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<div class="moz-cite-prefix">Hi Andreas,<br>
<br>
On 13/02/13 02:08, Andreas Tille wrote:<br>
</div>
<blockquote cite="mid:20130212160831.GC20516@an3as.eu" type="cite">
<pre wrap="">Hi,
when continuing a bit with MEME packaging for Debian I stumbled upon an
issue that needs to be discussed with upstream. Usually Debian installs
every binary a user should execute under /usr/bin. Thus in the case of
MEME the package in preparation puts 97 executable files into this
directory. Debian policy checker asks for having a manpage for any file
there and when trying to autocreate these using pod2man and help2man I
finally have drawn the conclusion that we might be on the wrong track
here.
There are some tools that really seem to be MEME *internal* which should
not be called by the user directly. One example for such an executable
is for instance
cat_max - Copies standard input to standard output and quits with $status 1
if more than <max> bytes are written.</pre>
</blockquote>
This script is only used by the script "download" which seems to
have been left over from an older method of updating the sequence
databases. I've now removed both from our source repository so they
won't be in future releases. There are more than a few fossils and
it's past time I dealt with them so I'll try to identify the rest.<br>
<blockquote cite="mid:20130212160831.GC20516@an3as.eu" type="cite">
<pre wrap="">
I can not really imagine that this is a user oriented tool but it rather
seems to be something that is used internally by other parts of MEME.
Moreover there are tools with quite generic names. For instance in the
current packaging attemt a file /usr/bin/tree would be installed which
would create a conflict with the tree package that contains the very
same file name. So it is not possible to put this executable here in
the meme package.</pre>
</blockquote>
The program "tree" can probably be renamed (maybe mhmm_tree) for
future releases to avoid this problem because I don't believe any
work has been published referencing that name. I don't think we can
do that with "purge" ( Neuwald <i>et al.</i>, "Gibbs motif
sampling: detection
of bacterial outer membrane protein repeats", Protein Science, <b>4</b>:1618--1632,
1995.
) or "dust" (
<a class="moz-txt-link-freetext" href="http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.1028">http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.1028</a> )
though because they're someone else's published programs. It's
possible they don't need to be included at all though we do have
documentation for purge so maybe it's part of some people's workflow
( <a class="moz-txt-link-freetext" href="http://xkcd.com/1172/">http://xkcd.com/1172/</a> ). They were originally used as filters for
sequences on the MEME webservice though they were disabled before I
started working on the MEME Suite (I have no idea why).<br>
<blockquote cite="mid:20130212160831.GC20516@an3as.eu" type="cite">
<pre wrap="">
The usual workaround in this situations is to move all those internal
tools to
/usr/bin/meme
and set the PATH if needed accordingly. Only those executables that
should be called by the user should reside in /usr/bin. Could you
perhaps help to identify what executables this are and whether the plan
to move other tools to some different place might be feasible?
Alternatively we could move *all* executables to /usr/bin/meme and write
some wrapper scripts for the user oriented executables to set the PATH
accordingly or to `cd /usr/bin/meme` and call the real executable there.
Any hint would be welcome.</pre>
</blockquote>
I'll work on a list of what each of the programs is used for and get
back to you. Even discounting the fossils there are probably quite a
few scripts and programs only relevant to installing the MEME Suite
on a webserver. For example a local user would almost never want to
use the update_db script as it's a very clumsy way to get sequence
data for specific tasks.<br>
<br>
~James<br>
<blockquote cite="mid:20130212160831.GC20516@an3as.eu" type="cite">
<pre wrap="">
Kind regards
Andreas.
</pre>
</blockquote>
<br>
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