trying to move meme to virtual/mpi from lam-mpi

svn path=/; revision=231

8 files changed, 2 insertions, 583 deletions

diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
index 75d2b28..4a83c46 100644
--- a/sci-biology/meme/Manifest
+++ b/sci-biology/meme/Manifest
@@ -1,8 +1,6 @@
 AUX meme-3.5.4-Makefile.am.patch 377 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad SHA1 96530d5a58b8c01c99ae2b5463b7448758d7fb3d SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8
-AUX meme-3.5.4-patch1.patch 8019 RMD160 c443da2f16552c488b77e897bdae543839a0738d SHA1 d37473061f4294d342521570729d65421ead0d99 SHA256 7f42f3de330e19630ab5eb335043749afd94652b8d2b1564ce8cd6856acf81e6
-AUX meme-3.5.4-patch2.patch 2496 RMD160 1d492e01a9e06aa0564e2c15235eb49f28f4d2b7 SHA1 cbc691788e2d30cde438f15d94a97f637fdce4a5 SHA256 2571bff727505cddfe59aefa931f2b2436ed2a2daf1e35b5a1d6c6014a753a21
-AUX meme_3.5.4.patch_1 7443 RMD160 6d72e74d6139d8c29bfcda9da750dc454f08ef0a SHA1 336c91ad5ecd44d49de0e940bb18315b62569a2b SHA256 306cee9c3c831494cf264ded84d248e5773c9a56d259a02e8da9c6dc31457f04
-AUX meme_3.5.4.patch_2 2074 RMD160 56520122dd1d35afa444414ea57199924e8492b5 SHA1 29edf295100721006aea8b76ff4c5bdfb9312020 SHA256 bf74f09bcd6c247f464f15b17e3a0e8f95149fdc5b92d8f17d06ede430d2d7be
+AUX meme-3.5.4-patch1.patch 7443 RMD160 6d72e74d6139d8c29bfcda9da750dc454f08ef0a SHA1 336c91ad5ecd44d49de0e940bb18315b62569a2b SHA256 306cee9c3c831494cf264ded84d248e5773c9a56d259a02e8da9c6dc31457f04
+AUX meme-3.5.4-patch2.patch 2074 RMD160 56520122dd1d35afa444414ea57199924e8492b5 SHA1 29edf295100721006aea8b76ff4c5bdfb9312020 SHA256 bf74f09bcd6c247f464f15b17e3a0e8f95149fdc5b92d8f17d06ede430d2d7be
 DIST meme_3.5.4.tar.gz 1045501 RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 SHA1 d780dba0b900f840a599cf69cfeba4eefd4856b4 SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86
 EBUILD meme-3.5.4-r1.ebuild 2822 RMD160 2855f8b8c529002cb498639f51779294d0d4f41e SHA1 ea3e3b23dce7ce2b3bbca1ea3b393fb3da283e1e SHA256 c3370cf5ad110a7a3e4a5b0c53ed8823c4b9e151dcf79aa3a46f8a5a0e80b0c7
 MISC ChangeLog 566 RMD160 74f3916e717ce84e593217bd53c0b99eb10a14c9 SHA1 799df7e3146993c26d897dd8224f302fd0970fcc SHA256 909bde96179b1488d0bcd854d9cd2d3a37a6e55c6c9756623fae0e77e8562dff
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/digest-meme-3.5.4-r1 b/sci-biology/meme/files/digest-meme-3.5.4-r1
deleted file mode 100644
index 01fad30..0000000
--- a/sci-biology/meme/files/digest-meme-3.5.4-r1
+++ /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 09a9498..0000000
--- a/sci-biology/meme/files/meme-3.5.4-patch1.patch
+++ /dev/null
@@ -1,210 +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: 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 &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 3854b83..0000000
--- a/sci-biology/meme/files/meme-3.5.4-patch2.patch
+++ /dev/null
@@ -1,78 +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-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
-+## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
- ##
- ## $Log: meme-3.5.4-patch2.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 1.12  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: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
-+## $Id: meme-3.5.4-patch2.patch,v 1.1 2007/09/17 02:41:56 je_fro Exp $
- ##
- ## $Log: meme-3.5.4-patch2.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 1.8  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/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 &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.patch_2 b/sci-biology/meme/files/meme_3.5.4.patch_2
deleted file mode 100644
index cc07a98..0000000
--- a/sci-biology/meme/files/meme_3.5.4.patch_2
+++ /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>