commit: 9c2dcdf491c442611763b878fba0c3240daf1d42 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Wed Feb 3 05:40:53 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Wed Feb 3 05:40:53 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c2dcdf4
sci-biology/polyphen: EAPI bump, fix configure, compile and install Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/polyphen/polyphen-2.2.2.ebuild | 38 ++++++++++++++++++++++++++++-- 1 file changed, 36 insertions(+), 2 deletions(-) diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild index 0995356fd..da07819a5 100644 --- a/sci-biology/polyphen/polyphen-2.2.2.ebuild +++ b/sci-biology/polyphen/polyphen-2.2.2.ebuild @@ -5,11 +5,21 @@ EAPI=7 DESCRIPTION="Predict effect of aminoacid substitution on human protein function" HOMEPAGE="http://genetics.bwh.harvard.edu/pph2/dokuwiki/start"; -SRC_URI="http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-${PV}r405d.tar.gz"; +SRC_URI=" + http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-${PV}r405d.tar.gz + http://mafft.cbrc.jp/alignment/software/mafft-7.221-without-extensions-src.tgz + http://prdownloads.sourceforge.net/weka/weka-3-6-12.zip +" LICENSE="polyphen" # for non-commercial use only SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" + +DEPEND=" + dev-perl/CGI + sci-biology/ncbi-blast+ +" +RDEPEND="${DEPEND}" # 3.7GB # ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2 @@ -19,3 +29,27 @@ KEYWORDS="" # 895MB # ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2 + +src_unpack() { + unpack "polyphen-${PV}r405d.tar.gz" + cp "${DISTDIR}/mafft-7.221-without-extensions-src.tgz" "${S}/src" || die + cp "${DISTDIR}/weka-3-6-12.zip" "${S}/src" || die +} + +src_configure() { + # non-standard configure script + ./configure +} + +src_compile() { + pushd src + emake -j1 + popd +} + +src_install() { + pushd src + default + popd + einstalldocs +}
