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

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

[Martin Mokrejs]

commit:     e5dded97493ddde7b18b92023fc77bb7822f64ad
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 20:31:23 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 20:31:23 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e5dded97

sci-biology/scaffold_builder: new package but with a missing LICENSE

---
 sci-biology/scaffold_builder/ChangeLog             | 10 +++++++
 sci-biology/scaffold_builder/metadata.xml          |  9 +++++++
 .../scaffold_builder-20130403.ebuild               | 31 ++++++++++++++++++++++
 3 files changed, 50 insertions(+)

diff --git a/sci-biology/scaffold_builder/ChangeLog b/sci-biology/scaffold_builder/ChangeLog
new file mode 100644
index 0000000..72c9e84
--- /dev/null
+++ b/sci-biology/scaffold_builder/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/scaffold_builder
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*scaffold_builder-20130403 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +scaffold_builder-20130403.ebuild, +metadata.xml:
+  new package but with a missing LICENSE
+

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

diff --git a/sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild
new file mode 100644
index 0000000..f32c0cbf
--- /dev/null
+++ b/sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+S="${WORKDIR}"
+
+DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference assembly"
+HOMEPAGE="http://sourceforge.net/projects/scaffold-b/"
+SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.py
+	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc
+	http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	dev-lang/python"
+
+src_install(){
+	echo "#! /usr/bin/env python" > scaffold_builder_v2.py || die
+	cat "${DISTDIR}"/scaffold_builder_v2.py >> scaffold_builder_v2.py || die
+	dobin scaffold_builder_v2.py
+	dodoc "${DISTDIR}"/scaffold_builder_v2_help.doc
+	cp "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder_v2_Manual.pdf || die
+	dodoc scaffold_builder_v2_Manual.pdf
+}

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

[Christoph Junghans]

commit:     1d0aad7555e7603f1b8c4b080458f79d65ec5512
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 03:10:48 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 03:10:48 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1d0aad75

added license

Package-Manager: portage-2.2.8-r1

---
 sci-biology/scaffold_builder/ChangeLog                        | 5 ++++-
 sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild | 5 +++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-biology/scaffold_builder/ChangeLog b/sci-biology/scaffold_builder/ChangeLog
index 72c9e84..1dec7cf 100644
--- a/sci-biology/scaffold_builder/ChangeLog
+++ b/sci-biology/scaffold_builder/ChangeLog
@@ -2,9 +2,12 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Sep 2014; Christoph Junghans <ottxor@gentoo.org>
+  scaffold_builder-20130403.ebuild:
+  added license
+
 *scaffold_builder-20130403 (23 Mar 2014)
 
   23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   +scaffold_builder-20130403.ebuild, +metadata.xml:
   new package but with a missing LICENSE
-

diff --git a/sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild
index f32c0cbf..9a4446d 100644
--- a/sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild
+++ b/sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
 S="${WORKDIR}"
 
@@ -12,7 +12,8 @@ SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.py
 	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc
 	http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
 
-LICENSE=""
+#http://www.scfbm.org/content/8/1/23
+LICENSE="CC-BY-2.0"
 SLOT="0"
 KEYWORDS=""
 IUSE=""

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

[Martin Mokrejs]

commit:     f90c619958049fd0417d0a27d42cf521e78bd8a9
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 30 12:46:25 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 30 12:46:25 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f90c6199

version bump

Package-Manager: portage-2.2.15

---
 sci-biology/scaffold_builder/ChangeLog                  |  8 +++++++-
 ...20130403.ebuild => scaffold_builder-20131122.ebuild} | 17 +++++++++--------
 2 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/sci-biology/scaffold_builder/ChangeLog b/sci-biology/scaffold_builder/ChangeLog
index 1dec7cf..5663f61 100644
--- a/sci-biology/scaffold_builder/ChangeLog
+++ b/sci-biology/scaffold_builder/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-biology/scaffold_builder
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*scaffold_builder-20131122 (30 Jan 2015)
+
+  30 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +scaffold_builder-20131122.ebuild, -scaffold_builder-20130403.ebuild:
+  version bump
+
   16 Sep 2014; Christoph Junghans <ottxor@gentoo.org>
   scaffold_builder-20130403.ebuild:
   added license

diff --git a/sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
similarity index 64%
rename from sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild
rename to sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
index 9a4446d..dc14a4d 100644
--- a/sci-biology/scaffold_builder/scaffold_builder-20130403.ebuild
+++ b/sci-biology/scaffold_builder/scaffold_builder-20131122.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: $
 
@@ -8,14 +8,14 @@ S="${WORKDIR}"
 
 DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference assembly"
 HOMEPAGE="http://sourceforge.net/projects/scaffold-b/"
-SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.py
+SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip
 	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc
 	http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
 
 #http://www.scfbm.org/content/8/1/23
 LICENSE="CC-BY-2.0"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE=""
 
 DEPEND=""
@@ -23,10 +23,11 @@ RDEPEND="${DEPEND}
 	dev-lang/python"
 
 src_install(){
-	echo "#! /usr/bin/env python" > scaffold_builder_v2.py || die
-	cat "${DISTDIR}"/scaffold_builder_v2.py >> scaffold_builder_v2.py || die
-	dobin scaffold_builder_v2.py
+	echo "#! /usr/bin/env python" > scaffold_builder.pyy || die
+	cat scaffold_builder.py >> scaffold_builder.pyy || die
+	mv scaffold_builder.pyy scaffold_builder.py || die
+	dobin scaffold_builder.py
 	dodoc "${DISTDIR}"/scaffold_builder_v2_help.doc
-	cp "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder_v2_Manual.pdf || die
-	dodoc scaffold_builder_v2_Manual.pdf
+	cp -p "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder.pdf || die
+	dodoc scaffold_builder.pdf
 }

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

[Martin Mokrejs]

commit:     a385fb23ce58638c74875eeca73e15321abe91de
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 26 21:33:32 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 26 21:33:32 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a385fb23

sci-biology/scaffold_builder: fixed RDEPEND, added second HOMEPAGE

Package-Manager: portage-2.2.18

 sci-biology/scaffold_builder/ChangeLog                        | 4 ++++
 sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild | 4 +++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/sci-biology/scaffold_builder/ChangeLog b/sci-biology/scaffold_builder/ChangeLog
index 5663f61..07ea526 100644
--- a/sci-biology/scaffold_builder/ChangeLog
+++ b/sci-biology/scaffold_builder/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  scaffold_builder-20131122.ebuild:
+  sci-biology/scaffold_builder: noted RDEPEND, added second HOMEPAGE
+
 *scaffold_builder-20131122 (30 Jan 2015)
 
   30 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
index dc14a4d..d642ff9 100644
--- a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
+++ b/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
@@ -7,7 +7,8 @@ EAPI=5
 S="${WORKDIR}"
 
 DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference assembly"
-HOMEPAGE="http://sourceforge.net/projects/scaffold-b/"
+HOMEPAGE="http://sourceforge.net/projects/scaffold-b
+	http://edwards.sdsu.edu/scaffold_builder"
 SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip
 	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc
 	http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
@@ -20,6 +21,7 @@ IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
+	sci-biology/mummer
 	dev-lang/python"
 
 src_install(){

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

[Martin Mokrejs]

commit:     9e96e99628c9d8aeb85f66c6fe4d0874acf1f0c1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 26 21:43:04 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 26 21:43:04 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9e96e996

sci-biology/scaffold_builder: set proper LICENSE to the one mentioned in the http://www.scfbm.org/content/pdf/1751-0473-8-23.pdf article and also in the COPYING.txt file in the distribution .zip file

Package-Manager: portage-2.2.18

 sci-biology/scaffold_builder/ChangeLog                        | 6 ++++++
 sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/sci-biology/scaffold_builder/ChangeLog b/sci-biology/scaffold_builder/ChangeLog
index 07ea526..0db66bf 100644
--- a/sci-biology/scaffold_builder/ChangeLog
+++ b/sci-biology/scaffold_builder/ChangeLog
@@ -4,6 +4,12 @@
 
   26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   scaffold_builder-20131122.ebuild:
+  sci-biology/scaffold_builder: set proper LICENSE to the one mentioned in the
+  http://www.scfbm.org/content/pdf/1751-0473-8-23.pdf article and also in the
+  COPYING.txt file in the distribution .zip file
+
+  26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  scaffold_builder-20131122.ebuild:
   sci-biology/scaffold_builder: noted RDEPEND, added second HOMEPAGE
 
 *scaffold_builder-20131122 (30 Jan 2015)

diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
index d642ff9..40110cc 100644
--- a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
+++ b/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
@@ -14,7 +14,7 @@ SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.
 	http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
 
 #http://www.scfbm.org/content/8/1/23
-LICENSE="CC-BY-2.0"
+LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""

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

[Justin Lecher]

commit:     a114d80f850c5d384988fd4120f7666fdb922151
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 23 10:19:39 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 23 10:19:39 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a114d80f

sci-biology/scaffold_builder: Properly use install python scripts

Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 ....ebuild => scaffold_builder-20131122-r1.ebuild} | 26 +++++++++++++---------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
similarity index 65%
rename from sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
rename to sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
index f6358fe..5e57eb5 100644
--- a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild
+++ b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
@@ -4,12 +4,16 @@
 
 EAPI=5
 
-S="${WORKDIR}"
+PYTHON_COMPAT=( python2_7 )
+
+inherit python-r1
 
 DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference assembly"
-HOMEPAGE="http://sourceforge.net/projects/scaffold-b
+HOMEPAGE="
+	http://sourceforge.net/projects/scaffold-b
 	http://edwards.sdsu.edu/scaffold_builder"
-SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip
+SRC_URI="
+	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip
 	http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc
 	http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
 
@@ -19,17 +23,19 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/mummer
-	dev-lang/python"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	sci-biology/mummer"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
 
 src_install(){
 	echo "#! /usr/bin/env python" > scaffold_builder.pyy || die
 	cat scaffold_builder.py >> scaffold_builder.pyy || die
 	mv scaffold_builder.pyy scaffold_builder.py || die
-	dobin scaffold_builder.py
+	python_foreach_impl python_doscript scaffold_builder.py
 	dodoc "${DISTDIR}"/scaffold_builder_v2_help.doc
-	cp -p "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder.pdf || die
-	dodoc scaffold_builder.pdf
+	newdoc "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder.pdf
 }

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

[Martin Mokrejs]

commit:     eb31c25db3a5f79c2c460fa49f43d22fe00d5d0f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 29 22:33:41 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 29 22:33:41 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=eb31c25d

sci-biology/scaffold_builder: clarify description

Package-Manager: portage-2.2.28

 sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
index 5e57eb5..0a7ae54 100644
--- a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
+++ b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 
 inherit python-r1
 
-DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference assembly"
+DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference genome"
 HOMEPAGE="
 	http://sourceforge.net/projects/scaffold-b
 	http://edwards.sdsu.edu/scaffold_builder"

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

[Andrew Ammerlaan]

commit:     6e366bae83219695f935daa55763ba202102ecce
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:30:57 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:30:57 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6e366bae

sci-biology/scaffold_builder: BDEPEND on unzip

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

 sci-biology/scaffold_builder/scaffold_builder-2.2.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/scaffold_builder/scaffold_builder-2.2.ebuild b/sci-biology/scaffold_builder/scaffold_builder-2.2.ebuild
index 3f0274551..9f60e82c6 100644
--- a/sci-biology/scaffold_builder/scaffold_builder-2.2.ebuild
+++ b/sci-biology/scaffold_builder/scaffold_builder-2.2.ebuild
@@ -25,6 +25,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 RDEPEND="${PYTHON_DEPS}
 	sci-biology/mummer"
 DEPEND="${RDEPEND}"
+BDEPEND="app-arch/unzip"
 
 S="${WORKDIR}"
 

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

[Andrew Ammerlaan]

commit:     d4d0d1524160afa9709b58edeb13c0dd1eff7c9f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb  1 04:51:13 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb  1 04:51:13 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d4d0d152

sci-biology/scaffold_builder: drop pack, py2 only

checked the code, and this is still py2 style

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/scaffold_builder/metadata.xml          | 15 ---------
 .../scaffold_builder/scaffold_builder-2.2.ebuild   | 39 ----------------------
 2 files changed, 54 deletions(-)

diff --git a/sci-biology/scaffold_builder/metadata.xml b/sci-biology/scaffold_builder/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/scaffold_builder/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>

diff --git a/sci-biology/scaffold_builder/scaffold_builder-2.2.ebuild b/sci-biology/scaffold_builder/scaffold_builder-2.2.ebuild
deleted file mode 100644
index 9f60e82c6..000000000
--- a/sci-biology/scaffold_builder/scaffold_builder-2.2.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds"
-HOMEPAGE="
-	https://sourceforge.net/projects/scaffold-b
-	https://edwards.sdsu.edu/scaffold_builder"
-SRC_URI="
-	https://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v${PV}.zip
-	https://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc
-	https://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	sci-biology/mummer"
-DEPEND="${RDEPEND}"
-BDEPEND="app-arch/unzip"
-
-S="${WORKDIR}"
-
-src_install(){
-	echo "#! /usr/bin/env python" > scaffold_builder.pyy || die
-	cat scaffold_builder.py >> scaffold_builder.pyy || die
-	mv scaffold_builder.pyy scaffold_builder.py || die
-	python_foreach_impl python_doscript scaffold_builder.py
-	dodoc "${DISTDIR}"/scaffold_builder_v2_help.doc
-	newdoc "${DISTDIR}"/Manual_v2.1.pdf scaffold_builder.pdf
-}