volvox example in gbrowse package tutorial uses invalid paths, is this a bug?

Asked by Alexander Bakker

I just installed the current amd64 gbrowse package (gbrowse 2.42~dfsg-1build1 (amd64 binary) in ubuntu precise) from universal including all necessary dependencies.
At first glance all seemed right, with all sample pages accessible via (apache2) localhost. I decided to try following the included tutorial (dated 2010, this might be part of the problem, if indeed there is any). ATthe volvoxexample, I encountered these minor inconvieniences (pasting some scribbles I made while trying to get this example to work):

Gbrowse2 tutorial volvox example (section 1. 'The Basics') Ubuntu 12.04 LTS (64bit) 20121016

instead of first series of commands
    # chown my_user_name /var/lib/gbrowse2/databases
    # chown my_user_name /etc/gbrowse2
    # exit

(sudo su)
    # chown my_user_name /var/lib/gbrowse/databases
    # chown my_user_name /etc/gbrowse
    # su my_user_name

gbrowse2 is in 'gbrowse' instead of 'gbrowse2' dirs (changing all other references accordingly)

instead of:
 % cd /var/www/gbrowse2
 % cp tutorial/data_files/volvox_remarks.gff3 databases/volvox

 % cd /usr/share/gbrowse/htdocs
 % cp tutorial/data_files/volvox_remarks.gff3 /var/lib/gbrowse/databases/volvox
 % cp tutorial/conf_files/volvox.conf /etc/gbrowse/

Apparently, all the stuff that was typically in /var/www is now in /usr/share/<content>/htdocs , or in /var/lib/<content> (/databases in the case of databases)

in /etc/gbrowse/Gbrowse.conf the stanza to be added at the end of the file was already present:

description = Tutorial database
path = volvox.conf

in volvox.conf, replace
  -dir '/home/<package-admin's username?>/GBrowse/htdocs/databases/volvox'
  -dir '/usr/share/gbrowse/htdocs/databases/volvox'
(or move the volvox db to your own homedir and replace the hardcoded username by yours)

I got this working by changing ownership of /var/lib/gbrowse/databases back to root (recursively).

Like I mentioned in the summary, I'm not exactly sure whether this qualifies as a bug or if it's even worthy of mentioning.

Alexander Bakker

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actionparsnip (andrew-woodhead666) said :

I would mention it, if the doc needs changing then it should be updated

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