diff options
Diffstat (limited to 'sci-biology/meme/files/meme_3.5.4.patch_1')
| -rw-r--r-- | sci-biology/meme/files/meme_3.5.4.patch_1 | 198 |
1 files changed, 0 insertions, 198 deletions
diff --git a/sci-biology/meme/files/meme_3.5.4.patch_1 b/sci-biology/meme/files/meme_3.5.4.patch_1 deleted file mode 100644 index b072d7e..0000000 --- a/sci-biology/meme/files/meme_3.5.4.patch_1 +++ /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 < 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> - |