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

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

[Martin Mokrejs]

commit:     2bd8167c9b0bea828111da63404724d0667cfbf3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May  5 15:10:02 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May  5 15:10:02 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2bd8167c

sci-biology/barnacle: a skeleton of a messy package

Package-Manager: portage-2.2.18

 sci-biology/barnacle/ChangeLog             |  9 +++++++
 sci-biology/barnacle/barnacle-1.0.3.ebuild | 39 ++++++++++++++++++++++++++++++
 sci-biology/barnacle/metadata.xml          |  9 +++++++
 3 files changed, 57 insertions(+)

diff --git a/sci-biology/barnacle/ChangeLog b/sci-biology/barnacle/ChangeLog
new file mode 100644
index 0000000..7d5b981
--- /dev/null
+++ b/sci-biology/barnacle/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/barnacle
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*barnacle-1.0.3 (05 May 2015)
+
+  05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +barnacle-1.0.3.ebuild, +metadata.xml:
+  sci-biology/barnacle: a skeleton of a messy package

diff --git a/sci-biology/barnacle/barnacle-1.0.3.ebuild b/sci-biology/barnacle/barnacle-1.0.3.ebuild
new file mode 100644
index 0000000..de565f3
--- /dev/null
+++ b/sci-biology/barnacle/barnacle-1.0.3.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="Check de novo assembly for chimeric contigs/transcripts"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/barnacle"
+#SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/1.0.0/"${P}".tar.gz"
+SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/${PV}/${P}.tar.gz"
+# ftp://ftp.bcgsc.ca/supplementary/Barnacle_BMC_Genomics/aml_data.tar.gz
+# http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/1.0.3
+
+LICENSE="bcca_2010"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${S}"
+
+# follow README.txt
+src_compile(){
+	cd src || die
+	# Run setup.py to compile the portions of Barnacle that require compilation, and download and setup the default annotations
+	./setup.py || die
+}
+
+src_install(){
+	dodoc README.txt
+	cd src || die
+	# do something
+}

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

[Martin Mokrejs]

commit:     81043e128c02e9a72bb99a36257d0b60dbca9ef1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 16:12:18 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 16:12:18 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=81043e12

sci-biology/barnacle: does not build due to a new build system

Package-Manager: portage-2.2.28

 sci-biology/barnacle/{barnacle-1.0.3.ebuild => barnacle-1.0.4.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/barnacle/barnacle-1.0.3.ebuild b/sci-biology/barnacle/barnacle-1.0.4.ebuild
similarity index 100%
rename from sci-biology/barnacle/barnacle-1.0.3.ebuild
rename to sci-biology/barnacle/barnacle-1.0.4.ebuild

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

[Martin Mokrejs]

commit:     9d66184475a6cff25507968662eafe9ca1f30dc6
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Sep 23 17:33:02 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Sep 23 17:33:02 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d661844

sci-biology/barnacle:  another attempt at a compile step

Package-Manager: portage-2.3.0

 sci-biology/barnacle/barnacle-1.0.4.ebuild | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/sci-biology/barnacle/barnacle-1.0.4.ebuild b/sci-biology/barnacle/barnacle-1.0.4.ebuild
index 2fb3123..e1f95ad 100644
--- a/sci-biology/barnacle/barnacle-1.0.4.ebuild
+++ b/sci-biology/barnacle/barnacle-1.0.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -29,7 +29,8 @@ S="${S}"
 src_compile(){
 	cd src || die
 	# Run setup.py to compile the portions of Barnacle that require compilation, and download and setup the default annotations
-	./setup.py || die
+	touch alignment_processing/gap_realigner_cluster || die # prevent compilation on a cluster
+	./setup.py localhost || die
 }
 
 src_install(){

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

[Horea Christian]

commit:     a47e7c6629898c630edc013392245b5613fbdeeb
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan  4 12:12:49 2021 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jan  5 06:07:59 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a47e7c66

sci-biology/barnacle: remove package, py2 only, does not compile

This is broken beyond repair, it is not compatible with py3.
I tried to save it with DISTUTILS_USE_SETUPTOOLS="no"
but it does not compile: EOFError: EOF when reading a line

We could patch it, but IMO it is not worth the effort
upstream is dead since 2016.

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/barnacle/barnacle-1.0.4.ebuild | 39 ------------------------------
 sci-biology/barnacle/metadata.xml          | 12 ---------
 2 files changed, 51 deletions(-)

diff --git a/sci-biology/barnacle/barnacle-1.0.4.ebuild b/sci-biology/barnacle/barnacle-1.0.4.ebuild
deleted file mode 100644
index 970f127fd..000000000
--- a/sci-biology/barnacle/barnacle-1.0.4.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Check de novo assembly for chimeric contigs/transcripts"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/barnacle"
-#SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/1.0.0/"${P}".tar.gz"
-SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/${PV}/${P}.tar.gz"
-# ftp://ftp.bcgsc.ca/supplementary/Barnacle_BMC_Genomics/aml_data.tar.gz
-# http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/1.0.3
-
-LICENSE="bcca_2010"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${S}"
-
-# follow README.txt
-src_compile(){
-	cd src || die
-	# Run setup.py to compile the portions of Barnacle that require compilation, and download and setup the default annotations
-	touch alignment_processing/gap_realigner_cluster || die # prevent compilation on a cluster
-	./setup.py localhost || die
-}
-
-src_install(){
-	dodoc README.txt
-	cd src || die
-	# do something
-}

diff --git a/sci-biology/barnacle/metadata.xml b/sci-biology/barnacle/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/barnacle/metadata.xml
+++ /dev/null
@@ -1,12 +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>
-</pkgmetadata>