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

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

[Martin Mokrejs]

commit:     fffb9359386b03cbe403bd3f0c7ef432cd982591
Author:     Martin Mokrejs <mmokrejs <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 17 20:16:06 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Feb 17 20:16:06 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fffb9359

sci-biology/seqclean: description line cleanup

(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/seqclean/seqclean-0.1.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-biology/seqclean/seqclean-0.1.ebuild b/sci-biology/seqclean/seqclean-0.1.ebuild
index ac7f202..eae3ef6 100644
--- a/sci-biology/seqclean/seqclean-0.1.ebuild
+++ b/sci-biology/seqclean/seqclean-0.1.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=3
 
-DESCRIPTION="SeqClean: perl scripts for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences with two binaries"
+DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences, low quality and low-complexity sequences with two binaries"
 HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software"
 for i in seqclean/{seqcl_scripts,mdust,trimpoly}; do
 	SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz"

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

[Martin Mokrejs]

commit:     a875b950fad1f054144a916a41d1c2b5b90673b4
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:41:41 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:41:41 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a875b950

sci-biology/seqclean: bump EAPI

Package-Manager: portage-2.2.18

 sci-biology/seqclean/ChangeLog              | 4 ++++
 sci-biology/seqclean/seqclean-110625.ebuild | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/sci-biology/seqclean/ChangeLog b/sci-biology/seqclean/ChangeLog
index e8b4cbb..f7c664a 100644
--- a/sci-biology/seqclean/ChangeLog
+++ b/sci-biology/seqclean/ChangeLog
@@ -4,6 +4,10 @@
 
   17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   seqclean-110625.ebuild:
+  sci-biology/seqclean: bump EAPI
+
+  17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  seqclean-110625.ebuild:
   sci-biology/seqclean: fix language
 
 *seqclean-110625 (25 Jun 2011)

diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild
index da1ef80..1de8c72 100644
--- a/sci-biology/seqclean/seqclean-110625.ebuild
+++ b/sci-biology/seqclean/seqclean-110625.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
 inherit eutils toolchain-funcs
 

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

[Martin Mokrejs]

commit:     315aa2bb53945cec10af0b07e6d16b3b8f60b8fe
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:40:17 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:40:17 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=315aa2bb

sci-biology/seqclean: fix language

Package-Manager: portage-2.2.18

 sci-biology/seqclean/ChangeLog              | 7 +++++--
 sci-biology/seqclean/seqclean-110625.ebuild | 4 ++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/sci-biology/seqclean/ChangeLog b/sci-biology/seqclean/ChangeLog
index b03c585..e8b4cbb 100644
--- a/sci-biology/seqclean/ChangeLog
+++ b/sci-biology/seqclean/ChangeLog
@@ -1,10 +1,13 @@
 # ChangeLog for sci-biology/seqclean
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  seqclean-110625.ebuild:
+  sci-biology/seqclean: fix language
+
 *seqclean-110625 (25 Jun 2011)
 
   25 Jun 2011; Justin Lecher <jlec@gentoo.org> -seqclean-0.1.ebuild,
   +seqclean-110625.ebuild, +files/seqclean-110625-build.patch:
   Cleaned ebuild
-

diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild
index 1078c0c..da1ef80 100644
--- a/sci-biology/seqclean/seqclean-110625.ebuild
+++ b/sci-biology/seqclean/seqclean-110625.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: $
 
@@ -48,7 +48,7 @@ src_install() {
 		dobin ${i}/${i}
 	done
 
-	einfo "Optionally, you might want to download UniVec from NCBI if you do not have your own"
+	einfo "Optionally, you may want to download UniVec from NCBI if you do not have your own"
 	einfo "fasta file with vector sequences you want to remove from sequencing"
 	einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html"
 }

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

[Andrew Ammerlaan]

commit:     68ad6456d75a15daa7604515cabae17c599a5f3d
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 14:03:43 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 14:03:43 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=68ad6456

sci-biology/seqclean: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/seqclean/seqclean-110625.ebuild | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild
index 67a98eb5a..f98fdf3b8 100644
--- a/sci-biology/seqclean/seqclean-110625.ebuild
+++ b/sci-biology/seqclean/seqclean-110625.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences"
 HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/"
@@ -14,7 +14,6 @@ done
 LICENSE="Artistic"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 
 DEPEND="
 	dev-lang/perl
@@ -23,13 +22,15 @@ RDEPEND="${DEPEND}"
 
 S=${WORKDIR}
 
+PATCHES=(
+	"${FILESDIR}"/${P}-build.patch
+)
+
 src_prepare() {
+	default
 	# disable the necessity to install Mailer.pm with this tool
 	einfo "Disabling mailer feature within seqclean"
 	sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die
-
-	epatch "${FILESDIR}"/${P}-build.patch
-
 	tc-export CC CXX
 }