[Gmod-ajax] Question about data store outside of jbrowse

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[Gmod-ajax] Question about data store outside of jbrowse

Marc Höppner-3
Hi,

hope this hasn't been answered in the recent past, but I have not been
able to figure out how to set a data store that is not within the
jbrowse folder. Specifically:

Jbrowse lives in: /usr/share/tomcat7/webapps/jbrowse

The data store should be: /jbrowse/data

This is basically because /usr is in the root file system which on our
machine has limited space (and I'd like to add various VCF and BAM
tracks). I have tried setting jbrowse.conf like so:

[datasets.hg19]
url = ?data=/jbrowse/data
name = Homo sapiens hg19

and copied the working jbrowse/data directory to /jbrowse/data as by the
url setting above. I then moved jbrowse/data to bak.data and restarted
tomcat. I get the data set selector, but JBrowse apparently cannot read
from /jbrowse/data (all permissions were transferred when copying it).

So how can I fix this? WebApollo can do this, but I am not sure how this
works under the hood.

Cheers,

Marc

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Re: Question about data store outside of jbrowse

Raymond Wan-2
Hi Marc,


On Thu, Jun 16, 2016 at 5:28 PM, Marc P. Hoeppner <[hidden email]> wrote:
> hope this hasn't been answered in the recent past, but I have not been
> able to figure out how to set a data store that is not within the
> jbrowse folder. Specifically:
>
> Jbrowse lives in: /usr/share/tomcat7/webapps/jbrowse


I've never tried running JBrowse under Tomcat -- I've only used Apache.

But does setting a symbolic link work?  (i.e., "ln" command so that
/usr/share/tomcat7/webapps/jbrowse/data links to /jbrowse/data)  Of
course, in addition to the Tomcat configuration to allow following of
symbolic links.


> tomcat. I get the data set selector, but JBrowse apparently cannot read
> from /jbrowse/data (all permissions were transferred when copying it).


At least for Apache, you will want the files owned by the process that
runs the Apache process.  Alternatively, by the same group is fine,
too.

I presume Tomcat is the same here...

Perhaps you should double check the permissions?  And maybe even do a
recursive chown/chmod.

Ray

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patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
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Re: Question about data store outside of jbrowse

nathandunn

Marc,

What is your goal?    I seem to remember you doing Apollo stuff.  You can always click on “public” under the organism tab and you can browse any organism directly (logout and then click “Browse Genomes”).

If you are wanting raw JBrowse (different views and feature-set), you have a few options:

1 - symlink.  I don’t recommend this as non-war files can have weird behavior.  Definitely not a bad first step.  You may have to turn on “allowLink” in server.xml though I think its on by default.  I think it is recommended not doing this for windows as well.

2 - You can add “Context” entry to your tomcat server.xml inside a <Host> . . .  <Context docBase="/path/to/files" path="/files" />.  http://stackoverflow.com/a/1812356/1739366  (see the very first part of this)

3 - You can add Apache 2 as a proxy.  http://genomearchitect.readthedocs.io/en/stable/Configure.html?highlight=proxy#apache-proxy and then add a separate directory for JBrowse.  This is what I typically do, but I serve up a lot of different things.


Nathan

> On Jun 16, 2016, at 2:35 AM, Raymond Wan <[hidden email]> wrote:
>
> Hi Marc,
>
>
> On Thu, Jun 16, 2016 at 5:28 PM, Marc P. Hoeppner <[hidden email]> wrote:
>> hope this hasn't been answered in the recent past, but I have not been
>> able to figure out how to set a data store that is not within the
>> jbrowse folder. Specifically:
>>
>> Jbrowse lives in: /usr/share/tomcat7/webapps/jbrowse
>
>
> I've never tried running JBrowse under Tomcat -- I've only used Apache.
>
> But does setting a symbolic link work?  (i.e., "ln" command so that
> /usr/share/tomcat7/webapps/jbrowse/data links to /jbrowse/data)  Of
> course, in addition to the Tomcat configuration to allow following of
> symbolic links.
>
>
>> tomcat. I get the data set selector, but JBrowse apparently cannot read
>> from /jbrowse/data (all permissions were transferred when copying it).
>
>
> At least for Apache, you will want the files owned by the process that
> runs the Apache process.  Alternatively, by the same group is fine,
> too.
>
> I presume Tomcat is the same here...
>
> Perhaps you should double check the permissions?  And maybe even do a
> recursive chown/chmod.
>
> Ray
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity planning
> reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax


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patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
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Re: Question about data store outside of jbrowse

Marc Höppner-3
Hi,

thanks for the hints. I am trying out JBrowse as a stand-alone (not
Apollo) for a specific project. I ended up "mount --bind" ing the data
store from our storage space - that seems to work fine. I will see if
this becomes a problem down the line and have a look at your other
suggestions.

Cheers,

Marc

Am 16.06.16 um 18:01 schrieb Nathan Dunn:

> Marc,
>
> What is your goal?    I seem to remember you doing Apollo stuff.  You can always click on “public” under the organism tab and you can browse any organism directly (logout and then click “Browse Genomes”).
>
> If you are wanting raw JBrowse (different views and feature-set), you have a few options:
>
> 1 - symlink.  I don’t recommend this as non-war files can have weird behavior.  Definitely not a bad first step.  You may have to turn on “allowLink” in server.xml though I think its on by default.  I think it is recommended not doing this for windows as well.
>
> 2 - You can add “Context” entry to your tomcat server.xml inside a <Host> . . .  <Context docBase="/path/to/files" path="/files" />.  http://stackoverflow.com/a/1812356/1739366  (see the very first part of this)
>
> 3 - You can add Apache 2 as a proxy.  http://genomearchitect.readthedocs.io/en/stable/Configure.html?highlight=proxy#apache-proxy and then add a separate directory for JBrowse.  This is what I typically do, but I serve up a lot of different things.
>
>
> Nathan
>
>> On Jun 16, 2016, at 2:35 AM, Raymond Wan <[hidden email]> wrote:
>>
>> Hi Marc,
>>
>>
>> On Thu, Jun 16, 2016 at 5:28 PM, Marc P. Hoeppner <[hidden email]> wrote:
>>> hope this hasn't been answered in the recent past, but I have not been
>>> able to figure out how to set a data store that is not within the
>>> jbrowse folder. Specifically:
>>>
>>> Jbrowse lives in: /usr/share/tomcat7/webapps/jbrowse
>>
>> I've never tried running JBrowse under Tomcat -- I've only used Apache.
>>
>> But does setting a symbolic link work?  (i.e., "ln" command so that
>> /usr/share/tomcat7/webapps/jbrowse/data links to /jbrowse/data)  Of
>> course, in addition to the Tomcat configuration to allow following of
>> symbolic links.
>>
>>
>>> tomcat. I get the data set selector, but JBrowse apparently cannot read
>>> from /jbrowse/data (all permissions were transferred when copying it).
>>
>> At least for Apache, you will want the files owned by the process that
>> runs the Apache process.  Alternatively, by the same group is fine,
>> too.
>>
>> I presume Tomcat is the same here...
>>
>> Perhaps you should double check the permissions?  And maybe even do a
>> recursive chown/chmod.
>>
>> Ray
>>
>> ------------------------------------------------------------------------------
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols are
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> J-Flow, sFlow and other flows. Make informed decisions using capacity planning
>> reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://sdm.link/zohomanageengine
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Re: Question about data store outside of jbrowse

nathandunn

Reading through various comments, that looks like a pretty robust solution for tomcat.    

Nathan

> On Jun 16, 2016, at 11:25 PM, Marc P. Hoeppner <[hidden email]> wrote:
>
> Hi,
>
> thanks for the hints. I am trying out JBrowse as a stand-alone (not Apollo) for a specific project. I ended up "mount --bind" ing the data store from our storage space - that seems to work fine. I will see if this becomes a problem down the line and have a look at your other suggestions.
>
> Cheers,
>
> Marc
>
> Am 16.06.16 um 18:01 schrieb Nathan Dunn:
>> Marc,
>>
>> What is your goal?    I seem to remember you doing Apollo stuff.  You can always click on “public” under the organism tab and you can browse any organism directly (logout and then click “Browse Genomes”).
>>
>> If you are wanting raw JBrowse (different views and feature-set), you have a few options:
>>
>> 1 - symlink.  I don’t recommend this as non-war files can have weird behavior.  Definitely not a bad first step.  You may have to turn on “allowLink” in server.xml though I think its on by default.  I think it is recommended not doing this for windows as well.
>>
>> 2 - You can add “Context” entry to your tomcat server.xml inside a <Host> . . .  <Context docBase="/path/to/files" path="/files" />.  http://stackoverflow.com/a/1812356/1739366  (see the very first part of this)
>>
>> 3 - You can add Apache 2 as a proxy.  http://genomearchitect.readthedocs.io/en/stable/Configure.html?highlight=proxy#apache-proxy and then add a separate directory for JBrowse.  This is what I typically do, but I serve up a lot of different things.
>>
>>
>> Nathan
>>
>>> On Jun 16, 2016, at 2:35 AM, Raymond Wan <[hidden email]> wrote:
>>>
>>> Hi Marc,
>>>
>>>
>>> On Thu, Jun 16, 2016 at 5:28 PM, Marc P. Hoeppner <[hidden email]> wrote:
>>>> hope this hasn't been answered in the recent past, but I have not been
>>>> able to figure out how to set a data store that is not within the
>>>> jbrowse folder. Specifically:
>>>>
>>>> Jbrowse lives in: /usr/share/tomcat7/webapps/jbrowse
>>>
>>> I've never tried running JBrowse under Tomcat -- I've only used Apache.
>>>
>>> But does setting a symbolic link work?  (i.e., "ln" command so that
>>> /usr/share/tomcat7/webapps/jbrowse/data links to /jbrowse/data)  Of
>>> course, in addition to the Tomcat configuration to allow following of
>>> symbolic links.
>>>
>>>
>>>> tomcat. I get the data set selector, but JBrowse apparently cannot read
>>>> from /jbrowse/data (all permissions were transferred when copying it).
>>>
>>> At least for Apache, you will want the files owned by the process that
>>> runs the Apache process.  Alternatively, by the same group is fine,
>>> too.
>>>
>>> I presume Tomcat is the same here...
>>>
>>> Perhaps you should double check the permissions?  And maybe even do a
>>> recursive chown/chmod.
>>>
>>> Ray
>>>
>>> ------------------------------------------------------------------------------
>>> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
>>> patterns at an interface-level. Reveals which users, apps, and protocols are
>>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>>> J-Flow, sFlow and other flows. Make informed decisions using capacity planning
>>> reports. http://pubads.g.doubleclick.net/gampad/clk?id=1444514421&iu=/41014381
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports. http://sdm.link/zohomanageengine
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