From 48332cb82e71e3d86b07335474ca3b7d5bf979fb Mon Sep 17 00:00:00 2001 From: Jeffrey Gardner Date: Thu, 26 Jun 2008 19:26:18 +0000 Subject: manifest svn path=/; revision=232 --- .../meme/files/meme-3.5.4-Makefile.am.patch | 17 ++ sci-biology/meme/files/meme-3.5.4-patch1.patch | 198 +++++++++++++++++++++ sci-biology/meme/files/meme-3.5.4-patch2.patch | 70 ++++++++ 3 files changed, 285 insertions(+) create mode 100644 sci-biology/meme/files/meme-3.5.4-Makefile.am.patch create mode 100644 sci-biology/meme/files/meme-3.5.4-patch1.patch create mode 100644 sci-biology/meme/files/meme-3.5.4-patch2.patch (limited to 'sci-biology/meme/files') 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 new file mode 100644 index 0000000..1293de0 --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch @@ -0,0 +1,17 @@ +--- 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 new file mode 100644 index 0000000..b072d7e --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-patch1.patch @@ -0,0 +1,198 @@ +--- 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 @@ +

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. +-
+-
+-
+- +

+

[ Top ]

+ diff --git a/sci-biology/meme/files/meme-3.5.4-patch2.patch b/sci-biology/meme/files/meme-3.5.4-patch2.patch new file mode 100644 index 0000000..cc07a98 --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-patch2.patch @@ -0,0 +1,70 @@ +--- 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. +
+--- 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. +
-- cgit v1.2.3-65-gdbad