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GBrowse

方健飞
Dear Proessor:
      Recently, I adopt the GBrowse software to construct own genome.
I folow the hg19 genome to config my data. But in the chromosomes
directory ,It doesn't auto create the directory.index. Can you tell me
how to auto create the directory.index file? The process is stored in
the accessory.

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Re: GBrowse

Scott Cain
Hello,

In order to create the directory.index file, the webserver needs access to the directory where it needs to be created, which means it needs execute and read privileges on every directory above the directory where you want to write (so they either have to be owned by the webserver user or have permissive read and execute permissions so that any user can get to that directory) and the webserver user must also have write permissions in the directory where you want it to be created.  I see from your config file that the directory is fairly deeply buried in your home directory--typically, a unix system would be configured to not allow the webserver user access to those directories.  Additionally, make sure that "apache" is the name of the webserver user on your system.  It could also be something like "www-data" or "nobody".

If these things are already in place, please check the apache error_log for messages related to why it won't create the file.

Scott



On Mon, Mar 31, 2014 at 9:34 AM, 方健飞 <[hidden email]> wrote:
Dear Proessor:
      Recently, I adopt the GBrowse software to construct own genome.
I folow the hg19 genome to config my data. But in the chromosomes
directory ,It doesn't auto create the directory.index. Can you tell me
how to auto create the directory.index file? The process is stored in
the accessory.

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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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