Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS
It's un-commented in both local and production. Still there is no icon in production. Cheers, Oksana On Mon, Jan 25, 2016 at 9:52 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi,
can you please check this setting?
https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L2...
Thanks, Bjoern
Thanks, Bjoern!
For my local install of Galaxy, logging in as a user worked and the icon is showing up (although I still had to manually go and change permissions on all the mako templates in ./database/compiled_templates directory). But our production instance of Galaxy (also v15.07 on CentOS 6.7) does not show the chart-symbol for Phyloviz, even when I'm logged in as a user. In production, it is not a clean install, but an upgrade from previous versions, so it is harder to figure out what's going on. There are no errors in the logs, so I'm still looking for any kind of clues of what could have gone wrong with the visualization.
Cheers, Oksana
Message: 1 Date: Sat, 23 Jan 2016 19:55:47 +0100 From: Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> To: Oksana Korol <okorol@gmail.com <mailto:okorol@gmail.com>>, galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS Message-ID: <56A3CCB3.9020503@gmail.com <mailto:56A3CCB3.9020503@gmail.com>> Content-Type: text/plain; charset=utf-8
Hi Oksana,
this work for me in 16.01 (upcoming). Please make sure you are logged into your Galaxy as some user, not anonymous and than the Phyloviz Visualisation will be available from the small chart-symbol next to
Am 25.01.2016 um 15:46 schrieb Oksana Korol: the
(i) symbol.
Hope this helps, Bjoern
Am 22.01.2016 um 23:53 schrieb Oksana Korol: > Hi, > > I'm having trouble getting visualization icons, like Phyloviz, to
show
> up on my Galaxy instance running in CentOS 6.7. Here are the steps
I
> took, expecting it to work: > > 1. cloned Galaxy tag v15.07 (that's the version we need to run in > production) > > 2. Followed the steps in https://wiki.galaxyproject.org/VisualizationSetup > - Renamed datatypes_conf.xml.sample to > datatypes_conf.xml > - Downloaded wigToBigWig, bedGraphToBigWig, and faToTwoBit > - Installed BED Tools > - Added above tools to my user path (galaxy_utils dir is where > wigToBigWig and others are): >
/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/galaxyuser/bin:/home/galaxyuser/bin:/home/galaxyuser/galaxy_utils:/home/galaxyuser/bin:/*home/galaxyuser/galaxy_utils:/home/galaxyuser/galaxy_utils/BEDTools/bedtools2/bin
> * > 3. Started Galaxy. > > 4. Uploaded a newick tree file (nhx), which is known to be
displayable
> in phyloviz on a Ubuntu instance of Galaxy > > 5. Made sure the datatype is nhx > > 6. Expecting to see a Phyloviz "graph" icon on the left, when I
expand
> the file in history, but there is nothing there. > > At this point I don't know where to dig to find how I can fix it.
Any
> feedback, including your own stories for visualization setup or
how I
> can debug what's not being picked up where, would be greatly appreciated. > > Cheers, > Oksana > --
This gets tricky, can you check if the visualisations are loacted under this path and do double-check the filetypes? The icon is only displayed with the correct datatype. Am 25.01.2016 um 17:37 schrieb Oksana Korol:
It's un-commented in both local and production. Still there is no icon in production.
Cheers, Oksana
On Mon, Jan 25, 2016 at 9:52 AM, Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> wrote:
Hi,
can you please check this setting?
https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L2...
Thanks, Bjoern
Am 25.01.2016 um 15:46 schrieb Oksana Korol: > Thanks, Bjoern! > > For my local install of Galaxy, logging in as a user worked and the icon > is showing up (although I still had to manually go and change > permissions on all the mako templates in ./database/compiled_templates > directory). But our production instance of Galaxy (also v15.07 on CentOS > 6.7) does not show the chart-symbol for Phyloviz, even when I'm logged > in as a user. In production, it is not a clean install, but an upgrade > from previous versions, so it is harder to figure out what's going on. > There are no errors in the logs, so I'm still looking for any kind of > clues of what could have gone wrong with the visualization. > > Cheers, > Oksana > > Message: 1 > Date: Sat, 23 Jan 2016 19:55:47 +0100 > From: Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com> > <mailto:bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>>> > To: Oksana Korol <okorol@gmail.com <mailto:okorol@gmail.com> <mailto:okorol@gmail.com <mailto:okorol@gmail.com>>>, > galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org> > <mailto:galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org>> > Subject: Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS > Message-ID: <56A3CCB3.9020503@gmail.com <mailto:56A3CCB3.9020503@gmail.com> > <mailto:56A3CCB3.9020503@gmail.com <mailto:56A3CCB3.9020503@gmail.com>>> > Content-Type: text/plain; charset=utf-8 > > Hi Oksana, > > this work for me in 16.01 (upcoming). Please make sure you are logged > into your Galaxy as some user, not anonymous and than the Phyloviz > Visualisation will be available from the small chart-symbol next to the > (i) symbol. > > Hope this helps, > Bjoern > > Am 22.01.2016 um 23:53 schrieb Oksana Korol: > > Hi, > > > > I'm having trouble getting visualization icons, like Phyloviz, to show > > up on my Galaxy instance running in CentOS 6.7. Here are the steps I > > took, expecting it to work: > > > > 1. cloned Galaxy tag v15.07 (that's the version we need to run in > > production) > > > > 2. Followed the steps in > https://wiki.galaxyproject.org/VisualizationSetup > > - Renamed datatypes_conf.xml.sample to > > datatypes_conf.xml > > - Downloaded wigToBigWig, bedGraphToBigWig, and faToTwoBit > > - Installed BED Tools > > - Added above tools to my user path (galaxy_utils dir is where > > wigToBigWig and others are): > > > /usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/galaxyuser/bin:/home/galaxyuser/bin:/home/galaxyuser/galaxy_utils:/home/galaxyuser/bin:/*home/galaxyuser/galaxy_utils:/home/galaxyuser/galaxy_utils/BEDTools/bedtools2/bin > > * > > 3. Started Galaxy. > > > > 4. Uploaded a newick tree file (nhx), which is known to be displayable > > in phyloviz on a Ubuntu instance of Galaxy > > > > 5. Made sure the datatype is nhx > > > > 6. Expecting to see a Phyloviz "graph" icon on the left, when I expand > > the file in history, but there is nothing there. > > > > At this point I don't know where to dig to find how I can fix it. Any > > feedback, including your own stories for visualization setup or how I > > can debug what's not being picked up where, would be greatly > appreciated. > > > > Cheers, > > Oksana > > --
It get even trickier... I just double-checked my local install, and I didn't have visualization_plugins_directory uncommented, and yet, it works on local install....
This gets tricky, can you check if the visualisations are loacted under this path
If you mean phyoviz and other plugin code from github, then yes, it's there. I doulbe-checked the files and permissions as well, just to be sure.
and do double-check the filetypes? The icon is only displayed with the correct datatype.
I did... I use exactly the same newick tree file for local and for production test. Upload it, selecting nhx as a datatype. Double-check the datatype by clicking on a pencil icon - it's nhx on both, but it works on local and doesn't on production. I'll keep digging and comparing the two installs. If you think of anything else, let me know. Thanks! Oksana
Hi, Oksana There are a few places to look and things to check in this situation. *First*, are other visualizations working on your production instance? Do you see the visualization icon/button and does the dropdown there have the 'charts' visualization on tabular files (like bed)? On the admin side for this, when your instance starts up you should see a section of logging data for visualizations that are loaded or error in the paster log. They're shown after the converter tools output logging info and before the job runners output theirs. They look something like: galaxy.web.base.pluginframework INFO 2016-01-26 09:57:37,989 VisualizationsRegistry, loaded plugin: phyloviz You should see the standard visualizations load there including 'phyloviz'. If there's a problem, then you'll see a stack trace and a message saying that it was skipped. *Second*, if visualizations are working well for other types, can you try uploading a phyloxml file and seeing if phyloviz will launch from that data? There's an example in this history: https://test.galaxyproject.org/u/carleberhard/h/phyloviz *Third*, it may be an issue with how the datatype is being referenced in the phyloviz config file (when compared with your datatypes_conf.xml file). Can you check the datatypes api on your production instance: $YOUR_ROOT/api/datatypes/mapping ...and search for the 'nhx' datatype? You should see something like towards the bottom of the response: "nhx": "galaxy.datatypes.data.Newick", I believe, this last part of this *should* match the line in phyloviz's config file: <test type="isinstance" test_attr="datatype" result_type="datatype"> data.Newick</test> Thanks, Carl On Mon, Jan 25, 2016 at 1:37 PM, Oksana Korol <okorol@gmail.com> wrote:
It get even trickier... I just double-checked my local install, and I didn't have visualization_plugins_directory uncommented, and yet, it works on local install....
This gets tricky, can you check if the visualisations are loacted under this path
If you mean phyoviz and other plugin code from github, then yes, it's there. I doulbe-checked the files and permissions as well, just to be sure.
and do double-check the filetypes? The icon is only displayed with the correct datatype.
I did... I use exactly the same newick tree file for local and for production test. Upload it, selecting nhx as a datatype. Double-check the datatype by clicking on a pencil icon - it's nhx on both, but it works on local and doesn't on production.
I'll keep digging and comparing the two installs. If you think of anything else, let me know.
Thanks!
Oksana
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Thanks for the detailed breakdown of the places to check, Carl! I was able to fix the issue following the steps you've outlined. For the benefit of other readers, here is what I did to fix it: On Tue, Jan 26, 2016 at 10:09 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hi, Oksana
There are a few places to look and things to check in this situation.
*First*, are other visualizations working on your production instance? Do you see the visualization icon/button and does the dropdown there have the 'charts' visualization on tabular files (like bed)?
Yes, I am able to see other visualizations.
On the admin side for this, when your instance starts up you should see a section of logging data for visualizations that are loaded or error in the paster log. They're shown after the converter tools output logging info and before the job runners output theirs. They look something like:
galaxy.web.base.pluginframework INFO 2016-01-26 09:57:37,989 VisualizationsRegistry, loaded plugin: phyloviz
You should see the standard visualizations load there including 'phyloviz'. If there's a problem, then you'll see a stack trace and a message saying that it was skipped.
Logs where showing no problems.
*Second*, if visualizations are working well for other types, can you try uploading a phyloxml file and seeing if phyloviz will launch from that data? There's an example in this history:
Uploaded phyloxml sample and it was showing visualization icon.
*Third*, it may be an issue with how the datatype is being referenced in the phyloviz config file (when compared with your datatypes_conf.xml file).
I've checked datatypes_conf.xml file and the lines that describe newick and nexus datatypes where commented out. A bit silly, but that was what was breaking it. Uncommenting them fixed the issue. Thanks for all your help, guys! Cheers, Oksana
participants (3)
-
Björn Grüning -
Carl Eberhard -
Oksana Korol