[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/snphylo/

[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/snphylo/

[Andrew Ammerlaan]

commit:     331823c3e421263be84719b492e2cff006c99447
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 09:12:28 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 09:12:40 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=331823c3

sci-biology/snphylo: fix fetching, version bump

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

 profiles/package.mask                              |  1 -
 ...-20140701.ebuild => snphylo-0_p20181005.ebuild} | 23 +++++++++++-----------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 076004dee..9232daefe 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -103,4 +103,3 @@ sci-biology/sgp2
 sci-biology/skewer-bin
 sci-biology/smalt
 sci-biology/SnpEff
-sci-biology/snphylo

diff --git a/sci-biology/snphylo/snphylo-20140701.ebuild b/sci-biology/snphylo/snphylo-0_p20181005.ebuild
similarity index 58%
rename from sci-biology/snphylo/snphylo-20140701.ebuild
rename to sci-biology/snphylo/snphylo-0_p20181005.ebuild
index c10401184..48506d759 100644
--- a/sci-biology/snphylo/snphylo-20140701.ebuild
+++ b/sci-biology/snphylo/snphylo-0_p20181005.ebuild
@@ -1,29 +1,30 @@
-# 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
+
+COMMIT="55cc9a45dc1d0064c94a3e8bea8fdb7c00656556"
 
 DESCRIPTION="Pipeline to generate phylogenetic tree from SNP data"
-HOMEPAGE="http://chibba.pgml.uga.edu/snphylo"
-SRC_URI="http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz -> ${P}.tar.gz"
-# http://github.com/thlee/SNPhylo
-# http://www.biomedcentral.com/1471-2164/15/162
+HOMEPAGE="https://github.com/thlee/SNPhylo"
+SRC_URI="https://github.com/thlee/SNPhylo/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}
+RDEPEND="
 	sci-biology/fastdnaml
 	sci-biology/muscle
-	sci-biology/phylip"
+	sci-biology/phylip
+	dev-lang/R
+"
+DEPEND="${RDEPEND}"
 # http://chibba.pgml.uga.edu/snphylo/install_on_linux.html
 # R packages (phangorn, gdsfmt, SNPRelate and getopt)
 # $ apt-get -y install r-base-dev r-cran-getopt r-cran-rgl
 
-S="${WORKDIR}"/"${PN}"
+S="${WORKDIR}/SNPhylo-${COMMIT}"
 
 src_compile(){
 	bash setup.sh || die