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

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

[Martin Mokrejs]

commit:     44e3ae771a3aa414d91c4687cb707b2d16b32ff7
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 20 12:50:03 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 20 12:50:03 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=44e3ae77

sci-biology/canu: add live package of a new tool

Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/canu/canu-9999.ebuild | 50 +++++++++++++++++++++++++++++++++++++++
 sci-biology/canu/metadata.xml     | 12 ++++++++++
 2 files changed, 62 insertions(+)

diff --git a/sci-biology/canu/canu-9999.ebuild b/sci-biology/canu/canu-9999.ebuild
new file mode 100644
index 000000000..bef85d20f
--- /dev/null
+++ b/sci-biology/canu/canu-9999.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit java-pkg-2 git-r3
+
+DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences"
+HOMEPAGE="http://canu.readthedocs.io/en/latest"
+EGIT_REPO_URI="https://github.com/marbl/canu.git"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+RDEPEND="
+	>=virtual/jre-1.8:*
+	dev-lang/perl
+	virtual/perl-File-Path
+	sci-visualization/gnuplot
+	"
+# =sci-biology/mhap-2.1.3 if we unbundle it
+DEPEND="${RDEPEND}
+	>=virtual/jdk-1.8:*
+	dev-java/ant-core
+	"
+
+# Perl 5.12.0, or File::Path 2.08
+# Java SE 8
+# https://github.com/marbl/MHAP uses Apache maven
+S="${WORKDIR}"/"${P}"
+
+# contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON
+
+src_compile(){
+	cd src || die
+	emake
+}
+
+src_install(){
+	# installs
+	#  /usr/bin
+	#  /usr/lib/libcanu.a
+	#  /usr/lib/site_perl/canu
+	#  /usr/share/java/classes/mhap-2.1.3.jar
+	rm -rf Linux-amd64/obj
+	insinto /usr
+	doins -r Linux-amd64/{bin,lib,share}
+}

diff --git a/sci-biology/canu/metadata.xml b/sci-biology/canu/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/canu/metadata.xml
@@ -0,0 +1,12 @@
+<?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>

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

[Andrew Ammerlaan]

commit:     91dc0a8eec9e69d105e3d0534173ea59a4de80dd
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Feb 13 11:32:37 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Feb 13 11:32:37 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=91dc0a8e

sci-biology/canu: dolib --> dolib.a

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/canu/canu-2.1.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild
index 1993440de..201058fad 100644
--- a/sci-biology/canu/canu-2.1.1.ebuild
+++ b/sci-biology/canu/canu-2.1.1.ebuild
@@ -63,7 +63,7 @@ src_install(){
 	insinto /usr
 	doins -r Linux-amd64/{bin,share}
 	insinto /usr/$(get_libdir)
-	dolib Linux-amd64/lib/libcanu.a
+	dolib.a Linux-amd64/lib/libcanu.a
 	rm Linux-amd64/lib/libcanu.a || die
 	perl_set_version
 	insinto ${VENDOR_LIB}

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

[Martin Mokrejs]

commit:     a59c6f6546b9556a99d35f05abc3d96557f8bac2
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Wed Mar 17 19:26:26 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 17 19:26:26 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a59c6f65

sci-biology/canu: add missing dependency

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/canu/canu-2.1.1.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild
index 201058fad..10e4f485a 100644
--- a/sci-biology/canu/canu-2.1.1.ebuild
+++ b/sci-biology/canu/canu-2.1.1.ebuild
@@ -22,6 +22,7 @@ RDEPEND="${PYTHON_DEPS}
 	dev-lang/perl
 	virtual/perl-File-Path
 	sci-visualization/gnuplot
+	sci-biology/minimap2
 "
 # =sci-biology/mhap-2.1.3 if we unbundle it
 DEPEND="${RDEPEND}

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

[Andrew Ammerlaan]

commit:     5d981c778add96cbea7ea24c75031a2fa9df04e4
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:52:26 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:52:26 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5d981c77

sci-biology/canu: use perl_domodule

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/canu/canu-2.1.1.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild
index 10e4f485a..a92b6e581 100644
--- a/sci-biology/canu/canu-2.1.1.ebuild
+++ b/sci-biology/canu/canu-2.1.1.ebuild
@@ -67,6 +67,5 @@ src_install(){
 	dolib.a Linux-amd64/lib/libcanu.a
 	rm Linux-amd64/lib/libcanu.a || die
 	perl_set_version
-	insinto ${VENDOR_LIB}
-	doins -r Linux-amd64/lib
+	perl_domodule -r Linux-amd64/lib
 }

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

[Andrew Ammerlaan]

commit:     50bd4cc7fea01fd32cf7b09878eb8e58887a8658
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 15:31:21 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 15:31:21 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=50bd4cc7

sci-biology/canu: drop non-existing blocker

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/canu/canu-2.1.1.ebuild | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild
index e14efe3af..987fb99f2 100644
--- a/sci-biology/canu/canu-2.1.1.ebuild
+++ b/sci-biology/canu/canu-2.1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -28,8 +28,7 @@ RDEPEND="${PYTHON_DEPS}
 DEPEND="${RDEPEND}
 	>=virtual/jdk-1.8:*
 	dev-java/ant-core
-	!sci-biology/wgs-assembler
-	"
+"
 
 # Detected file collision(s):
 #  * sci-biology/wgs-assembler-8.3_rc2:0::science