Basic setup question

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Basic setup question

Malcolm Tobias

All,

I manage a cluster and have been asked to set up a local instance of galaxy. I'm neither a galaxy user nor a biologist, so apologies in advance if my terminology is off.

I have a basic setup running now, but have been asked to include the option to "display at UCSC Main" when a user uploads a bam and clicks on the dataset. Currently I have the options of "display in IGB Local Web". I've tried this at a few of the other Galaxy sites, and the behavior seems unpredictable. Uploading the same data set to some sites gives me this option, while others don't. I'm assuming this is determined by the option in the universe_wsgi.ini file:

# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt

ucsc_display_sites = main,test,archaea,ucla

but uncommenting this option and restarting the server doesn't help. Increasing the log_level to DEBUG doesn't provide any insight.

Any suggestions about how to proceed? Could there be any firewall-related issues? I ask because of this in the configuration file:

# If use_remote_user = True, display application servers will be denied access

# to Galaxy and so displaying datasets in these sites will fail.

# display_servers contains a list of hostnames which should be allowed to

# bypass security to display datasets. Please be aware that there are security

# implications if this is allowed. More details (including required changes to

# the proxy server config) are available in the Apache proxy documentation on

# the wiki.

Thanks in advance,

Malcolm

--

Malcolm Tobias

314.362.1594


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Re: Basic setup question

Hans-Rudolf Hotz
Hi Malcolm

Displaying your data in browser outside of Galaxy is always a little bit
tricky. And there are two issues:

  - first, getting the 'display at UCSC main' option to show up in
    the history item

  - second, getting the actual display (at UCSC) to work


As far as I understand your e-mail, you currently struggle with the first?

There are a few points to check

a) (as you have written) make sure to have the option turned on in  the
    ~/universe_wsgi.ini file, eg:

   "ucsc_display_sites = main"


b) make sure two edit ~/tool-data/shared/ucsc/ucsc_build_sites.txt
    by listing all genomes you are interested to use for the display, eg:

    main http://genome.ucsc.edu/cgi-bin/hgTracks? mm7,mm8,mm9

    The database attribute of your dataset (ie history item) has to be
    set to either mm7 or mm8 or mm9. You will not get the the display
    option if the database is set to mm10 or hg18

c) make sure two edit ~/datatypes_conf.xml, eg

    <display file="ucsc/bam.xml" />

   should not be commented-out.



If all of this is correctly set up, you should get the 'display at UCSC
main' for your mouse (mm9) bam file.


Now comes the second issue, getting the display to work and here you
might run into firewall-related issues. Check: "Display Sites" at
http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy

Unfortunately, at this point we struggle as well on our main production
galaxy server which relies on external authentication.


Regards, Hans-Rudolf



On 06/06/2013 07:43 PM, Malcolm Tobias wrote:

> All,
>
> I manage a cluster and have been asked to set up a local instance of
> galaxy. I'm neither a galaxy user nor a biologist, so apologies in
> advance if my terminology is off.
>
> I have a basic setup running now, but have been asked to include the
> option to "display at UCSC Main" when a user uploads a bam and clicks on
> the dataset. Currently I have the options of "display in IGB Local Web".
> I've tried this at a few of the other Galaxy sites, and the behavior
> seems unpredictable. Uploading the same data set to some sites gives me
> this option, while others don't. I'm assuming this is determined by the
> option in the universe_wsgi.ini file:
>
> # UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
>
> ucsc_display_sites = main,test,archaea,ucla
>
> but uncommenting this option and restarting the server doesn't help.
> Increasing the log_level to DEBUG doesn't provide any insight.
>
> Any suggestions about how to proceed? Could there be any
> firewall-related issues? I ask because of this in the configuration file:
>
> # If use_remote_user = True, display application servers will be denied
> access
>
> # to Galaxy and so displaying datasets in these sites will fail.
>
> # display_servers contains a list of hostnames which should be allowed to
>
> # bypass security to display datasets. Please be aware that there are
> security
>
> # implications if this is allowed. More details (including required
> changes to
>
> # the proxy server config) are available in the Apache proxy
> documentation on
>
> # the wiki.
>
> Thanks in advance,
>
> Malcolm
>
> --
>
> Malcolm Tobias
>
> 314.362.1594
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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Re: Basic setup question

Malcolm Tobias

Hans-Rudolf,

First off, thanks for the response.

On Friday 07 June 2013 03:00:40 Hans-Rudolf Hotz wrote:

> b) make sure two edit ~/tool-data/shared/ucsc/ucsc_build_sites.txt

> by listing all genomes you are interested to use for the display, eg:

>

> main http://genome.ucsc.edu/cgi-bin/hgTracks? mm7,mm8,mm9

>

> The database attribute of your dataset (ie history item) has to be

> set to either mm7 or mm8 or mm9. You will not get the the display

> option if the database is set to mm10 or hg18

That's it! The test dataset I've been given is part of the "hg19" database, but that isn't included in:

[galaxy@login002 galaxy-dist]$ grep main tool-data/shared/ucsc/ucsc_build_sites.txt

main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2

When I uploaded the same dataset to the "Main" galaxy server: https://main.g2.bx.psu.edu/, it did give me the "display at UCSC" option, so they must have updated their database list.

Thanks again,

Malcolm

--

Malcolm Tobias

314.362.1594


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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