diff options
| -rw-r--r-- | profiles/package.mask | 6 | ||||
| -rw-r--r-- | sci-biology/tgi-tools/ChangeLog | 31 | ||||
| -rw-r--r-- | sci-biology/tgi-tools/Manifest | 14 | ||||
| -rw-r--r-- | sci-biology/tgi-tools/metadata.xml | 11 | ||||
| -rw-r--r-- | sci-biology/tgi-tools/tgi-tools-0.1.ebuild | 51 |
5 files changed, 0 insertions, 113 deletions
diff --git a/profiles/package.mask b/profiles/package.mask index fc36b2937..2e14758c9 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -53,12 +53,6 @@ =media-tv/ati-genericv4l-2.6 =games-util/pbsetup-2.0 -# Michał Górny <mgorny.3ehbo@mailnull.com> (06 Jul 2010) -# The distfiles are unversioned and the Manifest checksums are outdated. -# Additionally, the ebuild coexists in science overlay. Masking -# for removal in 30 days. Bug #157827. -=sci-biology/tgi-tools-0.1 - # Michael Weber <gentoo@xmw.de> (20 Jun 2010) # Highly experimental new interface version =sys-power/phc-intel-0.3.199.3_pre diff --git a/sci-biology/tgi-tools/ChangeLog b/sci-biology/tgi-tools/ChangeLog deleted file mode 100644 index a145ec1bc..000000000 --- a/sci-biology/tgi-tools/ChangeLog +++ /dev/null @@ -1,31 +0,0 @@ -# ChangeLog for sci-biology/tgi-tools -# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 31 Aug 2008; Thomas Sachau (Tommy[D]) <tommy@gentoo.org> metadata.xml: - Add local useflags to metadata.xml (GLEP 56) - - 26 Oct 2007; Charlie Shepherd <masterdriverz@gentoo.org> - tgi-tools-0.1.ebuild: - Remove extraneous $S from paths in src_compile to shut up repoman. - - 12 Jul 2007; David Shakaryan <omp@gentoo.org> tgi-tools-0.1.ebuild: - Place $S in quotes. - - 15 Apr 2007; Stefan Schweizer <genstef@gentoo.org> tgi-tools-0.1.ebuild: - Remove RESTRICT=mirror, Artistic license allows redistribution - - 14 Dec 2006; Markus Ullmann <jokey@gentoo.org> tgi-tools-0.1.ebuild: - Whiteys - - 12 Dec 2006; Jakub Moc <jakub@gentoo.org> tgi-tools-0.1.ebuild: - QA: quoting, formatting, nomirror -> mirror etc. - - 12 Dec 2006; Andrei K. (azazello) <gentoo@horizon.ath.cx> - tgi-tools-0.1.ebuild: - add pvm use flag, install docs - - 12 Dec 2006; Andrei K. (azazello) <gentoo@horizon.ath.cx> - +tgi-tools-0.1.ebuild, +metadata.xml: - New ebuild, Bug 157827 - diff --git a/sci-biology/tgi-tools/Manifest b/sci-biology/tgi-tools/Manifest deleted file mode 100644 index 64925685d..000000000 --- a/sci-biology/tgi-tools/Manifest +++ /dev/null @@ -1,14 +0,0 @@ -DIST cdbfasta.tar.gz 23470 RMD160 d587deaac94eced97728b0596022ea5e6a1bc75e SHA1 c7455ad2ac92cd1ee1293f0100fd871d71e4d630 SHA256 6862061d923f49579568e62be06bf434e79dbb56dfafe573353b4eb7d8ab9c9c -DIST mdust.tar.gz 7526 RMD160 c04a6ba5a56724bfee70b8fe31f0bf4132b74885 SHA1 8885f206d61a76c6623c4115af02793bb52911c4 SHA256 9722806920fc6772dc92f99e7a59554c5f7c35b596dca0df9ed03ff2e5c6440d -DIST nrcl.tar.gz 13151 RMD160 65f2e829fcf2da0134873eaa13098995b4472e15 SHA1 a9bf20a6f0f10201a03fb51644fa64e2519abd84 SHA256 3402a3efb38e3c7320831ca07e228374bbbba34d5b8a161446a7fc0bf4397808 -DIST psx.tar.gz 7797 RMD160 2b6de75126f19cbb60e1ed0b9988a935ad021a45 SHA1 3e0ac61f9ef2e546ff571bfc269e904138b445b9 SHA256 6759f1001be93fcfca9cebd0c764088c4942f2d7feee100d10cf2fbb39e4cd5a -DIST pvmsx.tar.gz 10963 RMD160 1d14cb6e25a533f8a9879b04c5eb9e04532874e5 SHA1 562ea8628e47739ec7b98c622c894fe45e210c98 SHA256 c403534a0d13c2457a50c8ff5e9aeb5979d91a56307478b6420b5caf40e62230 -DIST sclust.tar.gz 14370 RMD160 1334a6a555c6ed3c8ad03ed697887bba76e8441e SHA1 19afe2272cb8b01e631313d57c38cd7fc575fc3c SHA256 4550350993a56d4e5e7163247965d4af91c32cc40ff7e0eeff3a0c6e04fd8ef4 -DIST seqclean.tar.gz 181383 RMD160 d3faae9e342e95dcbd66d39d80eb7e53f0527275 SHA1 8b3871cc0d70d71ff1bc7bfedc3638ff60e4c889 SHA256 4175b6ca7d93a7ea39e6dfb513500205c29a61b393a96bb2a7861a5540fd0d6d -DIST tclust.tar.gz 8864 RMD160 e77a8ce86fa779bbce7c46efbce2245ec7735681 SHA1 35793ddc161c31ce0827073e993f4f6456dbbd35 SHA256 d4f9714f56f77c0e31f0ec9cd9da374899184f40fd688b06292e40412fbb7445 -DIST tgi_cpp_library.tar.gz 58212 RMD160 a85d0e0232a3956f93e521a73075d81d5ecfaaf3 SHA1 1039291f5f0ca617d025bcfacf4f271a3a225001 SHA256 555a81a63233d725868f6179cf3f5d74cceaa040058e2e4ded20f95487c89875 -DIST trimpoly.tar.gz 12562 RMD160 7345812dbbcea3d7fd2018ba1b04254863d171a4 SHA1 3558e9663cba6e6c179ca6f9a019f95d7aa1d4db SHA256 aa8f4a47d45ee534a15edf8e325f341a72d0ce0fa659ccfd8591c15bef44da4f -DIST zmsort.tar.gz 5537 RMD160 cf6599dbd417f5ea50ec41db7909a2415ac28e68 SHA1 27a88033d99da8671fcae598f21e5b8cb7089e40 SHA256 32c5b72e22ae0fbd1784174dcff74e1a40817e29e98b2a0a32a21d83ace6b7fd -EBUILD tgi-tools-0.1.ebuild 1550 RMD160 a1a28c953031c4dccda85e16d8a193eeb132bbaf SHA1 3add5dc0d8caac1a08c176cb15fcfba8273a2aa3 SHA256 8a7e0100ad1bcc3986aab9fa94f2ad0058cb601ac253fba080207e3c94b7f1b8 -MISC ChangeLog 1074 RMD160 7c28798705aad06db6b8f229f5ff6662fc0a95bb SHA1 b35d953aa50d512d5e46264070d408c49bbf7bc1 SHA256 70a377853213bedeee10f64d578f0c2d351746900e4145846b7cb13c320bd51b -MISC metadata.xml 365 RMD160 84b7b418e77601aa884c417642c291e8c70b4523 SHA1 d419ab4faec170345a59de081ec0ec2299d7b28f SHA256 7f31aa6845152d5d7c6bb322e23d67ac3d7221cebbb2f56d1ea17132d61dfbd1 diff --git a/sci-biology/tgi-tools/metadata.xml b/sci-biology/tgi-tools/metadata.xml deleted file mode 100644 index 1ca299553..000000000 --- a/sci-biology/tgi-tools/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>no-herd</herd> - <maintainer><email>maintainer-wanted@gentoo.org</email></maintainer> - <use> - <flag name='pvm'>Use <pkg>sys-cluster/pvm</pkg> - (Parallel Virtual Machine) and build the pvmsx - utility</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/tgi-tools/tgi-tools-0.1.ebuild b/sci-biology/tgi-tools/tgi-tools-0.1.ebuild deleted file mode 100644 index 8e9b2fb37..000000000 --- a/sci-biology/tgi-tools/tgi-tools-0.1.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx" -HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" - -for i in seqclean/{seqclean,mdust,trimpoly} cdbfasta/cdbfasta tgicl/{psx,pvmsx,zmsort,tclust,sclust,nrcl,tgi_cpp_library}; do - SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz" -done - -LICENSE="Artistic" -SLOT="0" -IUSE="pvm" -KEYWORDS="~x86" - -DEPEND="pvm? ( sys-cluster/pvm )" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_unpack() { - unpack {seqclean,mdust,trimpoly,cdbfasta,tgi_cpp_library}.tar.gz - for i in nrcl sclust tclust zmsort psx pvmsx; do - mkdir "${S}"/${i} - cd "${S}"/${i} - unpack ${i}.tar.gz - done -} - -src_compile() { - sed -i 's/use Mailer;/#use Mailer;/' seqclean/seqclean - sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' zmsort/zmsort.cpp - # TODO: fix error in nrcl - for i in cdbfasta mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do - sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \ - ${i}/Makefile - cd "${S}/${i}" || die "cd ${i} failed" - emake || die "emake failed in ${i}" - done -} - -src_install() { - dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx} - for i in mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do - dobin ${i}/${i} - done - for i in cdbfasta seqclean; do - newdoc ${i}/README README.${i} - done -} |