[Gmod-ajax] Tracks missing from re-installation of JBrowse

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[Gmod-ajax] Tracks missing from re-installation of JBrowse

Raymond Wan-2
Hi all,

Sorry if I'm missing the obvious but I can't seem to figure out the
problem I'm having.

In short, I had a JBrowse 1.11.6 instance working and through an
upgrade that went south, I had to basically lose where JBrowse was
installed (i.e., this wasn't JBrowse's fault).  So, I started from the
beginning, with the latest 1.12.1 .

Repeating what I did wasn't hard since I kept a record.  But, not
surprisingly, I couldn't get it working.  Only the sequence track was
showing; not any of the other tracks.

So, I decided to go back to basics and try to get the sample data sets
working.  And I was getting the same problem!  So, I think I'm missing
something...

My Apache error log has two notable error messages:

[Sat Jul 09 23:42:03.750061 2016] [core:error] [pid 121654]
(13)Permission denied: [client XXX:34250] AH00035: access to
/jbrowse/sample_data/json/yeast/names/root.json denied (filesystem
path '/var/www/html/jbrowse/sample_data/json/yeast/names') because
search permissions are missing on a component of the path, referer:
XXX/jbrowse/?data=sample_data/json/yeast

[Sat Jul 09 23:42:03.815065 2016] [core:error] [pid 121654]
(13)Permission denied: [client XXX:34250] AH00035: access to
/jbrowse/sample_data/json/yeast/seq/refSeqs.json denied (filesystem
path '/var/www/html/jbrowse/sample_data/json/yeast/seq') because
search permissions are missing on a component of the path, referer:
XXX/jbrowse/?data=sample_data/json/yeast

The first one is asking for "root.json", which does not exist at that
path.  The file that I think it should be looking for is meta.json .
I can't seem to figure out where this is coming from, other than maybe
compat_121.html, but I doubt it.

As for permissions, I think if all files are readable by the Apache2
process (and directories have x permission), this is enough?  I've
assigned them to the group www-data (i.e., Ubuntu) instead of the
user, but I think that is ok.

Are there other logs I can look to for help besides my Apache2 error log?

And setup.log has not errors after running setup.sh...  Not sure where
else I should look...

Thank you!

Ray

PS: Has the format for trackList.json or any configuration file
changed since 1.11.6?

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Re: Tracks missing from re-installation of JBrowse

Colin
Sometimes even if permissions are right on a file, it might be restricted on a folder upwards in the directory tree, causing these errors. Try checking out this guide


Perhaps if sudo was used to unzip jbrowse or something similar, then it needs to fix permissions up to the jbrowse root dir

The other things should fall into place after that. No changes in data directory structures or file formats occurred. The root.json thing corresponds to a file that is downloaded when generate-names.pl wasn't run, it's not really a problem maybe and might go away once permission issues are fixed http://gmod.org/wiki/JBrowse_Configuration_Guide#generate-names.pl


-Colin

On Sat, Jul 9, 2016 at 11:03 AM, Raymond Wan <[hidden email]> wrote:
Hi all,

Sorry if I'm missing the obvious but I can't seem to figure out the
problem I'm having.

In short, I had a JBrowse 1.11.6 instance working and through an
upgrade that went south, I had to basically lose where JBrowse was
installed (i.e., this wasn't JBrowse's fault).  So, I started from the
beginning, with the latest 1.12.1 .

Repeating what I did wasn't hard since I kept a record.  But, not
surprisingly, I couldn't get it working.  Only the sequence track was
showing; not any of the other tracks.

So, I decided to go back to basics and try to get the sample data sets
working.  And I was getting the same problem!  So, I think I'm missing
something...

My Apache error log has two notable error messages:

[Sat Jul 09 23:42:03.750061 2016] [core:error] [pid 121654]
(13)Permission denied: [client XXX:34250] AH00035: access to
/jbrowse/sample_data/json/yeast/names/root.json denied (filesystem
path '/var/www/html/jbrowse/sample_data/json/yeast/names') because
search permissions are missing on a component of the path, referer:
XXX/jbrowse/?data=sample_data/json/yeast

[Sat Jul 09 23:42:03.815065 2016] [core:error] [pid 121654]
(13)Permission denied: [client XXX:34250] AH00035: access to
/jbrowse/sample_data/json/yeast/seq/refSeqs.json denied (filesystem
path '/var/www/html/jbrowse/sample_data/json/yeast/seq') because
search permissions are missing on a component of the path, referer:
XXX/jbrowse/?data=sample_data/json/yeast

The first one is asking for "root.json", which does not exist at that
path.  The file that I think it should be looking for is meta.json .
I can't seem to figure out where this is coming from, other than maybe
compat_121.html, but I doubt it.

As for permissions, I think if all files are readable by the Apache2
process (and directories have x permission), this is enough?  I've
assigned them to the group www-data (i.e., Ubuntu) instead of the
user, but I think that is ok.

Are there other logs I can look to for help besides my Apache2 error log?

And setup.log has not errors after running setup.sh...  Not sure where
else I should look...

Thank you!

Ray

PS: Has the format for trackList.json or any configuration file
changed since 1.11.6?

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everyone, including kids. Get more information and register today.
http://sdm.link/attshape
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everyone, including kids. Get more information and register today.
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Re: Tracks missing from re-installation of JBrowse

Raymond Wan-2
Hi Colin,

Thanks for your thoughts!  At least I didn't dwell on root.json for
too long and looked into something else.

I finally got it working.  I don't know everything I did (I kept
trying multiple things) but it seems I had the permission of .htaccess
wrong and also did not enable "AllowOverride FileInfo" in my web
server configuration.  I guess I had this setting in the previous
setup of the system and forgot about it!

It seems to work now; I haven't yet ran generate-names.pl on this new
setup, but will do so tomorrow.

Thanks a lot for your help!

Ray


On Sun, Jul 10, 2016 at 2:21 AM, Colin <[hidden email]> wrote:

> Sometimes even if permissions are right on a file, it might be restricted on
> a folder upwards in the directory tree, causing these errors. Try checking
> out this guide
>
> https://wiki.apache.org/httpd/13PermissionDenied
>
> Perhaps if sudo was used to unzip jbrowse or something similar, then it
> needs to fix permissions up to the jbrowse root dir
>
> The other things should fall into place after that. No changes in data
> directory structures or file formats occurred. The root.json thing
> corresponds to a file that is downloaded when generate-names.pl wasn't run,
> it's not really a problem maybe and might go away once permission issues are
> fixed http://gmod.org/wiki/JBrowse_Configuration_Guide#generate-names.pl
>
>
> -Colin
>
> On Sat, Jul 9, 2016 at 11:03 AM, Raymond Wan <[hidden email]> wrote:
>>
>> Hi all,
>>
>> Sorry if I'm missing the obvious but I can't seem to figure out the
>> problem I'm having.
>>
>> In short, I had a JBrowse 1.11.6 instance working and through an
>> upgrade that went south, I had to basically lose where JBrowse was
>> installed (i.e., this wasn't JBrowse's fault).  So, I started from the
>> beginning, with the latest 1.12.1 .
>>
>> Repeating what I did wasn't hard since I kept a record.  But, not
>> surprisingly, I couldn't get it working.  Only the sequence track was
>> showing; not any of the other tracks.
>>
>> So, I decided to go back to basics and try to get the sample data sets
>> working.  And I was getting the same problem!  So, I think I'm missing
>> something...
>>
>> My Apache error log has two notable error messages:
>>
>> [Sat Jul 09 23:42:03.750061 2016] [core:error] [pid 121654]
>> (13)Permission denied: [client XXX:34250] AH00035: access to
>> /jbrowse/sample_data/json/yeast/names/root.json denied (filesystem
>> path '/var/www/html/jbrowse/sample_data/json/yeast/names') because
>> search permissions are missing on a component of the path, referer:
>> XXX/jbrowse/?data=sample_data/json/yeast
>>
>> [Sat Jul 09 23:42:03.815065 2016] [core:error] [pid 121654]
>> (13)Permission denied: [client XXX:34250] AH00035: access to
>> /jbrowse/sample_data/json/yeast/seq/refSeqs.json denied (filesystem
>> path '/var/www/html/jbrowse/sample_data/json/yeast/seq') because
>> search permissions are missing on a component of the path, referer:
>> XXX/jbrowse/?data=sample_data/json/yeast
>>
>> The first one is asking for "root.json", which does not exist at that
>> path.  The file that I think it should be looking for is meta.json .
>> I can't seem to figure out where this is coming from, other than maybe
>> compat_121.html, but I doubt it.
>>
>> As for permissions, I think if all files are readable by the Apache2
>> process (and directories have x permission), this is enough?  I've
>> assigned them to the group www-data (i.e., Ubuntu) instead of the
>> user, but I think that is ok.
>>
>> Are there other logs I can look to for help besides my Apache2 error log?
>>
>> And setup.log has not errors after running setup.sh...  Not sure where
>> else I should look...
>>
>> Thank you!
>>
>> Ray
>>
>> PS: Has the format for trackList.json or any configuration file
>> changed since 1.11.6?
>>
>>
>> ------------------------------------------------------------------------------
>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

------------------------------------------------------------------------------
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Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
Gmod-ajax mailing list
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