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<div class="moz-cite-prefix">Hi Rafael,<br>
<br>
We have changed the way in which you set the path to these files,
the variable you now need to set is DATAFILE_BASE_PATH and this
should be set in SiteDefs.pm. The instructions for setting up
these files for use are in the README file on the ftp site where
you would have downloaded the files from.<br>
<br>
<a class="moz-txt-link-freetext" href="ftp://ftp.ensembl.org/pub/current_data_files/homo_sapiens/GRCh37/result_feature/README">ftp://ftp.ensembl.org/pub/current_data_files/homo_sapiens/GRCh37/result_feature/README</a><br>
<br>
Hope this helps,<br>
Beth<br>
<br>
On 22/02/13 12:18, Rafael Hernández wrote:<br>
</div>
<blockquote
cite="mid:CAK3SC65Xevd4bqeikg22TKigLw79iuHm08hFiJDD+KmyUsyGFQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div class="im"
style="font-family:arial,sans-serif;font-size:13px">
<div style="font-size:12.727272033691406px">Hi,</div>
<div style="font-size:12.727272033691406px"><br>
</div>
<div style="font-size:12.727272033691406px">
<span
style="font-size:12.727272033691406px;color:rgb(34,34,34)">I've
installed a local version of Ensembl release 70 following
the provided documentation and everything works fine
except the Regulation tools (</span><a
moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Regulation/Cell_line?db=funcgen;fdb=funcgen;r=17:46617590-46621119;rf=ENSR00001348194"
target="_blank" style="font-size:12.727272033691406px">example</a><span
style="font-size:12.727272033691406px;color:rgb(34,34,34)"> of
regulation tool).</span><br>
</div>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">
<div class="im">
<div style="font-size:12.727272033691406px">When I query
Ensembl looking for regulation info, it produces an AJAX
error and no graphics are showed.<br>
</div>
</div>
<div style="font-size:12.727272033691406px">Below the error
message:</div>
<div style="font-size:12.727272033691406px">
<div><br>
</div>
<div class="im"><b><font face="courier new, monospace">AJAX
error - Runtime Error in component
EnsEMBL::Web::Component::Regulation::FeaturesByCellLine
[content]"</font></b></div>
<div class="im">
<div><font face="courier new, monospace">Function
EnsEMBL::Web::Component::Regulation::FeaturesByCellLine
fails to execute due to the following error:<br>
</font></div>
<div><font face="courier new, monospace"><br>
</font></div>
<div><font face="courier new, monospace"><span
style="white-space:pre-wrap"> </span>--------------------
EXCEPTION --------------------</font></div>
<div><font face="courier new, monospace"><span
style="white-space:pre-wrap"> </span>MSG: Failed to
open: </font></div>
<div><font face="courier new, monospace"><span
style="white-space:pre-wrap"> </span>...
/result_feature/GM12878_DNase1_ENCODE_Uw/result_features.GM12878_DNase1_ENCODE_Uw.130.col</font></div>
<div><font face="courier new, monospace"><span
style="white-space:pre-wrap"> </span>No such file
or directory</font></div>
</div>
</div>
</div>
<div class="gmail_extra"
style="font-family:arial,sans-serif;font-size:13px">
<div style="font-size:12.727272033691406px"><br>
</div>
<div style="font-size:12.727272033691406px"><br>
</div>
<div style="font-size:12.727272033691406px">
I know the cause of the problem: Ensembl tries to read some
files from a directory located in the root of the file
system (e.g. <span style="font-family:'courier
new',monospace"> /result_feature/GM12878_</span><span
style="font-family:'courier new',monospace">DNase1_ENCODE_Uw/result_</span><span
style="font-family:'courier new',monospace">features.GM12878_DNase1_</span><span
style="font-family:'courier new',monospace">ENCODE_Uw.130.col</span>),
however the directory <span style="font-family:'courier
new',monospace">/result_feature/</span> doesn't exists and
the query crashes.</div>
<div style="font-size:12.727272033691406px"><br>
</div>
<div style="font-size:12.727272033691406px">If I move the <span
style="font-family:'courier new',monospace">/result_feature/ </span>folder
to the root of my file system, then Ensembl works, however I
don't want to put there those files, and I want to know how
could I change this. I found in the ensembl-dev page a
thread talking about this problem (<a moz-do-not-send="true"
href="http://lists.ensembl.org/pipermail/dev/2012-April/007279.html"
target="_blank">here</a>) and they suggested to set a
variable ENSEMBL_REGULATION_FILE_PATH pointing to the
desired folder in the DEFAULT.ini file.</div>
<div class="im">
<div style="font-size:12.727272033691406px"><font
color="#000000">In my case should look like this:</font></div>
<div style="font-size:12.727272033691406px"><font
color="#000000"><br>
</font></div>
<div style="font-size:12.727272033691406px">
<span style="font-family:'courier new',monospace">ENSEMBL_REGULATION_FILE_PATH=/usr/local/ensembl/regulation_files/</span><font
color="#000000"><br>
</font></div>
<div style="font-size:12.727272033691406px"><br>
</div>
<div style="font-size:12.727272033691406px">However it
doesn't works. Nothing change when using this setting and
Ensembl still looking for the files in the previous
directory. Any idea?</div>
<div style="font-size:12.727272033691406px">
<br>
</div>
</div>
<div style="font-size:12.727272033691406px"><span
style="font-size:12.727272033691406px">Thank you and best
regards,</span>
<div class="">
<div id=":1p8" class="" tabindex="0"><img
moz-do-not-send="true" class=""
src="https://mail.google.com/mail/u/0/images/cleardot.gif"
style=""></div>
</div>
<div class=""><br>
</div>
</div>
<div class="im"><br style="font-size:12.727272033691406px"
clear="all">
<div style="font-size:12.727272033691406px"><font
style="color:rgb(102,102,102)"><span
style="font-family:tahoma,sans-serif">Rafa Hernández
de Diego </span></font><br>
<div><span style="color:rgb(153,153,153)"><br>
</span></div>
<div><br>
</div>
</div>
</div>
</div>
</div>
<br>
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<pre wrap="">_______________________________________________
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</blockquote>
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