commit: ceed30c6026675c078281eb668ef28bedbbd0999 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Jan 19 12:17:16 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Jan 19 12:17:16 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ceed30c6
sci-biology/manatee-igs: EAPI bump, fix fetch, use https Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 27 ++++++----------------- 1 file changed, 7 insertions(+), 20 deletions(-) diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild index 65dda0367..8a21f8f36 100644 --- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild +++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild @@ -1,18 +1,15 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema" HOMEPAGE="http://manatee.sourceforge.net/igs"; # no https -SRC_URI=" - https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz - http://manatee.sourceforge.net/igs/docs/README_Linux.txt"; +SRC_URI="https://downloads.sourceforge.net/project/manatee/igs_manatee/${PV}/manatee-${PV}_linux.tgz"; LICENSE="Artistic-Manatee" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" DEPEND=" >=dev-libs/expat-1.95.8 @@ -45,26 +42,16 @@ RDEPEND="${DEPEND} >=virtual/mysql-5:* >=www-servers/apache-2.2" -S="${WORKDIR}"/manatee-"${PV}"_linux +S="${WORKDIR}/manatee-${PV}_linux" src_prepare(){ + default find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done } -#src_configure(){ -# there used to be manateee-="${PV}".tgz file which contained configure script in the past -# now the layout is different, temporarily commenting out untill we find the current full sources back again -# econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld || die -#} -# -#src_compile(){ -# default -#} - src_install(){ - dodoc ${DISTDIR}"/README_Linux.txt" dodir /var/www/localhost/cgi-bin cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin dodir /var/www/localhost/htdocs/manatee @@ -72,7 +59,7 @@ src_install(){ einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database" - einfo "You have to fetch the 1.1 GB large file from http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"; + einfo "You have to fetch the 1.1 GB large file from https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"; einfo "You need to update it regularly." - einfo "Also fetch http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)" + einfo "Also fetch https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)" }
