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diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
deleted file mode 100644
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--- a/sci-biology/ncbi-tools/ChangeLog
+++ /dev/null
@@ -1,334 +0,0 @@
-# ChangeLog for sci-biology/ncbi-tools
-# Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.53 2007/06/05 11:00:49 armin76 Exp $
-
-  05 Jun 2007; Raúl Porcel <armin76@gentoo.org> ncbi-tools-20060507.ebuild:
-  alpha stable wrt #152292
-
-  10 Mar 2007; Olivier Fisette <ribosome@gentoo.org>
-  +files/ncbi-tools-extra_vib.patch:
-  Added missing patch. Thanks to Walter Meinl <wuno@lsvw.de> for reporting
-  (bug #170202).
-
-*ncbi-tools-20061015-r1 (09 Mar 2007)
-
-  09 Mar 2007; Olivier Fisette <ribosome@gentoo.org>
-  -ncbi-tools-20061015.ebuild, +ncbi-tools-20061015-r1.ebuild:
-  Install ans2all utility. Added support for compiling/installing arbitrary
-  NCBI utilities. Thanks to José María Fernández González
-  <jmfernandez@cnio.es> for his work (see bug #169822). Pruned old version.
-
-  03 Nov 2006; Olivier Fisette <ribosome@gentoo.org>
-  -ncbi-tools-20050605-r2.ebuild:
-  Pruned old version.
-
-*ncbi-tools-20061015 (03 Nov 2006)
-
-  03 Nov 2006; Olivier Fisette <ribosome@gentoo.org>
-  +ncbi-tools-20061015.ebuild:
-  New upstream version.
-
-  30 Oct 2006; Christian Faulhammer <opfer@gentoo.org>
-  ncbi-tools-20060507.ebuild:
-  stable x86 as requested in bug #152292
-
-  25 Oct 2006; Lars Weiler <pylon@gentoo.org> ncbi-tools-20060507.ebuild:
-  Stable on ppc; bug #152292.
-
-  25 Oct 2006; Fabian Groffen <grobian@gentoo.org>
-  ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild:
-  Dropped ppc-macos, see you in prefix.
-
-  24 Oct 2006; Fabian Groffen <grobian@gentoo.org>
-  ncbi-tools-20060507.ebuild:
-  Dropped ppc-macos, we don't have pmake
-
-  24 Oct 2006; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20060507.ebuild:
-  Stable on amd64.
-
-  23 Oct 2006; Markus Rothe <corsair@gentoo.org> ncbi-tools-20060507.ebuild:
-  Stable on ppc64; bug #152292
-
-  23 Oct 2006; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20060507.ebuild:
-  Stable on sparc - bug #152292
-
-  27 Jun 2006; Brent Baude <ranger@gentoo.org> ncbi-tools-20060507.ebuild:
-  Keywording ncbi-tools-20060507 ~ppc64 for bug #138082
-
-  27 Jun 2006; Olivier Fisette <ribosome@gentoo.org>
-  -files/ncbi-tools-20050605-lop.patch, +files/ncbi-tools-lop.patch,
-  ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild,
-  ncbi-tools-20060507.ebuild:
-  Fixed ppc64 lop patch (my mistake).
-
-*ncbi-tools-20060507 (26 Jun 2006)
-
-  26 Jun 2006; Olivier Fisette <ribosome@gentoo.org>
-  +files/ncbi-tools-asn2all.patch, +ncbi-tools-20060507.ebuild:
-  New upstream version. Switched from GNU make to pmake as GNU make 3.81 is
-  confused by some Makefiles (fixes bug #136904, thanks to Greg Wilson for
-  reporting). Compile and install asn2all (fixes bug #136206, thanks to José
-  María Fernández González for the suggestion). Minor bugfixes and ebuild
-  clean-up. ppc64 keyword dropped as pmake is not available for that arch.
-
-  01 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>;
-  ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild:
-  (#121066) Port to modular X. Add some die messages to -r2 so the die's
-  aren't completely unhelpful. Fix the path expansion for html docs so it
-  doesn't break the installation -- not sure how it got committed as is:
-  {*.html *.gif} is missing a comma.
-
-  21 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
-  -ncbi-tools-20050605-r1.ebuild:
-  Removed buggy version.
-
-*ncbi-tools-20050605-r2 (14 Dec 2005)
-
-  14 Dec 2005; Olivier Fisette <ribosome@gentoo.org>
-  +ncbi-tools-20050605-r2.ebuild:
-  Fixed file collisions with "dev-libs/libpcre" (bug #115463).
-
-  16 Nov 2005; Olivier Fisette <ribosome@gentoo.org>
-  ncbi-tools-20050605-r1.ebuild:
-  Readded ~sparc (closes bug #111807).
-
-  15 Nov 2005; Fernando J. Pereda <ferdy@gentoo.org>
-  ncbi-tools-20050605-r1.ebuild:
-  re-add ~alpha wrt bug #111807
-
-*ncbi-tools-20050605-r1 (15 Nov 2005)
-
-  15 Nov 2005; Olivier Fisette <ribosome@gentoo.org>
-  +ncbi-tools-20050605-r1.ebuild:
-  Added MPI support for the BLAST family of programs. Thanks to Brady
-  Catherman <bradyc@uidaho.edu> for his work (fixes bug #111807).
-
-  09 Nov 2005; Jason Wever <weeve@gentoo.org> ncbi-tools-20050605.ebuild:
-  Stable on SPARC wrt bug #108334.
-
-  22 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -files/21ncbi,
-  -ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20050429.ebuild:
-  Pruning old versions.
-
-  22 Oct 2005; Fabian Groffen <grobian@gentoo.org>
-  ncbi-tools-20050605.ebuild:
-  Marked ppc-macos per bug #108334
-
-  18 Oct 2005; Aron Griffis <agriffis@gentoo.org>
-  ncbi-tools-20050605.ebuild:
-  Mark 20050605 stable on alpha
-
-  12 Oct 2005; Michael Hanselmann <hansmi@gentoo.org>
-  ncbi-tools-20050605.ebuild:
-  Stable on ppc.
-
-  11 Oct 2005; Luis Medinas <metalgod@gentoo.org>
-  ncbi-tools-20050605.ebuild:
-  Marked Stable on amd64
-
-  09 Oct 2005; Mark Loeser <halcy0n@gentoo.org> ncbi-tools-20050605.ebuild:
-  Stable on x86
-
-  07 Oct 2005; Brent Baude <ranger@gentoo.org> ncbi-tools-20050605.ebuild:
-  Marking ncbi-tools-200506 ppc64 stable for bug 108334
-
-  19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
-  Maintainer changed from Stephen Diener (MIA) to Olivier Fisette.
-
-  16 Sep 2005; Aron Griffis <agriffis@gentoo.org>
-  ncbi-tools-20050429.ebuild:
-  Mark 20050429 stable on alpha
-
-  19 Aug 2005; Michael Hanselmann <hansmi@gentoo.org>
-  ncbi-tools-20050429.ebuild:
-  Removed from ppc (xlc not available).
-
-  09 Aug 2005; Brent Baude <ranger@gentoo.org>
-  +files/ncbi-tools-20050605-lop.patch,
-  -files/ncbi-tools-20050605-lop.patch.gz, ncbi-tools-20050605.ebuild:
-  For the ebuild ncbi-tools-20050605, I was asked to remove the gz patch and
-  submit it as plain text. This commit will remove the gz patch and replace it
-  with a plain text one. The patch name change is also reflected in the
-  ebuild.
-
-  08 Aug 2005; Brent Baude <ranger@gentoo.org>
-  +files/ncbi-tools-20050605-lop.patch.gz, ncbi-tools-20050605.ebuild:
-  Added patch for 20050506 which when ppc64, will patch the makefile to use
-  gcc instead of the default xlc (IBM compiler) which doesnt exist on gentoo.
-
-  08 Aug 2005; Brent Baude <ranger@gentoo.org> ncbi-tools-20050429.ebuild:
-  ncbi-tools-20050429.ebuild does not compile on ppc64; will fix later ebuild
-
-*ncbi-tools-20050605 (06 Aug 2005)
-
-  06 Aug 2005; Olivier Fisette <ribosome@gentoo.org>
-  -ncbi-tools-20040616.ebuild, ncbi-tools-20050429.ebuild,
-  +ncbi-tools-20050605.ebuild:
-  New version. Added 20050429 to x86. Removed old version.
-
-  09 Jun 2005; Markus Rothe <corsair@gentoo.org>
-  ncbi-tools-20041020-r1.ebuild:
-  Stable on ppc64
-
-  02 Jun 2005; Olivier Fisette <ribosome@gentoo.org> ChangeLog:
-  Use "virtual/motif" instead of "x11-libs/openmotif".
-
-  16 May 2005; Olivier Fisette <ribosome@gentoo.org>
-  ncbi-tools-20050429.ebuild:
-  Fixed CFLAGS not being applied properly (bug #92564).
-
-*ncbi-tools-20050429 (13 May 2005)
-
-  13 May 2005; Olivier Fisette <ribosome@gentoo.org>
-  +ncbi-tools-20050429.ebuild:
-  New version.
-
-  29 Apr 2005; Markus Rothe <corsair@gentoo.org>
-  ncbi-tools-20041020-r1.ebuild:
-  Added ~ppc64 to KEYWORDS
-
-  24 Apr 2005; Michael Hanselmann <hansmi@gentoo.org>
-  ncbi-tools-20041020-r1.ebuild:
-  Stable on ppc.
-
-*ncbi-tools-20041020-r1 (06 Mar 2005)
-
-  06 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +files/21ncbi-r1,
-  +ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20041020.ebuild:
-  Added the "BLASTMAT" environment variable to the env.d file.
-
-  02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> ncbi-tools-20041020.ebuild:
-  Stable ppc-macos
-
-  01 Mar 2005; Olivier Fisette <ribosome@gentoo.org>
-  ncbi-tools-20041020.ebuild:
-  Added to x86.
-
-  02 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> ncbi-tools-20040616.ebuild:
-  Stable ppc-macos
-
-  30 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
-  ncbi-tools-20041020.ebuild:
-  Ebuild cleanup.
-
-*ncbi-tools-20041020 (18 Jan 2005)
-
-  18 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
-  +ncbi-tools-20041020.ebuild:
-  New version.
-
-  02 Jan 2005; Olivier Fisette <ribosome@gentoo.org> :
-  Added to x86. Use toolchain-funcs rather than gcc eclass.
-
-  29 Dec 2004; Ciaran McCreesh <ciaranm@gentoo.org> :
-  Change encoding to UTF-8 for GLEP 31 compliance
-
-*ncbi-tools-20040616 (23 Dec 2004)
-
-  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
-  +files/21ncbi, +files/ncbirc, +ncbi-tools-20040616.ebuild:
-  Moved from app-sci/ncbi-tools to sci-biology/ncbi-tools.
-
-  30 Nov 2004; <j4rg0n@gentoo.org> ncbi-tools-20040616.ebuild:
-  Keyworded ~ppc-macos.
-
-  22 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org>
-  ncbi-tools-20040616.ebuild:
-  Added to ~amd64
-
-  14 Oct 2004; Olivier Fisette <ribosome@gentoo.org>
-  ncbi-tools-20040616.ebuild:
-  Use gcc-getCC from gcc.eclass rather than ${CC}.
-
-  04 Oct 2004; Olivier Fisette <ribosome@gentoo.org>
-  ncbi-tools-20040616.ebuild:
-  Fixed potential bug in "SRC_URI".
-
-*ncbi-tools-20040616 (03 Oct 2004)
-
-  03 Oct 2004; Olivier Fisette <ribosome@gentoo.org> files/21ncbi,
-  -files/dot-ncbirc, +files/ncbirc, -ncbi-tools-20031103.ebuild,
-  -ncbi-tools-20040202-r1.ebuild, +ncbi-tools-20040616.ebuild:
-  Updated version and new ebuild. This fixes bug #65941.
-
-  02 Jun 2004; Aron Griffis <agriffis@gentoo.org> ncbi-tools-20031103.ebuild,
-  ncbi-tools-20040202-r1.ebuild:
-  Fix use invocation
-
-  05 May 2004; Bryan Østergaard <kloeri@gentoo.org>
-  ncbi-tools-20040202-r1.ebuild:
-  Stable on alpha.
-
-  19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org>
-  ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild,
-  ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild,
-  ncbi-tools-20040202.ebuild:
-  Cleanup, removing S=... with no effect
-
-  30 Mar 2004; Donnie Berkholz <spyderous@gentoo.org>;
-  ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild,
-  ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild,
-  ncbi-tools-20040202.ebuild:
-  Change x11-base/xfree dependency to virtual/x11.
-
-  21 Mar 2004; Martin Holzer <mholzer@gentoo.org>
-  ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild,
-  ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild,
-  ncbi-tools-20040202.ebuild:
-  adding categorie. see 45110 for details
-
-*ncbi-tools-20040202-r1 (06 Feb 2004)
-
-  06 Feb 2004; Stephen Diener <sediener@gentoo.org>
-  ncbi-tools-20040202-r1.ebuild:
-  Replaced buggy tarball with new one.  Bumped revision to propogate.
-
-*ncbi-tools-20040202 (05 Feb 2004)
-
-  05 Feb 2004; Stephen Diener <sediener@gentoo.org>
-  ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003.ebuild,
-  ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild,
-  ncbi-tools-20040202.ebuild:
-  Bumped 20031103 to x86, removed old ebuilds, added new release 20040202
-
-*ncbi-tools-20040202 (04 Feb 2004)
-
-  04 Feb 2004; Stephen Diener <sediener@gentoo.org>
-  ncbi-tools-20031103.ebuild, ncbi-tools-20040202.ebuild:
-  Version bump.  Changes -O3 -> -O2 so X11 apps will work.
-
-  11 Jan 2004; Heinrich Wendel <lanius@gentoo.org>
-  ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003-r2.ebuild,
-  ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild:
-  fixed motif dep
-
-*ncbi-tools-20031103 (13 Dec 2003)
-
-  13 Dec 2003; Stephen Diener <sediener@gentoo.org>
-  ncbi-tools-20031103.ebuild:
-  Added november release of ncbi-tools (blast-2.2.6 included);
-  Added support for -X
-
-*ncbi-tools-20030422 (11 Nov 2003)
-
-  11 Nov 2003; <sediener@gentoo.org> ncbi-tools-20030422.ebuild:
-  added bl2seq to list of installed binaries; changed date format from 04222003
-  to 20030422; renamed files to have date appended to not collide and changed
-  SRC_URI to mirror://gentoo/
-
-*ncbi-tools-04222003-r2 (08 Oct 2003)
-
-  08 Oct 2003; Robin H. Johnson <robbat2@gentoo.org>
-  ncbi-tools-04222003-r2.ebuild:
-  modified patch from #30656, corrected two pathes in the postinst message
-
-*ncbi-tools-04222003-r1 (05 May 2003)
-
-  05 May 2003; Jon Portnoy <avenj@gentoo.org> ncbi-tools-04222003-r1.ebuild :
-  A few enhancements from Gontran Zepeda <gontran@gontran.net>.
-
-*ncbi-tools-04222003 (03 May 2003)
-
-  03 May 2003; Jon Portnoy <avenj@gentoo.org> ncbi-tools-04222003 :
-  Initial important. Ebuild submitted by Steve Diener 
-  <sediener@unity.ncsu.edu>.
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
deleted file mode 100644
index 58ff038..0000000
--- a/sci-biology/ncbi-tools/Manifest
+++ /dev/null
@@ -1,38 +0,0 @@
-AUX 21ncbi-r1 232 RMD160 ba65fe937c9a29f4cc185d99db18522343bbb28b SHA1 5674f379f7a70e71394bca272fedd72a1622a7da SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411
-MD5 a5f54430f6f7422d75320e91068cae0b files/21ncbi-r1 232
-RMD160 ba65fe937c9a29f4cc185d99db18522343bbb28b files/21ncbi-r1 232
-SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411 files/21ncbi-r1 232
-AUX ncbi-tools-asn2all.patch 1190 RMD160 3aaccc677bd8b9bad6c6424f5080c71cdac553d7 SHA1 ae22c77cfcd7d416a89ea3fe1e0331264473669d SHA256 e2fd71fdaa07b9e1c9cf646b2d3aa02c2ec822d41dcd45cadfced4164f458bed
-MD5 b89cb833887b3e3efda83d074b4b8edb files/ncbi-tools-asn2all.patch 1190
-RMD160 3aaccc677bd8b9bad6c6424f5080c71cdac553d7 files/ncbi-tools-asn2all.patch 1190
-SHA256 e2fd71fdaa07b9e1c9cf646b2d3aa02c2ec822d41dcd45cadfced4164f458bed files/ncbi-tools-asn2all.patch 1190
-AUX ncbi-tools-extra_vib.patch 1393 RMD160 05e2dcf17b6af9475625eb0aa0be6bc96071a923 SHA1 bb92aeada6786d4573f9ad98e3d50b4a4201ba10 SHA256 b7639937d59c8bd636c6b02a65a4469d188645b9a10fffd0c8680fb861a7a8e1
-MD5 81e003b746faf22d3f1b1df37ffdcf41 files/ncbi-tools-extra_vib.patch 1393
-RMD160 05e2dcf17b6af9475625eb0aa0be6bc96071a923 files/ncbi-tools-extra_vib.patch 1393
-SHA256 b7639937d59c8bd636c6b02a65a4469d188645b9a10fffd0c8680fb861a7a8e1 files/ncbi-tools-extra_vib.patch 1393
-AUX ncbi-tools-lop.patch 701 RMD160 1b9d8d196b1d4f27b090e616c9ac03cb9b4e6a09 SHA1 be28d340be72b9840342b407d95dc2a558e39de9 SHA256 9e5c57e944d23920f196f36912933653c236998729f69f28be8b55964865dfbc
-MD5 6b62beda180ee6d7d4d4a52507acc3ff files/ncbi-tools-lop.patch 701
-RMD160 1b9d8d196b1d4f27b090e616c9ac03cb9b4e6a09 files/ncbi-tools-lop.patch 701
-SHA256 9e5c57e944d23920f196f36912933653c236998729f69f28be8b55964865dfbc files/ncbi-tools-lop.patch 701
-AUX ncbirc 33 RMD160 3bfa36288b608b4e29252ad1972bb8c06cded3e1 SHA1 eb14976d464f4fa0e14085c8dd58886b0c684a56 SHA256 8687909c83658049cbad656b6d99c8e6143365286e2fa981fbdddc87b178ab8e
-MD5 23986a001c85eb8c2c319aacfa9cb40c files/ncbirc 33
-RMD160 3bfa36288b608b4e29252ad1972bb8c06cded3e1 files/ncbirc 33
-SHA256 8687909c83658049cbad656b6d99c8e6143365286e2fa981fbdddc87b178ab8e files/ncbirc 33
-DIST mpiblast-20060625.tar.gz 165096 RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 SHA1 e0acdde2770973b752396a6ba1a99b47ea4ddcde SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097
-DIST ncbi-tools-20070826.tar.gz 17076175 RMD160 00daadd503bf729c15ada0008e305492a076fe15 SHA1 5e61f4f73ef52d145d0df86bb00f03f2db833ee9 SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8
-DIST ncbi-tools-sdk-doc.tar.bz2 263568 RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b SHA1 6fd259b1fc75684db43bd817fc4720e92f56e81c SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2
-EBUILD ncbi-tools-20070826.ebuild 6379 RMD160 a1bdac06154ed9ced4a70231470487c491b504a8 SHA1 dd57b5279a538aa5b843f50ed09ebfcfaa4f1eb2 SHA256 846d90c089f5496d524ae814b6d4e553c989f9c215c3d3cf7163314d33ed3a4f
-MD5 07e2b6278efd8b172d9827478646d10f ncbi-tools-20070826.ebuild 6379
-RMD160 a1bdac06154ed9ced4a70231470487c491b504a8 ncbi-tools-20070826.ebuild 6379
-SHA256 846d90c089f5496d524ae814b6d4e553c989f9c215c3d3cf7163314d33ed3a4f ncbi-tools-20070826.ebuild 6379
-MISC ChangeLog 12046 RMD160 f5da07dae177d685279cfc8cb1e808195a324d59 SHA1 2c500e98f4078d01e7e07bb5fbec1b9969b54947 SHA256 9c61bf118f77126decdf8f68383fd4581488e411c23e51e9543487412d5754a2
-MD5 84765ef98775eb5a866921708cff3f5e ChangeLog 12046
-RMD160 f5da07dae177d685279cfc8cb1e808195a324d59 ChangeLog 12046
-SHA256 9c61bf118f77126decdf8f68383fd4581488e411c23e51e9543487412d5754a2 ChangeLog 12046
-MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
-MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262
-RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262
-SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f metadata.xml 262
-MD5 03f6be617d48b4f2a475c697390a2a99 files/digest-ncbi-tools-20070826 706
-RMD160 50e74fe0a0f4174a503bc4deed45c3527326bf0d files/digest-ncbi-tools-20070826 706
-SHA256 61f6572f086b8f5fb0728a44d49814b6fb003579b173e88d7da077ebd8ac27ae files/digest-ncbi-tools-20070826 706
diff --git a/sci-biology/ncbi-tools/files/21ncbi-r1 b/sci-biology/ncbi-tools/files/21ncbi-r1
deleted file mode 100644
index d4de68e..0000000
--- a/sci-biology/ncbi-tools/files/21ncbi-r1
+++ /dev/null
@@ -1,6 +0,0 @@
-# Location of the formatdb data sets
-BLASTDB="/usr/share/ncbi/formatdb"
-# Location of the BLAST matrixes.
-BLASTMAT="/usr/share/ncbi/data"
-# Location of the ".ncbi.rc" file which sets the default path for shared data.
-NCBI=/etc/ncbi
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1
deleted file mode 100644
index a80231e..0000000
--- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1
+++ /dev/null
@@ -1,8 +0,0 @@
-MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096
-RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096
-SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096
-MD5 8eca84753fd7a1d39bab256a4944f65e ncbi-tools-20061015.tar.gz 15772715
-RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 ncbi-tools-20061015.tar.gz 15772715
-SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de ncbi-tools-20061015.tar.gz 15772715
-RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568
-SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826
deleted file mode 100644
index 3c82f07..0000000
--- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826
+++ /dev/null
@@ -1,8 +0,0 @@
-MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096
-RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096
-SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096
-MD5 c17f7b08c12823e4320661894110dcb1 ncbi-tools-20070826.tar.gz 17076175
-RMD160 00daadd503bf729c15ada0008e305492a076fe15 ncbi-tools-20070826.tar.gz 17076175
-SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8 ncbi-tools-20070826.tar.gz 17076175
-RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568
-SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch
deleted file mode 100644
index 1cd7976..0000000
--- a/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- ncbi-20050605/make/makedis.csh	2005-05-13 05:42:12.000000000 +0200
-+++ ncbi/make/makedis.csh	2005-09-20 22:02:38.000000000 +0200
-@@ -472,6 +472,24 @@
- 
- set net_stat = $status
- 
-+if ("$?NCBI_MT_OTHERLIBS" == "1") then
-+	set CMD='make $MFLG -f makenet.unx \
-+		CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
-+		LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
-+		AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
-+		THREAD_OBJ=$NCBI_THREAD_OBJ \
-+		THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
-+		NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all'
-+else
-+	set CMD='make $MFLG -f makenet.unx \
-+		CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
-+		LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
-+		AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
-+		NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all'
-+endif
-+eval echo $CMD
-+eval echo $CMD | sh 
-+
- if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then
-    echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat
- 	cat <<EOF
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch
deleted file mode 100644
index cb7d1ad..0000000
--- a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- ncbi-20061015/make/makedis.csh	2006-09-14 17:37:03.000000000 +0200
-+++ ncbi/make/makedis.csh	2007-03-07 21:00:36.090836460 +0100
-@@ -485,6 +485,34 @@
- 
- set net_stat = $status
- 
-+if ( $net_stat == 0 ) then
-+	# Compile additional tools, usually hidden
-+	if ( ! $?EXTRA_VIB ) then
-+		set EXTRA_VIB = ( asn2all )
-+	endif
-+	
-+	if ("$?NCBI_MT_OTHERLIBS" == "1") then
-+		set CMD='make $MFLG -f makenet.unx \
-+			CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
-+			LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
-+			AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
-+			THREAD_OBJ=$NCBI_THREAD_OBJ \
-+			THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
-+			NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB'
-+	else
-+		set CMD='make $MFLG -f makenet.unx \
-+			CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
-+			LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
-+			AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
-+			NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB'
-+	endif
-+	eval echo $CMD
-+	eval echo $CMD | sh
-+	
-+	set net_stat = $status
-+	
-+endif
-+
- if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then
-    echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat
- 	cat <<EOF
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch
deleted file mode 100644
index 867b203..0000000
--- a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- platform/linux-power.ncbi.mk.bak	2005-08-04 22:45:13.000000000 -0500
-+++ platform/linux-power.ncbi.mk	2005-08-04 22:45:35.000000000 -0500
-@@ -9,10 +9,10 @@
- #it appears the flags above do not work anymore with newer libc,
- #the new flags should work. Dima. 08/23/01
- NCBI_AR=ar
--NCBI_CC = xlc_r -w -qcpluscmt -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-+NCBI_CC = gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
- NCBI_CFLAGS1 = -c 
- NCBI_LDFLAGS1 = -O3 -D_LARGE_FILES 
--NCBI_OPTFLAG = -O3 -qmaxmem=-1 -D_LARGE_FILE
-+NCBI_OPTFLAG = -O3  -D_LARGE_FILE
- NCBI_BIN_MASTER = /vol/stcfs/rchen/LoP/ncbi/bin
- NCBI_BIN_COPY = /vol/stcfs/rchen/LoP/ncbi/bin
- NCBI_INCDIR = /vol/stcfs/rchen/LoP/ncbi/include
diff --git a/sci-biology/ncbi-tools/files/ncbirc b/sci-biology/ncbi-tools/files/ncbirc
deleted file mode 100644
index 625dc6a..0000000
--- a/sci-biology/ncbi-tools/files/ncbirc
+++ /dev/null
@@ -1,2 +0,0 @@
-[NCBI]
-Data=/usr/share/ncbi/data
diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml
deleted file mode 100644
index ebbff81..0000000
--- a/sci-biology/ncbi-tools/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>ribosome@gentoo.org</email>
-		<name>Olivier Fisette</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-</pkgmetadata>
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild
deleted file mode 100644
index e60875c..0000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild
+++ /dev/null
@@ -1,200 +0,0 @@
-# Copyright 1999-2007 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit flag-o-matic toolchain-funcs eutils autotools
-
-DESCRIPTION="Development toolkit and applications for computational biology"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-SRC_URI="mirror://gentoo/${P}.tar.gz
-	doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )
-	mpi? ( mirror://gentoo/mpiblast-20060625.tar.gz )"
-
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
-IUSE="doc mpi X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	sys-devel/pmake
-	mpi? ( virtual/mpi )
-	X? ( virtual/motif )"
-
-S="${WORKDIR}/ncbi"
-
-EXTRA_VIB="asn2all asn2asn"
-
-pkg_setup() {
-	echo
-	ewarn 'Please note that the NCBI toolkit (and especially the X'
-	ewarn 'applications) are known to have compilation and run-time'
-	ewarn 'problems when compiled with agressive compilation flags. The'
-	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
-	ewarn 'X support is enabled.'
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${PN}-extra_vib.patch
-
-	if use ppc64; then
-		epatch "${FILESDIR}"/${PN}-lop.patch
-	fi
-
-	if use mpi; then
-		cd "${WORKDIR}"
-		epatch "${WORKDIR}"/mpiblast/ncbi_Dec2005_evalue.patch
-	fi
-
-	if ! use X; then
-		cd "${S}"/make
-		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
-			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
-			-i makedis.csh || die
-	else
-		if use x86; then
-			# X applications segfault on startup on x86 with -O3.
-			replace-flags '-O3' '-O2'
-		fi
-	fi
-
-	# Apply user C flags...
-	cd "${S}"/platform
-	# ... on x86...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \
-		-i linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i ppclinux.ncbi.mk || die
-	# ... on generic Linux.
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux.ncbi.mk || die
-
-	# Put in our MAKEOPTS (doesn't work).
-	# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh
-
-	# Set C compiler...
-	# ... on x86...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die
-	# ... on generic Linux.
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-
-	# GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake
-	# instead. The right solution would be to fix the Makefiles. (Be my guest.)
-	cd "${S}"/make
-	sed -i -e "s%CMD='make%CMD='/usr/bin/pmake%" makedis.csh || die \
-			"Failed to replace make by pmake."
-}
-
-src_compile() {
-	export EXTRA_VIB
-	cd "${WORKDIR}"
-	ncbi/make/makedis.csh || die
-	mkdir "${S}"/cgi
-	mkdir "${S}"/real
-	mv "${S}"/bin/*.cgi "${S}"/cgi || die
-	mv "${S}"/bin/*.REAL "${S}"/real || die
-
-	if use mpi; then
-		cd "${WORKDIR}"/mpiblast
-		AM_OPT="-a"
-		eautoreconf
-		econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die
-		emake || die
-	fi
-}
-
-src_install() {
-	dobin "${S}"/bin/* || die "Failed to install binaries."
-	for i in ${EXTRA_VIB}; do
-		dobin "${S}"/build/${i} || die "Failed to install binaries."
-	done
-	dolib "${S}"/lib/* || die "Failed to install libraries."
-	mkdir -p "${D}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
-		die "Failed to install headers."
-
-	if use mpi; then
-		cd "${WORKDIR}"/mpiblast
-		make install DESTDIR="${D}" || die "Failed to install MPI blast."
-	fi
-
-	# TODO: Web apps
-	#insinto /usr/share/ncbi/lib/cgi
-	#doins ${S}/cgi/*
-	#insinto /usr/share/ncbi/lib/real
-	#doins ${S}/real/*
-	# TODO: Add support for wwwblast.
-
-	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || \
-		die "Failed to install basic documentation."
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \
-		die "Failed renaming fa2htgs documentation."
-	newdoc "${S}"/config/README README.config || \
-		die "Failed renaming config documentation."
-	newdoc "${S}"/network/encrypt/README README.encrypt || \
-		die "Failed renaming encrypt documentation."
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib || \
-	die "Failed renaming nsclilib documentation."
-	newdoc "${S}"/sequin/README README.sequin || \
-		die "Failed renaming sequin documentation."
-	doman "${S}"/doc/man/* || \
-		die "Failed to install man pages."
-
-	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \
-		die "Failed to install HTML documentation."
-	insinto /usr/share/doc/${PF}/html/blast
-	doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
-	# Developer documentation
-	if use doc; then
-		# Hypertext SDK documentation
-		insinto /usr/share/doc/${PF}/html/sdk
-		doins "${WORKDIR}"/${PN}-sdk-doc/* || die
-
-		# Demo programs
-		mkdir "${D}"/usr/share/ncbi
-		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi/data
-	doins "${S}"/data/* || die "Failed to install shared data."
-	dodir /usr/share/ncbi/formatdb || die
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file."
-
-	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
-}