commit: 4a53300246ea9bcd0f7fbf801034c547d29d34eb Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Thu Feb 4 05:32:41 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Thu Feb 4 05:32:41 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a533002
sci-biology/snphylo: remove pack - this has missing deps - has not been fixed since it was added in 2015 - does not work, and will never work without some crazy workarounds. This package installs a script which looks for a config file and a directory named scripts in the same directory where the script is installed. At the moment only the master script is installed, which of course does not work because the config files and the .py files in the scripts dir are missing. We could of course add those, but then they would have to be in the same dir as the master script. (/opt would be an option, with a symlink of the executable script in a directory which is in PATH, though I am not sure if a symlink will work correctly with the way this package looks for it's config/scripts files) This was obviously designed for downloading and placing as is in some user directory. Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/snphylo/metadata.xml | 12 --------- sci-biology/snphylo/snphylo-0_p20181005.ebuild | 35 -------------------------- 2 files changed, 47 deletions(-) diff --git a/sci-biology/snphylo/metadata.xml b/sci-biology/snphylo/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/snphylo/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>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/snphylo/snphylo-0_p20181005.ebuild b/sci-biology/snphylo/snphylo-0_p20181005.ebuild deleted file mode 100644 index 48506d759..000000000 --- a/sci-biology/snphylo/snphylo-0_p20181005.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -COMMIT="55cc9a45dc1d0064c94a3e8bea8fdb7c00656556" - -DESCRIPTION="Pipeline to generate phylogenetic tree from SNP data" -HOMEPAGE="https://github.com/thlee/SNPhylo"; -SRC_URI="https://github.com/thlee/SNPhylo/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="" - -RDEPEND=" - sci-biology/fastdnaml - sci-biology/muscle - sci-biology/phylip - dev-lang/R -" -DEPEND="${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="${WORKDIR}/SNPhylo-${COMMIT}" - -src_compile(){ - bash setup.sh || die -} - -src_install(){ - dobin snphylo.sh -}
