Talk:Former How To Build A WormBase Mirror

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Some things to maybe add but most probably are installed anyways:

  • AceDB: You will need gdk/gtk+ maybe gtk2, X-Windows libraries/headers and readline to compile.
  • GTop: depends on gnome libraries.

Some other comments

about expat and libgd: it would be most probably a lot easier if you would use whatever package management system you use to install these together with their headers. something like: 


$: portinstall expat2 gd (for FreeBSD/portupgrade)

About XML::Simple

the force install throws errors, because the parser has errors ;-) namely: 

 Unable to recognise encoding of this document at /data/lib/perl5//XML/SAX/PurePerl/EncodingDetect.pm line 96

 #   Failed test 'CDATA section parsed correctly'
 #   in t/1_XMLin.t at line 426.
 #     Structures begin differing at:
 #          $got->{cdata} = '<greeting>Hello, world!</greeting>>'
 #     $expected->{cdata} = '<greeting>Hello, world!</greeting>'
 

 #   Failed test 'CDATA section containing markup characters parsed correctly'
 #   in t/1_XMLin.t at line 432.
 #     Structures begin differing at:
 #          $got->{x} = '<y>one</y>><y>two</y>>'
 #     $expected->{x} = '<y>one</y><y>two</y>'

and 

 
#   Failed test 'generated document with escaping'
#   in t/2_XMLout.t at line 302.
#     Structures begin differing at:
#          $got->{c} = '&amp;C&amp;'
#     $expected->{c} = '&C&'

for the last one the test seems to be buggy.

About robots.txt

The template allows the googlebot to index db/* .

About PrimerDesigner.pm

  • the CPAN module includes a linux x86 binary for testing which doesn't work on any other architecture
  • the tests check a connection to a remote server which doesn't work with my proxy setup

=> meaning force install or hack the code to use the proxy and recompile/copy over e-pcr

About configuring the DAS server

  • The configuration files are under conf/das.conf/ and need a working usernamae for mysql set if the apache runs under some abstract userid.
  • GBrowse external DAS sources are set in:
    • conf/das.servers
    • conf/das.servers.conf
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