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Gentoo's Bugzilla – Attachment 177109 Details for
Bug 253451
[new ebuild] sci-biology/consed-19
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consed-bin-20080723.ebuild
consed-bin-20080723.ebuild (text/plain), 3.66 KB, created by
Martin Mokrejš
on 2009-01-02 15:18:13 UTC
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Description:
consed-bin-20080723.ebuild
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Creator:
Martin Mokrejš
Created:
2009-01-02 15:18:13 UTC
Size:
3.66 KB
patch
obsolete
># Copyright 1999-2008 Gentoo Foundation ># Distributed under the terms of the GNU General Public License v2 ># $Header: $ > >DESCRIPTION="Consed: a genome sequence finishing X11 program (editor, autofinish, autoreport, >autoedit, and align reads to reference sequence)" >HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" > ># FIXME: change the SRC_URI based on the ARCH ># available files: ># consed_linux32bit.tar.Z ># consed_linux64bit.tar.Z ># consed_linux_itanium.tar.Z >SRC_URI="consed_linux32bit.tar.Z" > ># this is the sourcecode of consed apllication but no other tools are here ># SRC_URI="sources.tar.Z" > >LICENSE="phrap" >SLOT="0" >KEYWORDS="~x86 ~amd64" >IUSE="" > >DEPEND="" >RDEPEND="dev-lang/perl > >=sci-biology/phrap-1.080721 > >=sci-biology/phd2fasta-0.990622" > >S="${WORKDIR}" > >RESTRICT="fetch" > >pkg_nofetch() { > einfo "Please visit http://bozeman.mbt.washington.edu/consed/consed.html and obtain the file" > # einfo '"sources.tar.Z", and put it in' > einfo "consed_linux32bit.tar.Z or consed_linux64bit.tar.Z or" > einfo "consed_linux_itanium.tar.Z and optionally also sources.tar.Z put it in ${DISTDIR}" > einfo "The sources.tar.Z is at the moment not utilized by this ebuild as" > einfo "they lack some header file new.h" > einfo > einfo "In addition, you may download from your registered IP address also fixes from" > einfo "http://bozeman.mbt.washington.edu/consed/distributions/17.0/current_beta/phredPhrap" > einfo "and additional tools from" > einfo "http://bozeman.mbt.washington.edu/consed/distributions/17.0/current_beta/filter454Reads.perl" > einfo "http://bozeman.mbt.washington.edu/consed/distributions/17.0/current_beta/add454Reads.perl" > einfo "and the ebuild will place them into scripts/" > > einfo "There will be two consed* binaries installed. One statically linked" > einfo "and one dynamically linked against libstdc++-libc6.2-2.so.3 from" > einfo "authors. Finally, a soflink to the static binary will be created" > einfo "in your installation layout as /usr/bin/consed" >} > >src_compile() { > cd scripts > # zap the following three lines from the perl file phredPhrap and insert one > # pointing to a Gentoo place in /usr/share/phred/phredpar.dat > #$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat"; > ##$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat"; > ##$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat"; > ln -s phredPhrap polyphredPhrap > > pwd > cd .. > > #FIXME: cannot compile anyway because new.h is missing > einfo "Please test whether -DX86_GCC_LINUX works also on amd64 platforms, probably yes" > einfo "but how about other targets?" > > #FIXME: propagate $CFLAGS into the Makefile > # sed -i 's/#LXFLAGS= -DX86_GCC_LINUX/LXFLAGS= -DX86_GCC_LINUX/' Makefile > # make -f makefile_linux32bit || die "make -f makefile_linux32bit failed" > > # compile additional utilites > cd misc > > # co not overwrite /usr/bin/phd2fasta as user should install the updated > # version distributed always separately sci-biology/phd2fasta-20080822 > # cd phd2fasta > # make > # cd .. > > cd mktrace/ > make > cd .. > > cd 454/ > gcc sff2phdball.c -o sff2phdball > gcc sff2scf.c -o sff2scf > cd ../ >} > >src_install() { > ln -s consed_linux32bit consed > newenvd "${FILESDIR}"/consed 21consed|| die "Failed to install env file." > > dobin consed consed_linux32bit consed_linux32bit_dyn misc/454/sff2phdball misc/454/sff2scf misc/mktrace/mktrace scripts/phredPhrap scripts/polyphredPhrap scripts/*.perl contributions/*.perl > for i in {README,17.0_announcement}.txt ; do > dodoc ${i} > done > dodir /usr/share/consed-bin/examples > insinto /usr/share/consed-bin/examples > doins -r standard polyphred autofinish assembly_view 454_newbler align454reads align454reads_answer solexa_example solexa_example_answer selectRegions selectRegionsAnswer >}
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