-}
-
-pkg_postinst(){
- einfo "Proovread uses its own, modified version of bwa as bwa-proovread"
- einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr"
-}
diff --git a/sci-biology/proovread/proovread-.ebuild
b/sci-biology/proovread/proovread-.ebuild
deleted file mode 100644
index be1d610b0..0
--- a/sci-biology/proovread/proovread-.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="Error correct PacBio subreads using Illumina reads"
-HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread;
-if [ "$PV" == "" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread;
-else
-
SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz;
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Artistic-2 GPL-3 blasr"
-SLOT="0"
-
-# TODO: package shrimp and update blasr
-# blasr requires new dep libblasr, which
-# I cannot get to compile successfully
-RDEPEND="
- >=dev-lang/perl-5.10
- dev-perl/Log-Log4perl
- dev-perl/File-Which
- >=sci-biology/ncbi-tools++-2.2.24
- >=sci-biology/samtools-1.1
-"
-DEPEND="${RDEPEND}"
-
-src_install(){
- cd bin || die
- dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera
samfilter sam2cns proovread-flex proovread
- cd ../util/bwa || die
- dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1
- cd ../../util/SeqFilter || die
- dobin bin/SeqFilter
- cd ../../util/SeqChunker || die
- dobin bin/*
- cd ../../lib || die
- perl_domodule -r -C ${PN} *
- cd ../util/blasr-1.3.1 || die
- dobin blasr
-}
-
-pkg_postinst(){
- einfo "Proovread uses its own, modified version of bwa as bwa-proovread"
- einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr"
-}
[gentoo-commits] proj/sci:master commit in: sci-biology/proovread/
commit: 277e94d0c3028cae154e375195dcb5bb2e059f6d
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Mar 20 11:00:07 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sat Mar 20 11:00:07 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=277e94d0
sci-biology/proovread: fix MultipleKeywordsLines
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/proovread/proovread-2.14.1.ebuild | 1 -
sci-biology/proovread/proovread-.ebuild | 1 -
2 files changed, 2 deletions(-)
diff --git a/sci-biology/proovread/proovread-2.14.1.ebuild
b/sci-biology/proovread/proovread-2.14.1.ebuild
index 732817308..be1d610b0 100644
--- a/sci-biology/proovread/proovread-2.14.1.ebuild
+++ b/sci-biology/proovread/proovread-2.14.1.ebuild
@@ -10,7 +10,6 @@ HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread;
if [ "$PV" == "" ]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread;
- KEYWORDS=""
else
SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz;
KEYWORDS="~amd64 ~x86"
diff --git a/sci-biology/proovread/proovread-.ebuild
b/sci-biology/proovread/proovread-.ebuild
index 732817308..be1d610b0 100644
--- a/sci-biology/proovread/proovread-.ebuild
+++ b/sci-biology/proovread/proovread-.ebuild
@@ -10,7 +10,6 @@ HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread;
if [ "$PV" == "" ]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread;
- KEYWORDS=""
else
SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz;
KEYWORDS="~amd64 ~x86"
[gentoo-commits] proj/sci:master commit in: sci-biology/proovread/
commit: e8ed9acc2ba2166aeed1ebe534271fe724ba6980
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sun Jan 10 14:04:02 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sun Jan 10 14:04:02 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8ed9acc
sci-biology/proovread: add version 2.14.1
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
...oovread-.ebuild => proovread-2.14.1.ebuild} | 32 ++
sci-biology/proovread/proovread-.ebuild| 32 ++
2 files changed, 30 insertions(+), 34 deletions(-)
diff --git a/sci-biology/proovread/proovread-.ebuild
b/sci-biology/proovread/proovread-2.14.1.ebuild
similarity index 68%
copy from sci-biology/proovread/proovread-.ebuild
copy to sci-biology/proovread/proovread-2.14.1.ebuild
index d8d3dc913..732817308 100644
--- a/sci-biology/proovread/proovread-.ebuild
+++ b/sci-biology/proovread/proovread-2.14.1.ebuild
@@ -1,36 +1,35 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-[ "$PV" == "" ] && inherit git-r3
-
-inherit perl-functions toolchain-funcs
+inherit perl-functions
DESCRIPTION="Error correct PacBio subreads using Illumina reads"
HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread;
if [ "$PV" == "" ]; then
+ inherit git-r3
EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread;
KEYWORDS=""
else
- SRC_URI=""
- KEYWORDS="~amd64 ~x86" # issue #125
+
SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz;
+ KEYWORDS="~amd64 ~x86"
fi
-LICENSE="Artistic-2 GPL-3"
+LICENSE="Artistic-2 GPL-3 blasr"
SLOT="0"
-IUSE=""
-# needs Fasta::Parser
+# TODO: package shrimp and update blasr
+# blasr requires new dep libblasr, which
+# I cannot get to compile successfully
RDEPEND="
>=dev-lang/perl-5.10
dev-perl/Log-Log4perl
dev-perl/File-Which
>=sci-biology/ncbi-tools++-2.2.24
- >=sci-biology/samtools-1.1"
-DEPEND="${RDEPEND}
- >=sci-biology/shrimp-2
- sci-biology/blasr"
+ >=sci-biology/samtools-1.1
+"
+DEPEND="${RDEPEND}"
src_install(){
cd bin || die
@@ -43,9 +42,8 @@ src_install(){
dobin bin/*
cd ../../lib || die
perl_domodule -r -C ${PN} *
- # cd ../util/blasr-1.3.1 || die
- # dobin blasr
- # dodoc LICENSE.txt
+ cd ../util/blasr-1.3.1 || die
+ dobin blasr
}
pkg_postinst(){
diff --git a/sci-biology/proovread/proovread-.ebuild
b/sci-biology/proovread/proovread-.ebuild
index d8d3dc913..732817308 100644
--- a/sci-biology/proovread/proovread-.ebuild
+++ b/sci-biology/proovread/proovread-.ebuild
@@ -1,36 +1,35 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-[ "$PV" == "" ] && inherit git-r3
-
-inherit perl-functions toolchain-funcs
+inherit perl-functions
DESCRIPTION="Error correct PacBio subreads using Illumina reads"
HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread;
if [ "$PV" == "" ]; then
+ inherit git-r3
EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread;
KEYWORDS=""
else
- SRC_URI=""
- KEYWORDS="~amd64 ~x86" # issue #125
+
SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz;
+ KEYWORDS="~amd64 ~x86"
fi
-LICENSE="Artistic-2 GPL-3"
+LICENSE="Artistic-2 GPL-3 blasr"
SLOT="0"
-IUSE=""
-# needs Fasta::Parser
+# TODO: package shrimp and update blasr
+# blasr requires new dep libblasr, which
+# I cannot get to compile successfully
RDEPEND="
>=dev-lang/perl-5.10
dev-perl/Log-Log4perl
dev-perl/File-Which
>=sci-biology/ncbi-tools++-2.2.24
- >=sci-biology/samtools-1.1"
-DEPEND="${RDEPEND}
- >=sci-biology/shrimp-2
- sci-biology/blasr"
+ >=sci-biology/samtools-1.1
+"
+DEPEND="${RDEPEND}"
src_install(){
cd bin || die
@@ -43,9 +42,8 @@ src_install(){
dobin bin/*
cd ../../lib || die
perl_domodule -r -C ${PN} *
- # cd ../util/blasr-1.3.1 || die
- # dobin blasr
- # dodoc LICENSE.txt
+ cd ../util/blasr-1.3.1 || die
+ dobin blasr
}
pkg_postinst(){
[gentoo-commits] proj/sci:master commit in: sci-biology/proovread/
commit: af71a5d29200d0accf2890ef25c9393cd1a3fe32 Author: Justin Lecher gentoo org> AuthorDate: Mon Apr 2 20:23:27 2018 + Commit: Justin Lecher gentoo org> CommitDate: Mon Apr 2 20:23:27 2018 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=af71a5d2 sci-biology/proovread: Fix license Signed-off-by: Justin Lecher gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9 sci-biology/proovread/proovread-.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/proovread/proovread-.ebuild b/sci-biology/proovread/proovread-.ebuild index 5165ae6dd..d8d3dc913 100644 --- a/sci-biology/proovread/proovread-.ebuild +++ b/sci-biology/proovread/proovread-.ebuild @@ -17,7 +17,7 @@ else KEYWORDS="~amd64 ~x86" # issue #125 fi -LICENSE="proovread" # Artistic-2.0 or GPL-3 but not for commercial +LICENSE="Artistic-2 GPL-3" SLOT="0" IUSE=""
[gentoo-commits] proj/sci:master commit in: sci-biology/proovread/
commit: b1d6d2c3fc9cb4a1d918d0fb3424be2228b8e825
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sun Apr 1 22:17:42 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 1 22:17:42 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b1d6d2c3
sci-biology/proovread: call perl_domodule to install *.pm files
Package-Manager: Portage-2.3.27, Repoman-2.3.9
sci-biology/proovread/proovread-.ebuild | 4
1 file changed, 4 insertions(+)
diff --git a/sci-biology/proovread/proovread-.ebuild
b/sci-biology/proovread/proovread-.ebuild
index 11a78d2f8..5165ae6dd 100644
--- a/sci-biology/proovread/proovread-.ebuild
+++ b/sci-biology/proovread/proovread-.ebuild
@@ -5,6 +5,8 @@ EAPI=6
[ "$PV" == "" ] && inherit git-r3
+inherit perl-functions toolchain-funcs
+
DESCRIPTION="Error correct PacBio subreads using Illumina reads"
HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread;
if [ "$PV" == "" ]; then
@@ -39,6 +41,8 @@ src_install(){
dobin bin/SeqFilter
cd ../../util/SeqChunker || die
dobin bin/*
+ cd ../../lib || die
+ perl_domodule -r -C ${PN} *
# cd ../util/blasr-1.3.1 || die
# dobin blasr
# dodoc LICENSE.txt
[gentoo-commits] proj/sci:master commit in: sci-biology/proovread/
commit: a4e405144f304e63344c5228e1407fdff6bfab75
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sun Apr 1 21:49:26 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 1 21:49:26 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4e40514
sci-biology/proovread: new package
Will need more work from upstream to make it into Gentoo.
Package-Manager: Portage-2.3.27, Repoman-2.3.9
sci-biology/proovread/metadata.xml | 12 +++
sci-biology/proovread/proovread-.ebuild | 50 +
2 files changed, 62 insertions(+)
diff --git a/sci-biology/proovread/metadata.xml
b/sci-biology/proovread/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/proovread/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ mmokr...@fold.natur.cuni.cz
+ Martin Mokrejs
+
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
diff --git a/sci-biology/proovread/proovread-.ebuild
b/sci-biology/proovread/proovread-.ebuild
new file mode 100644
index 0..11a78d2f8
--- /dev/null
+++ b/sci-biology/proovread/proovread-.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+[ "$PV" == "" ] && inherit git-r3
+
+DESCRIPTION="Error correct PacBio subreads using Illumina reads"
+HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread;
+if [ "$PV" == "" ]; then
+ EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread;
+ KEYWORDS=""
+else
+ SRC_URI=""
+ KEYWORDS="~amd64 ~x86" # issue #125
+fi
+
+LICENSE="proovread" # Artistic-2.0 or GPL-3 but not for commercial
+SLOT="0"
+IUSE=""
+
+# needs Fasta::Parser
+RDEPEND="
+ >=dev-lang/perl-5.10
+ dev-perl/Log-Log4perl
+ dev-perl/File-Which
+ >=sci-biology/ncbi-tools++-2.2.24
+ >=sci-biology/samtools-1.1"
+DEPEND="${RDEPEND}
+ >=sci-biology/shrimp-2
+ sci-biology/blasr"
+
+src_install(){
+ cd bin || die
+ dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera
samfilter sam2cns proovread-flex proovread
+ cd ../util/bwa || die
+ dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1
+ cd ../../util/SeqFilter || die
+ dobin bin/SeqFilter
+ cd ../../util/SeqChunker || die
+ dobin bin/*
+ # cd ../util/blasr-1.3.1 || die
+ # dobin blasr
+ # dodoc LICENSE.txt
+}
+
+pkg_postinst(){
+ einfo "Proovread uses its own, modified version of bwa as bwa-proovread"
+ einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr"
+}
