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<?xml version="1.0"?>
<api>
  <query-continue>
    <allpages gapcontinue="Reproducing_gbrowse_img_functinality_with_JBrowse" />
  </query-continue>
  <query>
    <pages>
      <page pageid="1719" ns="0" title="Recompiling mod fcgid to avoid truncated Perl library paths">
        <revisions>
          <rev contentformat="text/x-wiki" contentmodel="wikitext" xml:space="preserve">Apache's [http://httpd.apache.org/mod_fcgid/ mod_fcgid] has many feature and performance advantages over the older mod_fastcgi, but has one major gotcha. Many people will install custom Perl libraries in non-standard locations, and then use the PERL5LIB environment variable to point GBrowse at those locations. The way to set environment variables for fcgid scripts is to use FcgidInitialEnv (or DefaultInitEnv in older versions of mod_fcgid) in the apache configuration file:

  # from /etc/apache2/conf.d/gbrowse2.conf
  Alias /fgb2 &quot;/usr/lib/cgi-bin/gb2&quot;
  &lt;Location /fgb2&gt;
    SetHandler   fcgid-script
    Options      ExecCGI
  &lt;/Location&gt;
  IdleTimeout    300
  FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
  FcgidInitialEnv PERL5LIB /home/lstein/projects/Bio-Graphics/trunk/lib:/home/lstein/projects/bioperl-
  live:/home/lstein/projects/Generic-Genome-Browser-Trunk/lib:/home/lstein/projects/Bio-
  BigFile/lib:/home/lstein/projects/Bio-BigFile/blib/arch

Unfortunately, you will find that PERL5LIB is truncated at 127 characters, causing Perl to complain that some libraries are missing and possibly causing an Internal Server Error.

The problem is that mod_fcgid limits environment variables to 127 characters and will truncate their values if they exceed this. To fix this problem, you must get the source, modify one line of a header file, reinstall the module. Here is the recipe:

 1% wget http://apache.sunsite.ualberta.ca/httpd/mod_fcgid/mod_fcgid-2.3.6.tar.gz
 2% tar zxvf mod_fcgid-2.3.6.tar.gz
 3% cd mod_fcgid-2.3.6
 4% perl -pi.bak -e 's/INITENV_VAL_LEN 128/INITENV_VAL_LEN 512/' modules/fcgid/fcgid_conf.h
 5% APXS=/usr/bin/apxs2 ./configure.apxs
 6% make
 7% sudo make install

Line 5 requires you to set the APXS environment variable to indicate where Apache's apxs2 compiler is located. Please change it to match where apxs2 is installed on your system. If you don't have apxs2, then you may need to install the development version of Apache. After reinstalling mod_fcgid, please restart Apache.</rev>
        </revisions>
      </page>
      <page pageid="1223" ns="0" title="Region panel">
        <revisions>
          <rev contentformat="text/x-wiki" contentmodel="wikitext" xml:space="preserve">Where should this page redirect? I think there should be a series of pages describing the various components of [[GBrowse]].

See also: the [[overview panel]].

[[Category:GBrowse]]</rev>
        </revisions>
      </page>
    </pages>
  </query>
</api>