proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

8 files changed, 527 insertions, 0 deletions

diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
new file mode 100644
index 000000000000..3ed08610b06e
--- /dev/null
+++ b/sci-biology/meme/Manifest
@@ -0,0 +1 @@
+DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e
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 000000000000..1293de0ea080
--- /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 000000000000..b072d7edc527
--- /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 @@
+ <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
new file mode 100644
index 000000000000..cc07a98307f2
--- /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.
+ 	<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>
diff --git a/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch b/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch
new file mode 100644
index 000000000000..1293de0ea080
--- /dev/null
+++ b/sci-biology/meme/files/meme-4.0.0-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-4.8.1-Makefile.am.patch b/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch
new file mode 100644
index 000000000000..e84006295735
--- /dev/null
+++ b/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch
@@ -0,0 +1,134 @@
+ Makefile.am                                        |  6 +++---
+ doc/Makefile.am                                    |  2 +-
+ doc/examples/Makefile.am                           | 24 +++++++++++-----------
+ .../Makefile.am                                    |  2 +-
+ doc/examples/sample_opal_scripts/Makefile.am       |  2 +-
+ doc/images/Makefile.am                             |  2 +-
+ scripts/Makefile.am                                |  2 +-
+ 7 files changed, 20 insertions(+), 20 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index 4a69e34..842e33f 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -18,11 +18,11 @@ ARCHIVE_REVISION:
+ install-data-hook: dbdir
+ 
+ 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/doc/Makefile.am b/doc/Makefile.am
+index e0d6af9..e7bcb4f 100644
+--- a/doc/Makefile.am
++++ b/doc/Makefile.am
+@@ -202,7 +202,7 @@ COMMON_DOC = \
+ if WEBSITE
+ MEME_DOC_DIR = $(WEBDIR)/doc
+ else
+-MEME_DOC_DIR = $(prefix)/doc
++MEME_DOC_DIR = $(docdir)/html
+ endif
+ 
+ memedocdir = $(MEME_DOC_DIR)
+diff --git a/doc/examples/Makefile.am b/doc/examples/Makefile.am
+index 12970b5..633492c 100644
+--- a/doc/examples/Makefile.am
++++ b/doc/examples/Makefile.am
+@@ -51,24 +51,24 @@ if WEBSITE
+ exdir = $(WEBDIR)/examples
+ other_exdir = $(WEBDIR)/doc/examples
+ else
+-exdir = $(prefix)/doc/examples
++exdir = $(prefix)/share/meme/examples
+ other_exdir = $(exdir)
+ endif
+ 
+ ex_DATA = $(EXAMPLES)
+ 
+ install-data-hook:
+-	tar xzvf centrimo_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf dreme_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf fimo_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf glam2_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf glam2scan_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf mast_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf mcast_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf meme_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf memechip_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf spamo_example_output_files.tgz -C $(other_exdir)
+-	tar xzvf tomtom_example_output_files.tgz -C $(other_exdir)
++	tar xzvf centrimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf dreme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf fimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf glam2_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf glam2scan_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf mast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf mcast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf meme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf memechip_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf spamo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
++	tar xzvf tomtom_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
+ 
+ # If .svnignore file doesn't exist
+ # create an empty one
+diff --git a/doc/examples/compute_prior_dist_example_output_files/Makefile.am b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
+index 747028d..a358f58 100644
+--- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am
++++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
+@@ -22,7 +22,7 @@ EXAMPLES = \
+ if WEBSITE
+ exdir = $(WEBDIR)/doc/examples/compute_prior_dist_example_output_files
+ else
+-exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files
++exdir = $(prefix)/share/meme/examples/compute_prior_dist_example_output_files
+ endif
+ 
+ ex_DATA = $(EXAMPLES)
+diff --git a/doc/examples/sample_opal_scripts/Makefile.am b/doc/examples/sample_opal_scripts/Makefile.am
+index 3a638b3..30925bb 100644
+--- a/doc/examples/sample_opal_scripts/Makefile.am
++++ b/doc/examples/sample_opal_scripts/Makefile.am
+@@ -18,7 +18,7 @@ EXAMPLES = \
+ if WEBSITE
+ exdir = $(WEBDIR)/doc/examples/sample_opal_scripts
+ else
+-exdir = $(prefix)/doc/examples/sample_opal_scripts
++exdir = $(prefix)/share/meme/examples/sample_opal_scripts
+ endif
+ 
+ ex_DATA = $(EXAMPLES)
+diff --git a/doc/images/Makefile.am b/doc/images/Makefile.am
+index c879621..a4696cd 100644
+--- a/doc/images/Makefile.am
++++ b/doc/images/Makefile.am
+@@ -28,7 +28,7 @@ MEME_IMAGES = \
+ if WEBSITE
+ memeimgdir = $(WEBDIR)/doc/images
+ else
+-memeimgdir = $(prefix)/doc/images
++memeimgdir = $(docdir)/html/images
+ endif
+ 
+ memeimg_DATA = $(MEME_IMAGES)
+diff --git a/scripts/Makefile.am b/scripts/Makefile.am
+index 4143e46..8a5c021 100644
+--- a/scripts/Makefile.am
++++ b/scripts/Makefile.am
+@@ -8,7 +8,7 @@
+ if WEBSITE
+ MEME_DOC_DIR = $(WEBDIR)/doc
+ else
+-MEME_DOC_DIR = $(prefix)/doc
++MEME_DOC_DIR = $(docdir)
+ endif
+ 
+ ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION)
diff --git a/sci-biology/meme/meme-4.8.1-r2.ebuild b/sci-biology/meme/meme-4.8.1-r2.ebuild
new file mode 100644
index 000000000000..8a1482c0b32d
--- /dev/null
+++ b/sci-biology/meme/meme-4.8.1-r2.ebuild
@@ -0,0 +1,85 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils python
+
+DESCRIPTION="The MEME/MAST system - Motif discovery and search"
+HOMEPAGE="http://meme.sdsc.edu/meme"
+SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz"
+
+LICENSE="meme"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="debug examples mpi"
+
+DEPEND="
+	app-shells/tcsh
+	dev-libs/libxml2:2
+	dev-libs/libxslt
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+#pkg_setup() {
+	# generate meme group to restrict logging to /var/log/meme
+#	enewgroup meme
+#	python_pkg_setup
+#	python_set_active_version 2
+#}
+
+src_prepare() {
+	use examples || sed -e '/SUBDIRS/s:examples::g' -i doc/Makefile.am
+	sed \
+		-e '/flags/s:-O3::g' \
+		-e '/opt/s:-O::g' \
+		-e '/debug/s:-ggdb::' \
+		-e '/debug/s:-g::' \
+		-e 's:CFLAGS=:CFLAGS+=:g' \
+		-i configure.ac || die
+	epatch \
+		"${FILESDIR}"/${P}-Makefile.am.patch
+	eautoreconf
+}
+
+src_configure() {
+	MY_PREFIX="${ROOT}opt/meme"
+	USE_DISABLE_MPI=""; if ! use mpi; then USE_DISABLE_MPI="--enable-serial"; fi
+	econf \
+		--sysconfdir="${EPREFIX}/etc/meme" \
+		--with-logs="${ROOT}var/log/meme" \
+		$(use_enable debug) \
+		$USE_DISABLE_MPI
+}
+
+src_test() {
+	# bug #297070
+	emake -j1 test
+}
+
+src_install() {
+	local i
+	default
+
+	for i in "${ED}"/usr/bin/*; do
+		mv "${ED}"/usr/bin/{,meme-}$(basename ${i}) || die
+	done
+
+	echo "PATH=/opt/${PN}/bin" > 99${PN}
+	doenvd 99${PN}
+
+	# allow logging only for members of meme group
+	# diropts -m 0770 -g meme -o root
+	diropts -m ugo+rwxt -o root
+	keepdir /var/log/meme
+}
+
+#pkg_postinst() {
+#	einfo 'Log files are produced in the "/var/log/meme" directory. Users'
+#	einfo 'need to be part of the meme group to use this facility.'
+#}
diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/meme/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>