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-rw-r--r--sci-biology/meme/Manifest20
-rw-r--r--sci-biology/meme/files/digest-meme-3.5.43
-rw-r--r--sci-biology/meme/files/meme-3.5.4-Makefile.am.patch17
-rw-r--r--sci-biology/meme/files/meme-3.5.4-patch1.patch198
-rw-r--r--sci-biology/meme/files/meme-3.5.4-patch2.patch70
-rw-r--r--sci-biology/meme/meme-3.5.4.ebuild88
6 files changed, 0 insertions, 396 deletions
diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
deleted file mode 100644
index 5640059..0000000
--- a/sci-biology/meme/Manifest
+++ /dev/null
@@ -1,20 +0,0 @@
-AUX meme-3.5.4-Makefile.am.patch 377 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad SHA1 96530d5a58b8c01c99ae2b5463b7448758d7fb3d SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8
-MD5 1340a30b4b010637181605a11e78a950 files/meme-3.5.4-Makefile.am.patch 377
-RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad files/meme-3.5.4-Makefile.am.patch 377
-SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8 files/meme-3.5.4-Makefile.am.patch 377
-AUX meme-3.5.4-patch1.patch 7443 RMD160 6d72e74d6139d8c29bfcda9da750dc454f08ef0a SHA1 336c91ad5ecd44d49de0e940bb18315b62569a2b SHA256 306cee9c3c831494cf264ded84d248e5773c9a56d259a02e8da9c6dc31457f04
-MD5 651579784b229f2fa7f566c5c655f562 files/meme-3.5.4-patch1.patch 7443
-RMD160 6d72e74d6139d8c29bfcda9da750dc454f08ef0a files/meme-3.5.4-patch1.patch 7443
-SHA256 306cee9c3c831494cf264ded84d248e5773c9a56d259a02e8da9c6dc31457f04 files/meme-3.5.4-patch1.patch 7443
-AUX meme-3.5.4-patch2.patch 2074 RMD160 56520122dd1d35afa444414ea57199924e8492b5 SHA1 29edf295100721006aea8b76ff4c5bdfb9312020 SHA256 bf74f09bcd6c247f464f15b17e3a0e8f95149fdc5b92d8f17d06ede430d2d7be
-MD5 9489e7cf0052442d5d1413e9e26b5b65 files/meme-3.5.4-patch2.patch 2074
-RMD160 56520122dd1d35afa444414ea57199924e8492b5 files/meme-3.5.4-patch2.patch 2074
-SHA256 bf74f09bcd6c247f464f15b17e3a0e8f95149fdc5b92d8f17d06ede430d2d7be files/meme-3.5.4-patch2.patch 2074
-DIST meme_3.5.4.tar.gz 1045501 RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 SHA1 d780dba0b900f840a599cf69cfeba4eefd4856b4 SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86
-EBUILD meme-3.5.4.ebuild 2863 RMD160 215da45e76c62eee3f44936ad9356e9625de6525 SHA1 c2a8424babf69e0109933ab8c799220931e77918 SHA256 f17c56140553a39f15ffeb3ceee750484281091a0d382998be95f729620a08a3
-MD5 e25f01559dd2b100758d7395ca82de71 meme-3.5.4.ebuild 2863
-RMD160 215da45e76c62eee3f44936ad9356e9625de6525 meme-3.5.4.ebuild 2863
-SHA256 f17c56140553a39f15ffeb3ceee750484281091a0d382998be95f729620a08a3 meme-3.5.4.ebuild 2863
-MD5 1eaad7de1310f43b70c0414c120687f6 files/digest-meme-3.5.4 235
-RMD160 ed97244306a01084ca6973c50c49726724212632 files/digest-meme-3.5.4 235
-SHA256 98b3e51f5544aa86ee4cfed70da0b3d9068cd677c3744e750b4f0bee2be5be8b files/digest-meme-3.5.4 235
diff --git a/sci-biology/meme/files/digest-meme-3.5.4 b/sci-biology/meme/files/digest-meme-3.5.4
deleted file mode 100644
index 01fad30..0000000
--- a/sci-biology/meme/files/digest-meme-3.5.4
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 9a8b3d21c6094616cc7b9b424352c697 meme_3.5.4.tar.gz 1045501
-RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 meme_3.5.4.tar.gz 1045501
-SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86 meme_3.5.4.tar.gz 1045501
diff --git a/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch
deleted file mode 100644
index 1293de0..0000000
--- a/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- Makefile.am.old 2007-04-24 10:36:50.000000000 -0400
-+++ Makefile.am 2007-04-24 10:37:37.000000000 -0400
-@@ -57,11 +57,11 @@
- endif
-
- dbdir:
-- mkdir -p $(MEME_DB)
-+ mkdir -p $(DESTDIR)$(MEME_DB)
-
- install-data-local:
-- mkdir -p $(MEME_LOGS)
-- chmod a+w $(MEME_LOGS)
-+ mkdir -p $(DESTDIR)$(MEME_LOGS)
-+ chmod a+w $(DESTDIR)$(MEME_LOGS)
-
- distdir = $(PACKAGE)_$(VERSION)
-
diff --git a/sci-biology/meme/files/meme-3.5.4-patch1.patch b/sci-biology/meme/files/meme-3.5.4-patch1.patch
deleted file mode 100644
index b072d7e..0000000
--- a/sci-biology/meme/files/meme-3.5.4-patch1.patch
+++ /dev/null
@@ -1,198 +0,0 @@
---- meme_3.5.4/website/cgi-bin/process_request.pl 2006-09-21 19:46:29.000000000 +0000
-+++ trunk/website/cgi-bin/process_request.pl 2007-05-30 01:35:02.000000000 +0000
-@@ -1,6 +1,6 @@
- #!@WHICHPERL@
- ##
--## $Id: process_request.pl 1339 2006-09-21 19:46:28Z tbailey $
-+## $Id: process_request.pl 1807 2007-05-30 01:34:31Z tbailey $
- ##
- ## $Log: process_request.pl,v $
- ## Revision 1.6.6.1 2006/02/16 23:22:35 nadya
-@@ -55,7 +55,8 @@
- $blocks_url = "http://blocks.fhcrc.org/blocks-bin/process_blocks.pl";
- #
- # You can change this if you wish to use a different JASPAR server
--$jaspar_root = "http://mordor.cgb.ki.se";
-+#$jaspar_root = "http://mordor.cgb.ki.se";
-+$jaspar_root = "http://asp.ii.uib.no:8090";
- $jaspar_url = "$jaspar_root/cgi-bin/jaspar2005/jaspar_db.pl";
- #
- # You can change this if you wish to use a different Meta-MEME server
-@@ -221,7 +222,7 @@
-
- $fasta = ""; # return value
- @lines = split(/\n/, $block); # split block into lines
-- for ($i = 1; $i<$#lines; $i++) {
-+ for ($i = 2; $i<$#lines; $i++) {
- last if $lines[$i] =~ /^\/\//;
- @words = split(/\s+/, $lines[$i]); # split line into words
- # get sequence line
-@@ -239,7 +240,7 @@
-
- $fasta = ""; # return value
- @lines = split(/\n/, $block); # split block into lines
-- for ($i = 1; $i<$#lines; $i++) {
-+ for ($i = 2; $i<$#lines; $i++) {
- last if $lines[$i] =~ /^\/\//;
- @words = split(/\s+/, $lines[$i]); # split line into words
- # get id line and sequence line
-@@ -311,7 +312,8 @@
- $content = $request->content;
-
- # fix bug in JASPAR output; add database field to view buttons
-- $content =~ s/rm=present/rm=present&db=$sub_db/g;
-+ # remove fix: JASPAR fixed the bug
-+ # $content =~ s/rm=present/rm=present&db=$sub_db/g;
-
- # display the page
- print $content;
---- meme_3.5.4/src/ureadseq.c 2006-09-21 19:46:28.000000000 +0000
-+++ trunk/src/ureadseq.c 2007-05-18 08:18:05.000000000 +0000
-@@ -1,5 +1,5 @@
- /*
-- * $Id: ureadseq.c 1339 2006-09-21 19:46:28Z tbailey $
-+ * $Id: ureadseq.c 1787 2007-05-18 08:17:28Z tbailey $
- *
- * $Log$
- * Revision 1.2 2006/03/08 20:50:11 nadya
-@@ -206,10 +206,9 @@
-
- Local void addinfo(char *s, struct ReadSeqVars *V)
- {
-- char s2[256], *si;
-+ char *si = (char *) malloc((strlen(s) + 40) * sizeof(char));
- boolean saveadd;
-
-- si = s2;
- while (*s == ' ') s++;
- sprintf(si, " %d) %s\n", V->nseq, s);
-
-@@ -217,6 +216,7 @@
- V->addit = true;
- V->isseqchar = isAnyChar;
- addseq( si, V);
-+ free(si);
- V->addit = saveadd;
- V->isseqchar = isSeqChar;
- }
-@@ -966,7 +966,6 @@
- } while ((l == 0) && !feof(V->f));
-
- if (feof(V->f)) V->err = eNoData;
--
- else switch (format_) {
- case kPlain : readPlain(V); break;
- case kIG : readIG(V); break;
-@@ -1181,7 +1180,7 @@
- int nlines= 0, k=0, splen= 0, otherlines= 0, aminolines= 0, dnalines= 0;
- char sp[MAXLINE];
- long linestart=0;
-- int maxlines2check=500;
-+ int maxlines2check=5000;
-
- #define ReadOneLine(sp) \
- { done |= (feof(fseq)); \
---- meme_3.5.4/src/include/ureadseq.h 2006-09-21 19:46:28.000000000 +0000
-+++ trunk/src/ureadseq.h 2007-05-18 08:18:05.000000000 +0000
-@@ -1,5 +1,5 @@
- /*
-- * $Id: ureadseq.h 1339 2006-09-21 19:46:28Z tbailey $
-+ * $Id: ureadseq.h 1048 2006-07-06 20:07:44Z cegrant $
- *
- * $Log$
- * Revision 1.1 2005/07/29 19:12:07 nadya
-@@ -15,7 +15,7 @@
- #include "config.h"
- #include "macros.h"
-
--#define MAXLINE 1024
-+#define MAXLINE 10240
-
- typedef char boolean;
- #define NEWLINE '\n'
---- meme_3.5.4/src/read_seq_file.c 2006-09-21 19:46:28.000000000 +0000
-+++ ./read_seq_file.c 2007-05-18 06:51:06.000000000 +0000
-@@ -433,6 +433,7 @@
- name[i++] = c; /* non-blank: add to name */
- }
- }
-+ Resize(name, i+1, char);
- name[i] = '\0';
-
- /* read in description */
---- meme_3.5.4/website/html/meme-install.html 2006-09-21 19:46:29.000000000 +0000
-+++ fred/meme-install.html 2007-05-30 02:00:56.000000000 +0000
-@@ -208,42 +208,39 @@
- <h2><a name="patch">Getting and installing the patches</a></h2>
- <p>The distribution may have patches associated with it. They are available
- from <a href="http://meme.nbcr.net/downloads/">http://meme.nbcr.net/downloads/</a>.
--The patch file name is <span class="command">filename.VERSION.patch</span>. In addition, a
--patched file is distributed as well and can be used as a drop-in substitute
--for the original file. The drop-in file is <span class="command">filename.VERSION</span>.
--It is necessary to download only one of the two files depending on the method used for
--patching. All patches for a specific version should be installed. The list
--below provides instructions for installation of availble patches for specific
--version.
-+Patch files are located in a directory named
-+<span class="command">VERSION.patches</span>,
-+for example, <span class="command">meme_3.5.4.patches</span>.
-+Patch file have names like:
-+<span class="command">VERSION.patch_SERIAL_NO</span>, for example, <span class="command">meme_3.5.4.patch_3</span>.
-+</p> <p> To install a patch, download the patch file from the URL given above.
-+Then perform the following commands to install it:
-+ <br><span class="command">$ cp PATCH_FILE VERSION </span> <br><span class="command">$ cd VERSION </span>
-+ <br><span class="command">$ patch -p1 < PATCH_FILE </span>
-+ <br><span class="command">$ make install </span>
-+ <br><span class="command">$ make test </span>
-+</p>
-+<p>
-+For example, to install the first patch to version meme_3.5.4, you would perform the following commands:
-+ <br><span class="command">$ cp meme_3.5.4.patch_1 meme_3.5.4 </span>
-+ <br><span class="command">$ cd meme_3.5.4 </span>
-+ <br><span class="command">$ patch -p1 < meme_3.5.4.patch_1 </span>
-+ <br><span class="command">$ make install </span>
-+ <br><span class="command">$ make test </span>
-+</p>
-+<p>
-+You must install all of the patches for a specific version in serial
-+number order. For example, if you wish to install patch number 3,
-+you must first have installed patches number 1 and 2 for that version.
-+This is easy to do. Just download all the patches for your current
-+version, copy them to your current versions's directory, and then
-+install them in order by repeating the <span class="command">patch</span>,
-+command above, with each patch file. You only need to run the
-+<span class="command">install</span> and
-+<span class="command">make test</span> commands once, after
-+the last <span class="command">patch</patch> command.
- </p>
-
--<center>
--<table class="large" border=1 cellspacing=0>
--<tr>
-- <th width=7% class="head">Version</th>
-- <th width=25% class="head">Patch list</th>
-- <th class="head">Installation</th>
--</tr>
--<tr>
-- <td align=center>3.5.0</td>
-- <td align=center>mast-client.txt</td>
-- <td>
-- <ol>
-- <li>If downloaded a patch file <code>mast-client.txt.3.5.0.patch</code>:
-- <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/</span>
-- <br><span class="command"># cd meme_3.5.0/scripts/</span>
-- <br><span class="command"># patch -p0 &lt; mast-client.txt.3.5.0.patch </span>
-- <br>
-- </li>
-- <li>If downloaded a patched file <code>mast-client.txt.3.5.0</code>:
-- <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/mast-client.txt</span>
-- </li>
-- </ol>
-- </td>
--</tr>
--</table>
--</center>
--
- <p>
- <p>[<a href="#top"> Top </a>]</p>
-
diff --git a/sci-biology/meme/files/meme-3.5.4-patch2.patch b/sci-biology/meme/files/meme-3.5.4-patch2.patch
deleted file mode 100644
index cc07a98..0000000
--- a/sci-biology/meme/files/meme-3.5.4-patch2.patch
+++ /dev/null
@@ -1,70 +0,0 @@
---- meme_3.5.4/website/cgi-bin/meme.pl 2006-09-21 19:46:29.000000000 +0000
-+++ trunk/website/cgi-bin/meme.pl 2007-09-10 00:28:33.000000000 +0000
-@@ -1,6 +1,6 @@
- #!@WHICHPERL@
- ##
--## $Id: meme.pl 1339 2006-09-21 19:46:28Z tbailey $
-+## $Id: meme.pl 2054 2007-09-10 00:27:42Z tbailey $
- ##
- ## $Log$
- ## Revision 1.12 2006/03/07 23:30:19 nadya
-@@ -467,21 +467,21 @@
-
- # check against allowed dna letters
- $x = $_;
-- $x =~ tr/ABCDGHKMNRSTUVWY//cd;
-+ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd;
- $new = length $x;
- if ($old == $new) {
- "dna";
- } else {
- # check against allowed protein letters
- $x = $_;
-- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd;
-+ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd;
- $new = length $x;
- if ($old == $new) {
- "protein";
- } else {
- # get the unknown letters
- $x = $_;
-- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d;
-+ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d;
- &whine("
- Your sequences contained the following unrecognized letters: $x.
- <BR>
---- meme_3.5.4/website/cgi-bin/mast.pl 2006-09-21 19:46:29.000000000 +0000
-+++ trunk/website/cgi-bin/mast.pl 2007-09-10 00:38:14.000000000 +0000
-@@ -1,6 +1,6 @@
- #!@WHICHPERL@
- ##
--## $Id: mast.pl 1339 2006-09-21 19:46:28Z tbailey $
-+## $Id: mast.pl 2055 2007-09-10 00:37:11Z tbailey $
- ##
- ## $Log$
- ## Revision 1.8 2006/03/07 23:30:19 nadya
-@@ -479,21 +479,21 @@
-
- # check against allowed nucleotide letters
- $x = $_;
-- $x =~ tr/ABCDGHKMNRSTUVWY//cd;
-+ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd;
- $new = length $x;
- if ($old == $new) {
- return("DNA");
- } else {
- # check against allowed protein letters
- $x = $_;
-- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd;
-+ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd;
- $new = length $x;
- if ($old == $new) {
- return("PROTEIN");
- } else {
- # get the unknown letters
- $x = $_;
-- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d;
-+ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d;
- &whine("
- Your sequences contained the following unrecognized letters: $x.
- <BR>
diff --git a/sci-biology/meme/meme-3.5.4.ebuild b/sci-biology/meme/meme-3.5.4.ebuild
deleted file mode 100644
index d05d8c5..0000000
--- a/sci-biology/meme/meme-3.5.4.ebuild
+++ /dev/null
@@ -1,88 +0,0 @@
-# Copyright 1999-2007 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-3.5.4.ebuild,v 1.1 2007/04/24 20:44:01 ribosome Exp $
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="The MEME/MAST system - Motif discovery and search"
-HOMEPAGE="http://meme.sdsc.edu/meme"
-SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz"
-LICENSE="meme"
-
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-# Other possible USE flags include "debug", "client", "server", "web",
-# "queue". Other variables must be set at compile time, but only when
-# the Web server is built. Right now, Web server and client are disabled.
-IUSE="mpi"
-
-# Works only with LAM-MPI.
-DEPEND=">=dev-lang/perl-5.6.1
- mpi? ( sys-cluster/lam-mpi )"
-
-S="${WORKDIR}/${PN}_${PV}"
-
-src_unpack() {
- unpack ${A}
-
- cd "${S}"
- epatch "${FILESDIR}/${P}-Makefile.am.patch"
- einfo "Regenerating autotools files..."
- eautoreconf
-}
-
-src_compile() {
- local EXTRA_CONF
- # Build system is too bugy to make the programs use standard locations.
- # Put everything in "/opt" instead.
- EXTRA_CONF="${EXTRA_CONF} --prefix=/opt/${PN}"
- EXTRA_CONF="${EXTRA_CONF} --with-logs=/var/log/${PN}"
- # Connect hyperlinks to official Web site.
- EXTRA_CONF="${EXTRA_CONF} --with-url=http://meme.nbcr.net/meme"
- # Disable Web server, client and Web site.
- EXTRA_CONF="${EXTRA_CONF} --disable-server --disable-client --disable-web"
- # Parallel implementation
- if ! use mpi; then
- EXTRA_CONF="${EXTRA_CONF} --enable-serial"
- fi
-
- ./configure ${EXTRA_CONF} || die "Configure failed."
- CC="$(tc-getCC)" ac_cc_opt="${CFLAGS}" make -e || die "Make failed."
-
-# Install parallel files only on x86, otherwise the install fails with the error:
-# i386 architecture of input file `mp.o' is incompatible with i386:x86-64 output
- if [[ "${ARCH}" == "x86" ]] ; then
- if use mpi; then
- cd src/parallel
- make || die "Parallel make failed."
- fi
- fi
-}
-
-src_install() {
- make install DESTDIR="${D}" || die "Failed to install program files."
- exeinto "/opt/${PN}/bin"
- if [[ "${ARCH}" == "x86" ]] ; then
- if use mpi; then
- doexe "${S}/src/parallel/${PN}_p" || \
- die "Failed to install parallel MEME implementation."
- fi
- fi
- keepdir "/var/log/${PN}"
- fperms 777 "/var/log/${PN}"
-}
-
-pkg_postinst() {
- echo
- einfo 'Prior to using MEME/MAST, you should source "/opt/meme/etc/meme.sh"'
- einfo '(or "/opt/meme/etc/meme.csh" if you use a csh-style shell). To do'
- einfo 'this automatically with bash, add the following statement to your'
- einfo '"~/.bashrc" file (without the quotes): "source /opt/meme/etc/meme.sh".'
- echo
- einfo 'Log files are produced in the "/var/log/meme" directory.'
- echo
-}
-
-src_test() {
- make test || die "Regression tests failed."
-}