commit: fdcbbfa6d96ef8d4eb5a39bc6366bba3a9a743f1 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Mon Jan 18 13:10:38 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Mon Jan 18 13:12:58 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdcbbfa6
sci-biology/twinscan: re-add, found the download link Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 69 +++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild new file mode 100644 index 000000000..6b9a5f57c --- /dev/null +++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit perl-module toolchain-funcs + +DESCRIPTION="iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure pred. pipeline" +HOMEPAGE="https://mblab.wustl.edu/software.html"; +#SRC_URI="https://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz" +# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’: +# Unable to locally verify the issuer's authority. +# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'. +RESTRICT="fetch" +SRC_URI="iscan-4.1.2.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND="dev-libs/glib:2" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/N-SCAN" +RESTRICT="test" + +src_prepare() { + default + sed "1 a use lib '/usr/share/${PN}/lib/perl5';" -i "${S}"/bin/*.pl || die + sed '/my $blast_param/ s/#//' -i "${S}/bin/runTwinscan2.pl" || die + tc-export CC AR RANLIB + + sed \ + -e 's:ar :$(AR) :g' \ + -e 's:ranlib :$(RANLIB) :g' \ + -e 's: -o : $(LDFLAGS) -o :g' \ + -i Makefile || die + + sed \ + -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \ + -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0) -DHAS_GLIB:g" \ + -i Makefile.include || die +} + +src_install() { + # TODO: prevent file collision with media-gfx/iscan by renaming iscan to iscan_twinscan + # also fix a Genscan++ToZoe.pl Nscan_driver.pl runTwinscan2.pl run_iscan.pl run_iscan_cons.pl run_iscan_cons_list.pl test.pl + rm src/test.pl || die + dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl + dolib.so lib/libzoe.a + insinto /usr/share/${PN} + doins -r parameters + insinto /usr/share/${PN}/src + doins src/*.zhmm + perl_set_version + insinto ${VENDOR_LIB}/${PN} + doins lib/perl5/*.pm + echo "TWINSCAN=/usr" > "${S}"/99${PN} + doenvd "${S}"/99${PN} + rm -rf examples/tmp + dodoc examples/* README* src/doc/*.txt +} + +pkg_postinst(){ + einfo "Pairagon acts on output from either: sci-biology/gmap sci-biology/blat." + einfo "It also works on blastn output from WU-BLAST (not provided in Gentoo)." + einfo "It also calls blastz (seems superseded by LASTZ) and genscan++ (not provided in Gentoo)." + einfo "For some reason we have pslCDnaFilter provided only by sci-biology/ucsc-genome-browser" +}
