--- 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 @@

Getting and installing the patches

The distribution may have patches associated with it. They are available from http://meme.nbcr.net/downloads/. -The patch file name is filename.VERSION.patch. 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 filename.VERSION. -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 +VERSION.patches, +for example, meme_3.5.4.patches. +Patch file have names like: +VERSION.patch_SERIAL_NO, for example, meme_3.5.4.patch_3. +

To install a patch, download the patch file from the URL given above. +Then perform the following commands to install it: +
$ cp PATCH_FILE VERSION
$ cd VERSION +
$ patch -p1 < PATCH_FILE +
$ make install +
$ make test +

+

+For example, to install the first patch to version meme_3.5.4, you would perform the following commands: +
$ cp meme_3.5.4.patch_1 meme_3.5.4 +
$ cd meme_3.5.4 +
$ patch -p1 < meme_3.5.4.patch_1 +
$ make install +
$ make test +

+

+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 patch, +command above, with each patch file. You only need to run the +install and +make test commands once, after +the last patch command.

-
- - - - - - - - - - - -
VersionPatch listInstallation
3.5.0mast-client.txt -
    -
  1. If downloaded a patch file mast-client.txt.3.5.0.patch: -
    # cp mast-client.txt.3.5.0 meme_3.5.0/scripts/ -
    # cd meme_3.5.0/scripts/ -
    # patch -p0 < mast-client.txt.3.5.0.patch -
    -
    2. -
  2. If downloaded a patched file mast-client.txt.3.5.0: -
    # cp mast-client.txt.3.5.0 meme_3.5.0/scripts/mast-client.txt -
    3. -
-
-
-

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