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--- 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: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
+## $Id: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
##
## $Log: meme-3.5.4-patch1.patch,v $
## Revision 1.1 2007/09/17 02:41:56 je_fro
## Add upstream patches and disable parallel install on amd64.
## (Portage version: 2.1.3.9)
##
## 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: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
+ * $Id: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
*
* $Log: meme-3.5.4-patch1.patch,v $
* Revision 1.1 2007/09/17 02:41:56 je_fro
* Add upstream patches and disable parallel install on amd64.
* (Portage version: 2.1.3.9)
*
* 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: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
+ * $Id: meme-3.5.4-patch1.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
*
* $Log: meme-3.5.4-patch1.patch,v $
* Revision 1.1 2007/09/17 02:41:56 je_fro
* Add upstream patches and disable parallel install on amd64.
* (Portage version: 2.1.3.9)
*
* 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 < 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>
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