Re: [galaxy-dev] Retrieving json files
Hi, Saket There's currently no json dataprovider. It's still relatively easy to get a JSON object, though. I'd recommend: 1. Using the 'line' dataprovider 2. Then, joining the strings returned from it (generally, you want all the strings so be careful using the regex, limit, or offset parameters) 3. Finally, parsing the joined text as JSON (in python: json.loads( your_string ), in javascript: JSON.parse( yourString )) Let me know if that doesn't work, Carl On Mon, Sep 1, 2014 at 2:25 AM, Saket Choudhary sake...@gmail.com wrote: Is there a way to retrieve fileX.json in history using the DataProviders? Using https://wiki.galaxyproject.org/DataProviders I tried base and line, but I am looking for retrieving the contents of fileX.json as a json object itself. Saket ___ 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/ ___ 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/
Re: [galaxy-dev] testing the visualization plugins
Ok - thanks! That is strange: the server seems to be configured properly
for all the new plugins but the client side believes only trackster is
available.
Let's try two things:
*First*, let's clear the browser cache to rule out that annoyance:
- In Chrome, I've had good luck with these instructions:
http://superuser.com/questions/89809/how-to-force-refresh-without-cache-in-google-chrome
- In Firefox, you can try:
http://superuser.com/questions/173210/how-can-i-clear-a-single-site-from-the-cache-in-firefox
Does the full menu of visualization options appear after you've done that
for the development server?
*Second*, let's see what the server ends up sending the client for
visualizations:
1. When you're logged into the dev server, open a new tab/window and
enter 'your dev server domain/api/histories' - this will return the
summary JSON data for your histories.
2. Look for the history you've been trying and add the 'id' value for it
(a hex string) and the word 'contents' to the url in your address bar like
this: 'your domain/api/histories/id/contents' - this will be the JSON
summaries of the datasets in that history
3. Finally, find a the JSON for a dataset in the summaries that should
work with charts - a bed file or a tabular file should work - and add the
'id' value for that dataset to the url in the address bar:
'domain/api/histories/history id/contents/dataset id' - this will be
JSON details for that dataset.
The detailed JSON dataset data should have a key/value pair for
'visualizations'. Since the plugin registry *should* be enabled, the server
should be returning an array of JSON objects for this key. Something like
this:
visualizations: [{ embeddable: false, href:
/visualization/show/charts?dataset_id=f597429621d6eb2b, html:
Charts, target: galaxy_main},{ embeddable:
false, href:
/visualization/show/scatterplot?dataset_id=f597429621d6eb2b,
html: Scatterplot, target: galaxy_main},{
embeddable: false, href:
/visualization/trackster?dataset_id=f597429621d6eb2bdbkey=%3Fhda_ldda=hda,
html: Trackster, target: _top} ]
If, for some reason, the registry is disabled (which strangely
*should* have shown in the logs), you'll instead see an array of plain
strings: [ 'trackster', ... ].
Does the array you see match the first structure? Are the JSON for
charts and scatterplot included?
Tedious work, I know, and I appreciate the help in diagnosing this bug.
On Thu, Aug 28, 2014 at 5:24 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Carl
What was the datatype (listed as 'format') of the dataset you tested
with here?:
However, if I hoover over the bar-plot icon, Visualize in
Trackster pops up (instead of just Visualize)
any data type, eg wig, tabular, bed, etc
I currently have: 'result_type=datatypedata.Data'
in ~/config/plugins/visualizations/trackster/config/trackster.xml
If I change that to 'result_type=datatypeinterval.Interval' (and do a
restart), I lose the bar-plot icon for wig and tabular. It is still there
for the bed file in the history.
Do the 'charts' and 'scatterplot' visualizations show up in the
visualization icon popup menu when you check on an interval or bed
datatype?
They never show up, I don't get the menu when I click on the bar-plot icon
(for bed and/or interval data typ). It goes straight to the Trackster page,
where, I am asked to define the Browser name and the Reference genome.
Hans-Rudolf
Thanks for the report and any info you can provide,
Carl
On Wed, Aug 27, 2014 at 4:03 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi
As part of my upgrade/testing work, I am looking at the
visualization plugins.
In a new galaxy installation (latest_2014.08.11), they (ie
'Charts', 'Scatterplot', and 'Trackster') seem to work fine.
All I have done was:
- I defined the visualization_plugins___directory in the
universe_wsgi.ini file
If I comment-out this line, I only get trackster, when I click on
the icon which looks like a bar-plot
Next, I have tried it on our development server (after I have
upgraded from release_2014.04.14 to latest_2014.08.11). I
changed the universe_wsgi.ini file.
I the logs I get:
galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,639
VisualizationsRegistry, loaded plugin: charts
galaxy.web.base.__pluginframework WARNING 2014-08-27 09:43:45,641
VisualizationsRegistry, plugin load failed or disabled:
./config/plugins/__visualizations/circster. Skipping...
galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,655
VisualizationsRegistry, loaded plugin: graphview
galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,657
VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.__pluginframework INFO 2014-08-27 09:43:45,675
Re: [galaxy-dev] testing the visualization plugins
Ok. Very strange. I'm unable to reproduce this with galaxy-dist 57d1b77
(stable).
Can you apply the attached patch, load a history with a simple bed file
(say: test-data/1.bed - or any bed file), and reply with what the logs say?
You can safely revert that change after we're done.
On Thu, Aug 28, 2014 at 9:29 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Carl
Thanks for your help - unfortunately no success so far
Let's try two things:
*First*, let's clear the browser cache to rule out that annoyance:
This didn't change anything. I have also tried different computers and
different browsers
*Second*, let's see what the server ends up sending the client for
visualizations:
it just looks like this:
visible: true,
visualizations: [
{
embeddable: false,
href:
/visualization/trackster?dataset_id=b1c72d84f3501797dbkey=%3Fhda_ldda=hda,
html: Trackster,
target: _top
}
]
}
Hans-Rudolf
140828.hans-visualizations.patch
Description: Binary data
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Re: [galaxy-dev] testing the visualization plugins
Hi, Hans, What was the datatype (listed as 'format') of the dataset you tested with here?: However, if I hoover over the bar-plot icon, Visualize in Trackster pops up (instead of just Visualize) Trackster by default accepts all datatypes (all subclasses inheriting data.Data) and is the only visualization that ships with Galaxy that allows visualization on all datatypes. You can change that by editing the 'Charts' and 'scatterplot' can work with any tabular datatype (or subclasses of). If a datatype isn't tabular, those visualizations won't appear as options in the menu. Do the 'charts' and 'scatterplot' visualizations show up in the visualization icon popup menu when you check on an interval or bed datatype? Thanks for the report and any info you can provide, Carl On Wed, Aug 27, 2014 at 4:03 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi As part of my upgrade/testing work, I am looking at the visualization plugins. In a new galaxy installation (latest_2014.08.11), they (ie 'Charts', 'Scatterplot', and 'Trackster') seem to work fine. All I have done was: - I defined the visualization_plugins_directory in the universe_wsgi.ini file If I comment-out this line, I only get trackster, when I click on the icon which looks like a bar-plot Next, I have tried it on our development server (after I have upgraded from release_2014.04.14 to latest_2014.08.11). I changed the universe_wsgi.ini file. I the logs I get: galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,639 VisualizationsRegistry, loaded plugin: charts galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,641 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/circster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,655 VisualizationsRegistry, loaded plugin: graphview galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,657 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,675 VisualizationsRegistry, loaded plugin: scatterplot galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,677 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/sweepster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,679 VisualizationsRegistry, loaded plugin: trackster wrt to 'Charts', 'Scatterplot', and 'Trackster', this looks fine to me. However, if I hoover over the bar-plot icon, Visualize in Trackster pops up (instead of just Visualize), and when I click on it I get straight to the Trackster page, where, I am asked to define the Browser name and the Reference genome. No links for 'Charts' and 'Scatterplot'. On the other hand, the plug in infrastructure seems to work: If I change ~/config/plugins/visualizations/trackster/config/trackster.xml I see the effects, ie if I change result_type=datatypedata.Data to result_type=datatypeinterval.Interval I can restrict the visualization to only the interval data. Somehow, I am running a mixture of the 'old' and the 'new' visualization set-up ? Has anyone seen similar problems when testing the new plug in infrastructure on an old/upgraded Galaxy installation Thank you very much for any hints and help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ 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/ ___ 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/
Re: [galaxy-dev] testing the visualization plugins
(oops, to continue the truncated sentence in the prev. email): You can change that by editing the ... config/trackster.xml 'datatype' as you did in your email to restrict what Trackster can run on. (sorry about that) On Wed, Aug 27, 2014 at 9:39 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Hi, Hans, What was the datatype (listed as 'format') of the dataset you tested with here?: However, if I hoover over the bar-plot icon, Visualize in Trackster pops up (instead of just Visualize) Trackster by default accepts all datatypes (all subclasses inheriting data.Data) and is the only visualization that ships with Galaxy that allows visualization on all datatypes. You can change that by editing the 'Charts' and 'scatterplot' can work with any tabular datatype (or subclasses of). If a datatype isn't tabular, those visualizations won't appear as options in the menu. Do the 'charts' and 'scatterplot' visualizations show up in the visualization icon popup menu when you check on an interval or bed datatype? Thanks for the report and any info you can provide, Carl On Wed, Aug 27, 2014 at 4:03 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi As part of my upgrade/testing work, I am looking at the visualization plugins. In a new galaxy installation (latest_2014.08.11), they (ie 'Charts', 'Scatterplot', and 'Trackster') seem to work fine. All I have done was: - I defined the visualization_plugins_directory in the universe_wsgi.ini file If I comment-out this line, I only get trackster, when I click on the icon which looks like a bar-plot Next, I have tried it on our development server (after I have upgraded from release_2014.04.14 to latest_2014.08.11). I changed the universe_wsgi.ini file. I the logs I get: galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,639 VisualizationsRegistry, loaded plugin: charts galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,641 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/circster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,655 VisualizationsRegistry, loaded plugin: graphview galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,657 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,675 VisualizationsRegistry, loaded plugin: scatterplot galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,677 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/sweepster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,679 VisualizationsRegistry, loaded plugin: trackster wrt to 'Charts', 'Scatterplot', and 'Trackster', this looks fine to me. However, if I hoover over the bar-plot icon, Visualize in Trackster pops up (instead of just Visualize), and when I click on it I get straight to the Trackster page, where, I am asked to define the Browser name and the Reference genome. No links for 'Charts' and 'Scatterplot'. On the other hand, the plug in infrastructure seems to work: If I change ~/config/plugins/visualizations/trackster/config/trackster.xml I see the effects, ie if I change result_type=datatypedata.Data to result_type=datatypeinterval.Interval I can restrict the visualization to only the interval data. Somehow, I am running a mixture of the 'old' and the 'new' visualization set-up ? Has anyone seen similar problems when testing the new plug in infrastructure on an old/upgraded Galaxy installation Thank you very much for any hints and help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ 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/ ___ 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/
Re: [galaxy-dev] IE 11 issues
That's what I was getting as well. It looks like this is an issue with IE11's event management API and our version of jQuery. I'll see if I can find a fix or alternately see if an updated jQuery will still cause this error. If this is blocking your analyses, I'd unfortunately recommend using either Chrome/Firefox or an older version of IE (10?). You might also try using IE's compatibility mode but this must be set on a per browser basis and might be tedious: https://kb.wisc.edu/page.php?id=35591 I'll update when I find out more and thanks for the report, Carl On Mon, Jul 28, 2014 at 1:24 PM, Sajdak, Doris dj...@buffalo.edu wrote: Hi Carl, Thanks for the help. Here’s what I get when I try to upload a new file: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: '$' is undefined File: tool_runner, Line: 64, Column: 13 SCRIPT5007: Unable to get property 'extend' of undefined or null reference File: galaxy.panels.js, Line: 28, Column: 1 SCRIPT5002: Function expected File: tool_runner, Line: 80, Column: 5 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 SCRIPT5002: Function expected File: galaxy.tools.js, Line: 9, Column: 5 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 I get the following when I click on the edit button next to one of the items in my history: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: 'jQuery' is undefined File: jquery.autocomplete.js, Line: 9, Column: 2 SCRIPT5009: 'jQuery' is undefined File: galaxy.autocom_tagging.js, Line: 20, Column: 1 SCRIPT5009: '$' is undefined File: edit, Line: 528, Column: 9 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 This is what I get from ‘hg summary:’ parent: 12442:29ce93a13ac7 tip Merge stable branch. branch: default commit: 1 modified, 177 unknown update: (current) Hope that helps. We’re very new to Galaxy so I won’t be surprised if it’s something wrong on my end. Thanks, Dori *From:* Carl Eberhard [mailto:carlfeberh...@gmail.com] *Sent:* Monday, July 28, 2014 10:55 AM *To:* Björn Grüning *Cc:* galaxy-dev@lists.bx.psu.edu; Sajdak, Doris *Subject:* Re: [galaxy-dev] IE 11 issues Hi, Dori Galaxy supports IE 10+ so this is definitely a bug. I'm checking for bugs in the history panel now, but in the meantime: - can you open the javascript console in your IE and see if any errors are displayed when doing the two tasks you mention? http://msdn.microsoft.com/en-us/library/ie/bg182326%28v=vs.85%29.aspx - What version of Galaxy does your lab use currently? (You can view the version by using the 'hg summary' command from the directory from which Galaxy is run) As an aside, IE has traditionally veered away from web standards and made it difficult to program compatible sites. Recent versions of IE have become much more standards compliant allowing us to support them well enough. Please don't hesitate to report IE (10+) bugs when using Galaxy. Thanks for the report and I'll update with my findings soon, Carl On Mon, Jul 28, 2014 at 10:42 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Dori, the IE is not really supported. There are many issues with IE and it's hard to deal with that. If possible please you Chrome or FF, both are supported and tested. Cheers, Bjoern Am 28.07.2014 um 16:40 schrieb Sajdak, Doris: We are having issues with using Galaxy in Internet Explorer 11 (these work fine in Chrome Firefox). 1. The jobs queued and history doesn't display unless you refresh the browser window. Clicking the history reload icon doesn't work. 2. If I click to edit something in the history, the tabs aren't clickable. Attributes are displayed but I can't click on Convert Format, Datatype, or Permissions. Anyone else having this problem? I
Re: [galaxy-dev] how to delete datasets or save space on local galaxy
You're absolutely right. That is a bug with that particular method of purging. I've created a card for it here: https://trello.com/c/bvOL9IBb. Thanks very much for finding that. On Mon, Apr 14, 2014 at 11:31 AM, Wang, Xiaofei xfw...@ku.edu wrote: Hi Carl, The size is changed when the page is reloaded. Here is how I purge the data: 1. Mark them deleted using the X button on the dataset 2. From the history options menu, select 'Purge Deleted Datasets' I think this will purge the deleted datasets too (correct?) because in the yellow box it shows that This dataset has been deleted and removed from disk. But I am not sure if there is any difference with the 3-steps that you advised. I think the difference might be that it can purge the dataset one by one in your advice, is it? Thanks Xiaofei *From:* Carl Eberhard [carlfeberh...@gmail.com] *Sent:* Monday, April 14, 2014 8:47 AM *To:* Wang, Xiaofei *Cc:* Dannon Baker; galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hello, That's a good question! Does the size in the top right change when the page is reloaded? Are these datasets copied from another history? How are you purging the datasets? As Dannon mentioned, if you click the 'X' button on the dataset it will 'mark' the dataset as deleted. To permanently deleted the datasets (or 'purge' them), you can: 1. Mark them deleted using the 'X' button on the dataset, 2. Then from the history options menu (the button that looks like a gear at the top of the history), select 'Include deleted datasets'. This will make the dataset you marked as deleted visible in the history again. 3. In the deleted dataset you'll see a yellow box explaining that the history has been deleted and showing two links: one for undeleting the dataset (which will undo the deletion of the dataset) and one for immediately removing it from disk - this link will purge the dataset. Click the second link. You can hide the deleted datasets again by clicking: history options menu - 'Include deleted datasets' again. If you do the above, does the size in the top right change or still remain the same? Let me know if you need more info, Carl On Fri, Apr 11, 2014 at 6:25 PM, Wang, Xiaofei xfw...@ku.edu wrote: Yes, it works. But, I am still a little bit confuse about the size on the top right corner. Why does not it change after purging datasets? -- *From:* Dannon Baker [dannon.ba...@gmail.com] *Sent:* Friday, April 11, 2014 4:57 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy I replied too soon. To answer your second question, yes, that's how to use the cleanup scripts from the command line. Enabling the option from my previous email will allow users to *immediately* purge datasets without waiting on those cleanup scripts. -Dannon On Fri, Apr 11, 2014 at 5:55 PM, Dannon Baker dannon.ba...@gmail.comwrote: Hey, sure. The option you're looking for is allow_user_dataset_purge, around line 650 or so. Good luck! -Dannon On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei xfw...@ku.edu wrote: Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets is how to use the command line, correct? Thanks a lot! Best, Xiaofei -- *From:* Dannon Baker [dannon.ba...@gmail.com] *Sent:* Friday, April 11, 2014 4:42 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the Purge Deleted Datasets option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei xfw...@ku.edu wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. Thank you so much! Best, Xiaofei ___ 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/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other
Re: [galaxy-dev] how to delete datasets or save space on local galaxy
Hello, That's a good question! Does the size in the top right change when the page is reloaded? Are these datasets copied from another history? How are you purging the datasets? As Dannon mentioned, if you click the 'X' button on the dataset it will 'mark' the dataset as deleted. To permanently deleted the datasets (or 'purge' them), you can: 1. Mark them deleted using the 'X' button on the dataset, 2. Then from the history options menu (the button that looks like a gear at the top of the history), select 'Include deleted datasets'. This will make the dataset you marked as deleted visible in the history again. 3. In the deleted dataset you'll see a yellow box explaining that the history has been deleted and showing two links: one for undeleting the dataset (which will undo the deletion of the dataset) and one for immediately removing it from disk - this link will purge the dataset. Click the second link. You can hide the deleted datasets again by clicking: history options menu - 'Include deleted datasets' again. If you do the above, does the size in the top right change or still remain the same? Let me know if you need more info, Carl On Fri, Apr 11, 2014 at 6:25 PM, Wang, Xiaofei xfw...@ku.edu wrote: Yes, it works. But, I am still a little bit confuse about the size on the top right corner. Why does not it change after purging datasets? -- *From:* Dannon Baker [dannon.ba...@gmail.com] *Sent:* Friday, April 11, 2014 4:57 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy I replied too soon. To answer your second question, yes, that's how to use the cleanup scripts from the command line. Enabling the option from my previous email will allow users to *immediately* purge datasets without waiting on those cleanup scripts. -Dannon On Fri, Apr 11, 2014 at 5:55 PM, Dannon Baker dannon.ba...@gmail.comwrote: Hey, sure. The option you're looking for is allow_user_dataset_purge, around line 650 or so. Good luck! -Dannon On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei xfw...@ku.edu wrote: Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets is how to use the command line, correct? Thanks a lot! Best, Xiaofei -- *From:* Dannon Baker [dannon.ba...@gmail.com] *Sent:* Friday, April 11, 2014 4:42 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the Purge Deleted Datasets option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei xfw...@ku.edu wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. Thank you so much! Best, Xiaofei ___ 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/ ___ 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/ inline: Screen Shot 2014-04-11 at 4.30.18 PM.png___ 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/
Re: [galaxy-dev] [CONTENT] Re: Unable to remove old datasets
Thanks, Ravi Peter I've added a card to get the allow_user_dataset_purge options into the client and to better show the viable options to the user: https://trello.com/c/RCPZ9zMF On Fri, Mar 14, 2014 at 11:10 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Fri, Mar 14, 2014 at 11:24 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Mar 13, 2014 at 6:40 PM, Sanka, Ravi rsa...@jcvi.org wrote: I do not think so. Several individual datasets have been deleted (clicked the upper-right X on the history item box) but no History has been permanently deleted. Is there any indication in the database if target dataset or datasets were marked for permanent deletion? In the dataset table, I see fields deleted, purged, and purgable, but nothing that says permanently deleted. I would welcome clarification from the Galaxy Team, here and on the wiki page which might benefit from a flow diagram? https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets My assumption is using permanently delete in the user interface marks an entry as purgable, and then it will be moved to purged (and the associated file on disk deleted) by the cleanup scripts - but I'm a bit hazy on this any why it takes a while for a user's usage figures to change. Hmm. Right now I've unable (via the web interface) to permanently delete a history - it stays stuck as deleted, and thus (presumably) won't get purged by the clean up scripts. I've tried: 1. Load problem history 2. Rename the history DIE DIE to avoid confusion 3. Top right menu, Delete permanently 4. Prompted Really delete the current history permanently? This cannot be undone, OK 5. Told History deleted, a new history is active 6. Top right menu, Saved Histories 7. Click Advanced Search, status all 8. Observe DIE DIE history is only deleted (while other older histories are deleted permanently) (BAD) 9. Run the cleanup scripts, $ sh scripts/cleanup_datasets/delete_userless_histories.sh $ sh scripts/cleanup_datasets/purge_histories.sh $ sh scripts/cleanup_datasets/purge_libraries.sh $ sh scripts/cleanup_datasets/purge_folders.sh $ sh scripts/cleanup_datasets/purge_datasets.sh 10. Reload the saved history list, no change. 11. Using the drop down menu, select Delete Permanently 12. Prompted History contents will be removed from disk, this cannot be undone. Continue, OK 13. No change to history status (BAD) 14. Tick the check-box, and use the Delete Permanently button at the bottom of the page 15. Prompted History contents will be removed from disk, this cannot be undone. Continue, OK 16. No change to history status (BAD) 17. Run the cleanup scripts, no change. Note that in my universe_wsgi.ini I have not (yet) set: allow_user_dataset_purge = True If this setting is important, then the interface seems confused - and if quotas are enforced, very frustrating :( Peter ___ 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/ ___ 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/
Re: [galaxy-dev] [CONTENT] Re: Unable to remove old datasets
I believe it's a (BAD) silent failure mode in the server code. If I understand correctly, the purge request isn't coughing an error when it gets to the 'allow_user_dataset_purge' check and instead is silently marking (or re-marking) the datasets as deleted. I would rather it fail with a 403 error if purge is explicitly requested. That said, it of course would be better to remove the purge operation based on the configuration then to show an error after we've found you can't do the operation. The same holds true for the 'permanently remove this dataset' link in deleted datasets. I'll see if I can find out the answer to your question on the cleanup scripts. On Tue, Mar 18, 2014 at 10:49 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Tue, Mar 18, 2014 at 2:14 PM, Carl Eberhard carlfeberh...@gmail.com wrote: Thanks, Ravi Peter I've added a card to get the allow_user_dataset_purge options into the client and to better show the viable options to the user: https://trello.com/c/RCPZ9zMF Thanks Carl - so this was a user interface bug, showing the user non-functional permanent delete (purge) options. That's clearer now. In this situation can the user just 'delete', and wait N days for the cleanup scripts to actually purge the files and free the space? (It seems N=10 in scripts/cleanup/purge_*.sh at least, elsewhere like the underlying Python script the default looks like N=60). Regards, Peter ___ 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/
Re: [galaxy-dev] [CONTENT] Re: Unable to remove old datasets
The cleanup scripts enforce a sort of lifetime for the datasets. The first time they're run, they may mark a dataset as deleted and also reset the update time and you'll have to wait N days for the next stage of the lifetime. The next time they're run, or if a dataset has already been marked as deleted, the actual file removal happens and purged is set to true (if it wasn't already). You can manually pass in '-d 0' to force removal of datasets recently marked as deleted. The purge scripts do not check 'allow_user_dataset_purge', of course. On Tue, Mar 18, 2014 at 11:50 AM, Carl Eberhard carlfeberh...@gmail.comwrote: I believe it's a (BAD) silent failure mode in the server code. If I understand correctly, the purge request isn't coughing an error when it gets to the 'allow_user_dataset_purge' check and instead is silently marking (or re-marking) the datasets as deleted. I would rather it fail with a 403 error if purge is explicitly requested. That said, it of course would be better to remove the purge operation based on the configuration then to show an error after we've found you can't do the operation. The same holds true for the 'permanently remove this dataset' link in deleted datasets. I'll see if I can find out the answer to your question on the cleanup scripts. On Tue, Mar 18, 2014 at 10:49 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Tue, Mar 18, 2014 at 2:14 PM, Carl Eberhard carlfeberh...@gmail.com wrote: Thanks, Ravi Peter I've added a card to get the allow_user_dataset_purge options into the client and to better show the viable options to the user: https://trello.com/c/RCPZ9zMF Thanks Carl - so this was a user interface bug, showing the user non-functional permanent delete (purge) options. That's clearer now. In this situation can the user just 'delete', and wait N days for the cleanup scripts to actually purge the files and free the space? (It seems N=10 in scripts/cleanup/purge_*.sh at least, elsewhere like the underlying Python script the default looks like N=60). Regards, Peter ___ 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/
Re: [galaxy-dev] History seems to load forever
Hi, Carrie
Can you (or the other user) open the javascript console and try to load the
history again in order to reproduce the problem?
You can open the console:
- by going to the menu command: Tools-Web Developer-Web Console in
Firefox.
- going to: the 'control menu' (the three horizontal bar button on the top
right)-Tools-Javascript Console in Chrome.
- by enabling the developer tools and going to Develop-Show Error Console
in Safari. Enable the developer menu by going to
preferences-advanced-Show develop menu in menu bar.
It may be there's an error on the client side involved and having this open
will show that error. Additionally, if an API call is returning a 400 range
http error - you won't see it in the server logs.
Thanks for the help and let me know what you find,
Carl
On Wed, Mar 12, 2014 at 10:22 AM, Ganote, Carrie L cgan...@iu.edu wrote:
Hi Hans,
Thanks for the advice! Sadly, I think our situations might not be the
same. We've been using external auth for a long time, so it's definitely
not a new change, and the user in question created their account after this
was in place. We log our users in with just their IU username, and tack the
@indiana.edu onto it with Apache to create the email address after
authenticating the username through IU. I checked the galaxy_user table,
and there doesn't seem to be any accidental duplicates or funny business
with the user name.
User is active, external, not deleted, not purged, and we don't enforce
any disk quotas.
I pulled the histories associated with the user id:
select * from history where user_id = '95' ;
id |create_time |update_time | user_id
|name| hid_counter | deleted | purged | genome_build |
importable | slug | published | importing
--+++-++-+-++--++--+---+---
1665 | 2014-02-23 18:42:23.497483 | 2014-03-11 19:04:55.614609 | 95
| Unnamed history| 5 | t | f | dm3 | f
| | f | f
1722 | 2014-02-28 20:46:50.292015 | 2014-03-11 19:06:47.498152 | 95
| RNAseq | 7 | f | f | ?|
f | | f | f
1811 | 2014-03-11 19:04:55.910381 | 2014-03-11 19:13:06.82213 | 95
| Unnamed history| 2 | f | f | ?| f
| | f | f
(3 rows)
I took a look at RNAseq:
select * from history_dataset_association where history_id = '1722';
id: 10027
history_id: 1722
dataset_id: 7258
create_time: 2014-02-28 20:51:32.369667
update_time: 2014-03-06 15:37:27.033951
copied_from_history_dataset_association_id: 9778
hid: 4
name :
https://usegalaxy.org/datasets/bbd44e69cb8906b52e29eb7a7c6c4900/display?to_ext=
peek:@HWI-B5-690_0086_FC:2:1:2711:936#CN/1 ... (this checks out with
the datafile)
extension: txt
metadata: {data_lines: 145087556, dbkey: dm3}
deleted: f
visible: t
purged: f
extended_metadata_id: uploaded txt file
I found this file in the dataset_files and there doesn't appear to be
anything wrong about it. It appears that the datasets in question were
downloaded from Galaxy main (by the looks of the upload URL).
I'm at a loss. I'll ask the user to clear all their browser information
just in case this is something simple like that. I'll ask them to re-upload
those files. In the meantime, any other sleuthing suggestions would be
greatly appreciated.
Sincerely,
Carrie Ganote
From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Wednesday, March 12, 2014 5:07 AM
To: Ganote, Carrie L
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] History seems to load forever
Hi Carrie
Was the history which is causing troubles created before you switched to
external authentication? Or has the user a slightly different e-mail
address now? eg different use of capital letters, like 'foo.bar@home'
and 'Foo.Bar@home' - we had such problems, when we switched to external
authentication.
I had to dig into our MySQL database and fix the galaxy_user table. In
your case, I recommend looking at the galaxy_user table and check
whether the user has more than one entry. Take the id (ie the number)
and search the history table using the id as 'user_id'. I would guess
you can fix your problem by changing the 'user_id' in the history
table for the history which is causing troubles.
BUT, BE VERY CAREFUL! you can do a lot of damage to the database. Switch
off the galaxy server first, and MAKE a back up the database before you
change anything.
Regards, Hans-Rudolf
On 03/11/2014 11:58 PM, Ganote, Carrie L wrote:
Hi List,
I just pulled and merged from galaxy-dist (I think it's dc067a95261d),
updated my database, and migrated my tools. The issues I am able to see
are minor, but I
Re: [galaxy-dev] Plugins
Hi, Michael It was good meeting you in Athens. You guys are doing amazing things. There currently is no mechanism to install a plugin (either hook or visualization) from the toolshed. I think it's certainly possible (and planned) in the future. I haven't added any hooks for plugins. I would hope there would be some discussion as to the which places in the code would be the most useful and desired within the community. Hopefully, that discussion can be sparked soon. As to the whether we can implement an admin link to reload the entire tool shed without restarting Galaxy: I talked a bit to Greg about it and it might be more possible and easier to reload entire tool sections (for example, 'Data sources'). Would that work for your use case? Carl On Thu, Mar 6, 2014 at 9:00 AM, Michael E. Cotterell mepcotter...@gmail.com wrote: Carl, Is there a way for a tool_shed installed tool to provide a plugin? Also, have you actually added any hooks anywhere? If so, where are they documented? Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ On Wednesday, September 18, 2013 at 11:00 AM, Carl Eberhard wrote: I've factored out the plugin discovery from the (page serving) plugin framework and subclassed an initial stab at a hook plugin manager. The page serving responsibilities are now in a separate subclass and the visualization registry is based on that: https://bitbucket.org/galaxy/galaxy-central/src/2d0bcb07596c4c688ed3908391d866831c65c042/lib/galaxy/web/base/pluginframework.py?at=default It should at least be easier modify. Have a look and let me know if you see any issues or have suggestions. On Tue, Sep 17, 2013 at 11:19 AM, Carl Eberhard carlfeberh...@gmail.com(mailto: carlfeberh...@gmail.com) wrote: Heya, Michael I'm currently working in this area as well now - so no worries if your schedule doesn't permit. The card is here: https://trello.com/c/c2AzV3Xf Any feedback is appreciated. On Mon, Sep 16, 2013 at 11:42 AM, Michael E. Cotterell mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote: Over next couple days, I'll take a look at what's in lib/galaxy/web/base/pluginframework.py and see if there is a way to refactor it with my stuff in order to get a general plugin framework (galaxy.pluginframework) as proposed by James. Sorry for the delay. Teaching a math class this semester is really eating up my time. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) (mailto: mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ On Tuesday, September 3, 2013 at 12:45 PM, Carl Eberhard wrote: It is web-specific and only handles the mako/static serving cases. I think the only areas we were generalizing at this point were the directory structures and main configuration. Agreed on more generalization and the hook system. Michael's stuff is a good direction to move in. I know John was looking to use it for dynamic job destinations and dynamic toolbox filters. I'd like to see some lab/community discussion on (even broad stroke) functional requirements and use cases. On Tue, Sep 3, 2013 at 12:27 PM, James Taylor ja...@jamestaylor.org (mailto:ja...@jamestaylor.org) (mailto: ja...@jamestaylor.org) wrote: Carl, is what you have now totally web specific? It would be great to have a general plugin framework (galaxy.pluginframework) which the web stuff could perhaps extend? On Tue, Sep 3, 2013 at 10:56 AM, Carl Eberhard carlfeberh...@gmail.com (mailto:carlfeberh...@gmail.com) (mailto: carlfeberh...@gmail.com) wrote: Heya, Michael Right now our only plugin code is located in lib/galaxy/web/base/pluginframework.py. It's only purpose so far is to: - allow locally modified/created code to serve mako templates and static pages/resources from paste. - serve as a super class for the visualization framework. I think your git repo has some great ideas. Carl On Fri, Aug 30, 2013 at 2:25 PM, Michael Cotterell mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) (mailto: mepcotter
Re: [galaxy-dev] Graph Datatypes
Hey, Bjoern Not sure whether a pull request or a toolshed repo would be best, but: if you decide on a toolshed repo, graphview as it is should be able to use your datatypes if they include a 'node-edge' dataprovider. Also, graphview is on my list - but most likely I won't get to it in the near future. Let me know if I can help with any of your changes, Carl On Mon, Mar 3, 2014 at 5:09 AM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi, we are currently working on a few graph based tools and we would like to add some new graph-datatypes, namely: gspan, gml, gexf, graphml, pajek. I saw that xgmml and sif are already integrated into core-galaxy and I'm wondering if a PR with these new datatypes would be appropriate or a new toolshed repository? Also, are there any plans to enhance graphview in the near future? Thanks, Bjoern ___ 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/
Re: [galaxy-dev] History panel filters
Hi, Federico Starting with the next distribution (and in the current 'galaxy-central'), you'll be able to do just that. Here's the documentation for it: https://wiki.galaxyproject.org/Learn/Managing%20Datasets#Searching_Datasets In future releases, we hope to enable the use of multiple selection and operations on multiple datasets with the search: https://bitbucket.org/galaxy/galaxy-central/commits/7ca065784d58e7aa77e5092952eacd963853df65 Good to see this will be useful for some and thanks for the suggestion, Carl On Mon, Feb 3, 2014 at 9:55 AM, Federico Zambelli federico.zambe...@gmail.com wrote: Dear Galaxy devs, I apologize if somebody has already proposed this idea. I think that it would be great to have a filter for the history panel based on name, data type and so on similar to the one on the tools panel. I really feel the need of it when working on histories with many datasets. Federico Zambelli ___ 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/ ___ 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/
Re: [galaxy-dev] galaxy local installation
Hello, Edgar - thanks for installing Galaxy! Regarding the screenshots: it looks like Galaxy's static css stylesheet isn't being loaded properly. Is this still occurring for you? Do you see anything when you try to go to http://localhost:8080/static/style/base.css in your browser? (You should see some text) Thanks, Carl On Thu, Dec 12, 2013 at 2:51 PM, fernandez Edgar edgar.fernan...@umontreal.ca wrote: Hello, Thank you very much for the quick answers. There were very useful. Now I hope I’m not bothering you with a couple more questions. I read more thoroughly the documentation for installing a production environment and I was wondering: 1. Is it possible to run the web server through apache but not as a proxy server? a. If so what are the steps exactly? I only found the explanation for a proxy server… 2. Will this kind of installation will work on red hat 6 enterprise server ? Cordialement / Regards, Edgar Fernandez *De :* Alistair Chilcott [mailto:alistair.chilc...@utas.edu.au] *Envoyé :* December-11-13 10:10 PM *À :* fernandez Edgar; galaxy-...@bx.psu.edu *Objet :* RE: galaxy local installation Edgar, I have been exploring similar outcomes and run into similar issues. I have recently found this post http://seqanswers.com/forums/showthread.php?t=23629 That I’m sure will prove helpful to you. This show how to get it working, including the dependancies and reference genomes .. advice on securing it is already on the galaxy websites. Another observation I would make is that the vast majority of help and advice you will find on the web relates to a galaxy environments built on Ubuntu, (12.04 LTS seem to be the version of choice). The instructions above will help you install it on SUSE but I found that having to translate the steps from Ubuntu to SUSE was occasionally problematic. Hope this helps. Regards, *Alistair * *From:* galaxy-dev-boun...@lists.bx.psu.edu [ mailto:galaxy-dev-boun...@lists.bx.psu.edugalaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *fernandez Edgar *Sent:* Thursday, 12 December 2013 4:31 AM *To:* galaxy-...@bx.psu.edu *Subject:* [galaxy-dev] galaxy local installation Hello, My name is Edgar Fernandez. I’m a sys. admin. at University of Montreal. I’ve been ask by a teacher to check out Galaxy. So I’ve installed locally on my computer galaxy (I’m running openSUSE x86_64 but I’ll install it on SUSE Linux ia64). I’ve executed the run.sh script and I’ve somewhat successfully made the website work. I say somewhat because I have a couple of issues: 1. The website is not well displayed (refer to the attachment) 2. I’ve changed the value of host to 0.0.0.0 in the universe_wsgi.ini file and it still launches to 127.0.0.1 I was also wondering if there is a step by step tutorial to install all the dependencies? I’m finding myself overwhelmed with all the different dependencies. Cordialement / Regards, *Edgar Fernandez* System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication ( Bur. : *1-514-343-6111 1-514-343-6111 poste 16568* *Université de Montréal* PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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/ ___ 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/
Re: [galaxy-dev] phyloviz: save visualization error
I've fixed both this error and another involving newick files. I've tested saving and loading with the three phyloviz compatible datatypes and it seems to be working. If you'd like, you can update to commit 11634:2e8596a621b4 on the stable branch and see if the fix works for your error. Let me know if I can help further. On Thu, Dec 5, 2013 at 3:08 PM, Carl Eberhard carlfeberh...@gmail.comwrote: Hello, Karen This is a bug and I wanted to let you know I'm looking into it now: https://trello.com/c/dzBmbyqF Sorry for the frustration and thanks for the report, Carl On Mon, Dec 2, 2013 at 6:23 PM, Karen Miga khm...@soe.ucsc.edu wrote: Hello, I am trying to use phyloviz on the cloud/Galaxy cloudman. Unfortunately, I am unable to save the visualization using the save/disk icon on the right hand side of the banner. Any help would be appreciated. Karen ___ 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/ ___ 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/
Re: [galaxy-dev] phyloviz: save visualization error
Hello, Karen This is a bug and I wanted to let you know I'm looking into it now: https://trello.com/c/dzBmbyqF Sorry for the frustration and thanks for the report, Carl On Mon, Dec 2, 2013 at 6:23 PM, Karen Miga khm...@soe.ucsc.edu wrote: Hello, I am trying to use phyloviz on the cloud/Galaxy cloudman. Unfortunately, I am unable to save the visualization using the save/disk icon on the right hand side of the banner. Any help would be appreciated. Karen ___ 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/ ___ 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/
Re: [galaxy-dev] Interacting with output views in Galaxy
Hello, Stephen Although still under initial development, you may want to look into the visualization registry for the infrastructure to render the region and allow the user to interact with it: http://wiki.galaxyproject.org/VisualizationsRegistry http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FAbstracts.2FTalks.How_to_Create_Your_Own_Web-based.2C_Interactive_Visualizations_for_Galaxy In a nutshell, it allows you to configure and include a link from the history panel to a custom page that you create with the mako templating system and the javascript you'll need for the interactivity. Galaxy resources (like your initial dataset) are parsed for you and available in the template. For the other half of the problem: creating new data from the interaction of the user, you'll want to look into the tools API (which is what Trackster uses). Still somewhat rough, there have been improvements to it lately that should allow you to run a tool based on user input and keep the chain of reproducibility. Two things to note: 1. I'd recommend not using the upload tool via the API: not because it doesn't work but because adding arbitrary data this way won't be reproducible. 2. Both the visualizations registry and the tools API are still under development. Feel free to contact me on IRC, email, or the mailing lists if you have any trouble though. I hope that helps and let me know if I can provide any more information, Carl On Fri, Nov 29, 2013 at 7:11 AM, Stephen Taylor stephen.tay...@imm.ox.ac.uk wrote: Hi, I was wondering, if anyone could point me to any resources and that allow the user to interact with the view of the output of a tool in Galaxy. So for example, I would like to load an image, draw a region of interest (ROI) (probably via some js routine) and then store that information in a file, generating an input in the History view. This input could then be used for further analysis. I guess Trackster does something like this, but I don't know if its routines are generic enough to handle this type of interaction. Thanks for any info! Steve ___ 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/ ___ 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/
Re: [galaxy-dev] latest galaxy-central version
Hello, Robert I'm having difficulty reproducing this with a fresh install of galaxy_central:default:11226:c67b9518c1e0. Is this an intermittent error or does it happen reliably each time with the steps above? Is it still the same javascript error you mentioned above? I'll investigate further. On Mon, Nov 4, 2013 at 7:29 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: I updated to the stable release and reproduced the issue. Step to reproduce 1. go to admin 2. Manage data librarieshttp://su2c-dev.ucsc.edu:8383/library_admin/browse_libraries 3. add dataset 4. select Upload files from filesystem paths 5. paste full path to any bam file. 6. leave defaults: auto-detect and copy files into galaxy 7. select role to restrict access 8. click upload to start Screen shows strange formatting and Job is running for Bam file. python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpJoasJl /data/galaxy-central/database/tmp/tmpzZO8t1 8877:/data/galaxy-central/database/job_working_directory/004/4548/dataset_8877_files:/data/galaxy-central/database/files/008/dataset_8877.dat If I do a firefox refresh and go back to the library, the formatting is normal. I'm assuming the fix is to just render the page before waiting for the job to complete. -Robert On Nov 4, 2013, at 12:45 PM, Martin Čech mar...@bx.psu.edu wrote: Hello, I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation. --Marten On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: It keeps doing posts, and I'm not seeing any new errors. POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in) Galaxy.currUser is undefined on Line 631 in history-panel.js When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things. -Robert On Nov 4, 2013, at 11:14 AM, James Taylor ja...@jamestaylor.org wrote: Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired. Are there any javascript errors? Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console. -- James Taylor, Associate Professor, Biology/CS, Emory University On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update. I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server. During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted Do you finish rendering the screen after the copy operation is complete? -Robert Screen Shot 2013-11-04 at 10.53.02 AM.png ___ 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/ ___ 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/
Re: [galaxy-dev] Deleting history entries not working, javascript void link?
Hello, Peter. Thanks for the report. There was an error in the javascript error handling of purge_async which is now fixed in stable:11227:151b7d3b2f1b. In the instances you mention, you should now see an error message in the history 'Unable to purge this dataset': This is because of two possible reasons: - the setting 'allow_user_dataset_purge' in universe_wsgi.ini is 'False' (or commented out) - there was an error in the call to purge_async on the server The 'href=javascript:void(0);' is a common idiom for creating links/anchors where the logic is handled on the client side. It tells the browser that, although the element has all the other properties of a link, it should not load it like another page and the click event will be handled by javascript on the current page. In the default branch, the error reporting has been (hopefully) improved to display appropriate messages for failed purging as well as better reporting overall. Sorry for the inconvenience. On Tue, Nov 5, 2013 at 7:02 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Hi all, I've just updated our main Galaxy to release_2013.11.04 but also see the following problem on galaxy-central, and on https://usegalaxy.org/ as well. (1) Go to any history with deleted files (2) Cog icon, tick Include Deleted datasets (3) Look at a deleted dataset in your history column, note the yellow Warning box with text: This dataset has been deleted. Click *here* to undelete it or *here* to immediately remove it from disk (4) Notice the first *here* link (undelete) has a sensible URL, e.g. as shown via your browser's status bar or right click to copy the URL. (5) Notice the second *here* (remove) has this as the URL: javascript:void(0) Unsurprisingly, the remove link has no effect as it is a JavaScript command to do nothing, and the user cannot therefore purge the file from their history. I've confirmed this on multiple browsers on multiple machines. Regards, Peter ___ 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/ ___ 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/
Re: [galaxy-dev] bug in handling sessions
Hi, Nikolai This should have been fixed with commit 10200:fd4113962c32 to the stable branch. What version are you using? Thanks On Wed, Oct 16, 2013 at 8:19 AM, Nikolai Vazov n.a.va...@usit.uio.nowrote: Hi, I have discovered the following weird Galaxy behaviour. If one sets log_actions = True in universe_wsgi.ini and tries to display the Saved Histories, then the Saved histories don't show up. The problem arises from ../lib/galaxy/web/framework/**helpers/grids.py line (around 230) trans.log_action( trans.get_user(), unicode( grid.view ), context, params) Until this line, the Query object 'query' has queried the DB and fetched the necessary data. Yet, in the file ../lib/galaxy/web/framework/__**init__.py in the function log_action self.sa_session.flush() seems to flush everything, including the data fetched by the 'query' object in grids.py Thus, the Saved Histories get No Items message. Commenting out the line log_actions = True does the job, but ... Any suggestions? Best regards Nikolay -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo __**_ 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/http://galaxyproject.org/search/mailinglists/ ___ 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/
Re: [galaxy-dev] masthead and history lost when embedding Galaxy in iframe
Heya, Andy Galaxy hasn't been designed to be loaded in an iframe yet. Currently, the javascript in Galaxy makes use of the window variable top - which points to the highest browser window in the DOM. There are many instances where we rely on both 'top' and the link target '_top' to control the iframes used inside the platform. In your implementation, top won't point to the Galaxy frame - but to the frame you've created. This can lead to pages/features that won't load (and fail silently unfortunately). We are currently working to remove our use of iframes within the platform which will help with embedding Galaxy into a frame. In the meantime, you may be able to alter those references to top to point to parent (which is context dependent) or to a named frame (naming the outer Galaxy frame and using that as a link target and replacement for top). Hope that helps. (with apologies to Andy for missing the mailing list in my first reply) On Thu, Oct 10, 2013 at 7:56 AM, Andy Saurin andrew.sau...@univ-amu.frwrote: Hi all, I really can't understand why this should be, but in recent versions of Galaxy if you have a simple html page with an iframe embedding Galaxy, you loose the masthead (no login, workflow etc) and the history panel no longer works. eg (newer Galaxy Versions) iframe src=https://galaxy.cbio.mskcc.org/; width=800px height=600px/iframe iframe src=https://galaxy.cbio.mskcc.org/; width=800px height=600px/iframe You can see the problems, whereas older versions of galaxy show no problems: iframe src=http://galaxy.berkeleybop.org:8080/; width=800px height=600px/iframe What could be causing this so that I can try to make amends? Thanks Andy ___ 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/ ___ 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/
Re: [galaxy-dev] Plugins
I've factored out the plugin discovery from the (page serving) plugin framework and subclassed an initial stab at a hook plugin manager. The page serving responsibilities are now in a separate subclass and the visualization registry is based on that: https://bitbucket.org/galaxy/galaxy-central/src/2d0bcb07596c4c688ed3908391d866831c65c042/lib/galaxy/web/base/pluginframework.py?at=default It should at least be easier modify. Have a look and let me know if you see any issues or have suggestions. On Tue, Sep 17, 2013 at 11:19 AM, Carl Eberhard carlfeberh...@gmail.comwrote: Heya, Michael I'm currently working in this area as well now - so no worries if your schedule doesn't permit. The card is here: https://trello.com/c/c2AzV3Xf Any feedback is appreciated. On Mon, Sep 16, 2013 at 11:42 AM, Michael E. Cotterell mepcotter...@gmail.com wrote: Over next couple days, I'll take a look at what's in lib/galaxy/web/base/pluginframework.py and see if there is a way to refactor it with my stuff in order to get a general plugin framework (galaxy.pluginframework) as proposed by James. Sorry for the delay. Teaching a math class this semester is really eating up my time. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ On Tuesday, September 3, 2013 at 12:45 PM, Carl Eberhard wrote: It is web-specific and only handles the mako/static serving cases. I think the only areas we were generalizing at this point were the directory structures and main configuration. Agreed on more generalization and the hook system. Michael's stuff is a good direction to move in. I know John was looking to use it for dynamic job destinations and dynamic toolbox filters. I'd like to see some lab/community discussion on (even broad stroke) functional requirements and use cases. On Tue, Sep 3, 2013 at 12:27 PM, James Taylor ja...@jamestaylor.org(mailto: ja...@jamestaylor.org) wrote: Carl, is what you have now totally web specific? It would be great to have a general plugin framework (galaxy.pluginframework) which the web stuff could perhaps extend? On Tue, Sep 3, 2013 at 10:56 AM, Carl Eberhard carlfeberh...@gmail.com (mailto:carlfeberh...@gmail.com) wrote: Heya, Michael Right now our only plugin code is located in lib/galaxy/web/base/pluginframework.py. It's only purpose so far is to: - allow locally modified/created code to serve mako templates and static pages/resources from paste. - serve as a super class for the visualization framework. I think your git repo has some great ideas. Carl On Fri, Aug 30, 2013 at 2:25 PM, Michael Cotterell mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote: Is this plugin code hosted anywhere (like in central)? On Monday, August 26, 2013, James Taylor wrote: Michael, Carl has been working on a plugin framework for Galaxy, and John Chilton has made some improvements. It would be great if you could look over what each other has done and come up with some suggestions. I personally am in favor of a very generic hook system where a hook can be defined anywhere in the code and then the user can provide any callable. I'm fond of the way sup implemented hooks, see the use of HookManager here: https://github.com/sup-heliotrope/sup/blob/develop/lib/sup/time.rb Your approach is quite similar and I like it. This makes it easy to have a script that can list all available hooks with their documentation. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Aug 23, 2013 at 10:29 AM, Michael E. Cotterell mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote: James, Has there been any more talk about this? I'd be willing to work in my reference implementation into central as a pull request, but I don't want to do that unless there is an agreed upon roadmap or something. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) (mailto: mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) (mailto:m
Re: [galaxy-dev] Plugins
Heya, Michael I'm currently working in this area as well now - so no worries if your schedule doesn't permit. The card is here: https://trello.com/c/c2AzV3Xf Any feedback is appreciated. On Mon, Sep 16, 2013 at 11:42 AM, Michael E. Cotterell mepcotter...@gmail.com wrote: Over next couple days, I'll take a look at what's in lib/galaxy/web/base/pluginframework.py and see if there is a way to refactor it with my stuff in order to get a general plugin framework (galaxy.pluginframework) as proposed by James. Sorry for the delay. Teaching a math class this semester is really eating up my time. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ On Tuesday, September 3, 2013 at 12:45 PM, Carl Eberhard wrote: It is web-specific and only handles the mako/static serving cases. I think the only areas we were generalizing at this point were the directory structures and main configuration. Agreed on more generalization and the hook system. Michael's stuff is a good direction to move in. I know John was looking to use it for dynamic job destinations and dynamic toolbox filters. I'd like to see some lab/community discussion on (even broad stroke) functional requirements and use cases. On Tue, Sep 3, 2013 at 12:27 PM, James Taylor ja...@jamestaylor.org(mailto: ja...@jamestaylor.org) wrote: Carl, is what you have now totally web specific? It would be great to have a general plugin framework (galaxy.pluginframework) which the web stuff could perhaps extend? On Tue, Sep 3, 2013 at 10:56 AM, Carl Eberhard carlfeberh...@gmail.com (mailto:carlfeberh...@gmail.com) wrote: Heya, Michael Right now our only plugin code is located in lib/galaxy/web/base/pluginframework.py. It's only purpose so far is to: - allow locally modified/created code to serve mako templates and static pages/resources from paste. - serve as a super class for the visualization framework. I think your git repo has some great ideas. Carl On Fri, Aug 30, 2013 at 2:25 PM, Michael Cotterell mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote: Is this plugin code hosted anywhere (like in central)? On Monday, August 26, 2013, James Taylor wrote: Michael, Carl has been working on a plugin framework for Galaxy, and John Chilton has made some improvements. It would be great if you could look over what each other has done and come up with some suggestions. I personally am in favor of a very generic hook system where a hook can be defined anywhere in the code and then the user can provide any callable. I'm fond of the way sup implemented hooks, see the use of HookManager here: https://github.com/sup-heliotrope/sup/blob/develop/lib/sup/time.rb Your approach is quite similar and I like it. This makes it easy to have a script that can list all available hooks with their documentation. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Aug 23, 2013 at 10:29 AM, Michael E. Cotterell mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote: James, Has there been any more talk about this? I'd be willing to work in my reference implementation into central as a pull request, but I don't want to do that unless there is an agreed upon roadmap or something. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) (mailto: mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ On Tuesday, July 16, 2013 at 2:08 PM, Michael E. Cotterell wrote: James, That's exactly what I was thinking. In my opinion, hooks are the way to go (as seen in my example), but if there's a better way then I'm game for that to. I just want to be able to extend Galaxy without modifying Galaxy itself. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia
Re: [galaxy-dev] Job listing exception
That's a great point. I've made a bug card for it here: https://trello.com/c/LsZoPtwv/1053-jobs-better-unicode-handling-in-stderr Thanks for reporting this. Carl On Sat, Jul 6, 2013 at 11:33 PM, Kyle Ellrott kellr...@soe.ucsc.edu wrote: This also took out my job handlers (exception below). So the introduction of non-ascii characters into the table (via the job stdout/stderr capture) can make a galaxy instance pretty useless. I was able to find the offending records using SELECT count(*) FROM job WHERE stderr similar to '%\x8b%'; Turns out it was the byproduct of doing a path paste of some gzipped fastq files (so they where never decompressed, just passed along), and then fastq_groomer.py complains about the file having an invalid header (line 22?) reports back an invalid header and prints it out, thus the non-ascii characters in the stderr. I 'cleaned' the database with 'update job set stderr = regexp_replace(stderr, '\x8b', '\x5f');'. But there should probably be some safe guards put in place to stop this from happening. Kyle galaxy.jobs.handler INFO 2013-07-06 12:35:32,033 job handler stop queue started Traceback (most recent call last): File /inside/depot4/galaxy/lib/galaxy/webapps/galaxy/buildapp.py, line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /inside/depot4/galaxy/lib/galaxy/app.py, line 164, in __init__ self.job_manager = manager.JobManager( self ) File /inside/depot4/galaxy/lib/galaxy/jobs/manager.py, line 36, in __init__ self.job_handler.start() File /inside/depot4/galaxy/lib/galaxy/jobs/handler.py, line 34, in start self.job_queue.start() File /inside/depot4/galaxy/lib/galaxy/jobs/handler.py, line 77, in start self.__check_jobs_at_startup() File /inside/depot4/galaxy/lib/galaxy/jobs/handler.py, line 92, in __check_jobs_at_startup ( model.Job.handler == self.app.config.server_name ) ): File /inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py, line 2341, in instances fetch = cursor.fetchall() File /inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py, line 3204, in fetchall l = self.process_rows(self._fetchall_impl()) File /inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py, line 3171, in _fetchall_impl return self.cursor.fetchall() UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 404: ordinal not in range(128) On Fri, Jul 5, 2013 at 11:43 PM, Kyle Ellrott kellr...@soe.ucsc.eduwrote: I'm getting an exception when trying to look at the admin job management screen. It looks like SQLAlchemy doesn't like non-ascii characters. Any ideas about what to do? Error - type 'exceptions.UnicodeDecodeError': 'ascii' codec can't decode byte 0x8b in position 404: ordinal not in range(128) URL: http://pk.kilokluster.ucsc.edu:8079/admin/jobs File '/inside/depot4/galaxy/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/inside/depot4/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/inside/depot4/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/inside/depot4/galaxy/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/inside/depot4/galaxy/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/inside/depot4/galaxy/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/inside/depot4/galaxy/lib/galaxy/web/base/controllers/admin.py', line 1053 in jobs for job in jobs: File '/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py', line 2341 in instances File '/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py', line 3204 in fetchall File '/inside/depot4/galaxy/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py', line 3171 in _fetchall_impl UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 404: ordinal not in range(128) ___ 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/ ___ Please keep all replies on the list by using reply all in your mail
Re: [galaxy-dev] Multiple output files do not appear in history
Hello, Cristopher
Thanks for noticing this. I've updated the wiki entry:
http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
Does the line starting with 'Alternately,' match the behavior you're seeing?
Thanks,
Carl
On Wed, Jul 3, 2013 at 8:59 AM, Christoph Malisi
christoph.mal...@computomics.com wrote:
Hi,
I found my problem:
in the production instances universe_wsgi.ini
the value for collect_outputs_from was different that in my VM.
It is set to:
collect_outputs_from = job_working_directory
Perhaps one could update the documentation that deals with multiple output
files and mention that the $__new_file_path__ variable is not necessary, it
is sufficient to name the output files correctly (i.e.
primary_123_output2_visible_fastq,…) in the job work dir.
Best,
Chris
universe_wsgi.ini
On Jul 3, 2013, at 10:36 AM, Christoph Malisi
christoph.mal...@computomics.com wrote:
Hey,
I'm writing a XML for a tool that produces a number of output files. As
the number is not known before the tool is run, I used the strategy
outlined here:
http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
First, I tried my tool definition in a galaxy instance in a virtual
machine to not interrupt our production instance (we have a local instance
set up). Here, everything worked fine. When trying the same code in our
production galaxy instance, it didn't: Regardless of how many output files
were produced, only one appears in the history. (the first one,
corresponding to output1 in the references wiki entry). When looking at
the temp directory provided to the tool by galaxy ($__new_file_dir__ in
the wiki, it always points to galaxy-dist/database/tmp/), the additional
output files have been created by my tool and are named correctly (e.g.
primary_123_output2_visible_fastq, primary_123_output3_visible_fastq, …)
Both instances are new, based on release_2013.06.03.
Is there any setting in galaxy somewhere that could prevent this from
working?
Thanks for your help
Chris
PS: I wrote a little python script that just creates multiple output
files, and the discrepancy between the two instances is reproducible. Here
is the code for the python script and the corresponding XML:
###
import subprocess
import argparse
import os
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-i', type=int)
parser.add_argument('output1')
parser.add_argument('output1_id')
parser.add_argument('out_dir')
args = parser.parse_args()
print 'Wrapper arguments:', args
with open(args.output1, 'w') as f:
f.write('output1')
for i in range(2, args.i+1):
name = 'output%i'%i
file_type = 'text'
fname = '%s_%s_%s_%s_%s' % ('primary', args.output1_id, name,
'visible', file_type)
with open(os.path.join(args.out_dir, fname), 'w') as f:
f.write('output%i'%i)
if __name__ == __main__:
main()
###
tool name=MultiOutTest id=multiouttest
descriptionMultiple Outputs test/description
command interpreter=python
multiout.py
-i $how_many
$output1
$output1.id
$__new_file_path__
/command
inputs
param name=how_many type=integer value=2 label=How many output
files?/
/inputs
outputs
data name=output1 format=txt/
/outputs
help
This is some help text.
/help
/tool
#
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Re: [galaxy-dev] lessc compiler error on blue_colors.ini
Hey, Seth I'm using npm less 1.3.3. That error isn't a known issue, no. Is that the full stack trace/error report? Which files have you edited? Thanks, Carl On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims seth.s...@gmail.com wrote: Dear Galaxy devs, I am attempting to create a style directory to match my school's look and feel. I am mainly trying to get the development environment setup to do this right now. My current problem is that when I attempt to compile the standard blue_colors.ini which comes with galaxy I am receiving a syntax error: ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:10 1 base_text=#303030 2 base_bg_top=#FF I have not edited that file at all. So the first question is, what version of lessc is being used to compile the styles for the basic installation? Also are there any pitfalls I should be aware of with this process. - Seth ___ 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/ ___ 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/
Re: [galaxy-dev] lessc compiler error on blue_colors.ini
The ini file is not a .less file so it will error if you call lessc directly with it. It may be that you're lacking some (not obvious) dependencies. Do you have pyparsing and PIL installed and available in your terminal (pip install will work with both)? You can also use npm to update/install your node modules (sudo npm install -g less) if you have npm installed. On Mon, Aug 5, 2013 at 11:28 AM, Seth Sims seth.s...@gmail.com wrote: Dear Carl, You are using a more recent version of lessc then I am so it is probably just a versioning error. Ubuntu Precise Pangolin's repositories are still at lessc-1.2.1. So apparently I need to manually install a more recent version of the compiler. Here is a description of the error if anyone else has this problem: I have not edited anything, when attempting to compile the vanilla blue_colors.ini from the repo I receive an error like so: $sudo lessc blue_colors.ini ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:9 1 base_text=#303030 2 base_bg_top=#FF However the only reason I used that command is because the makefile gives a different error: $ sudo make OUT=blue make[1]: Entering directory `/srv/galaxy-dist/static/style/blue' lessc -x ../base.less base.css TypeError: Cannot call method 'charAt' of undefined at getLocation (/usr/lib/nodejs/less/parser.js:204:34) at new LessError (/usr/lib/nodejs/less/parser.js:213:19) at Object.toCSS (/usr/lib/nodejs/less/parser.js:379:31) at /usr/bin/lessc:103:28 at /usr/lib/nodejs/less/parser.js:428:40 at /usr/lib/nodejs/less/parser.js:94:48 at /usr/lib/nodejs/less/index.js:113:15 at /usr/lib/nodejs/less/parser.js:428:40 at /usr/lib/nodejs/less/parser.js:94:48 at /usr/lib/nodejs/less/index.js:113:15 make[1]: *** [base.css] Error 2 make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue' make: *** [all] Error 2 Which is apparently a bug in the version of lessc I have. On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard carlfeberh...@gmail.comwrote: Hey, Seth I'm using npm less 1.3.3. That error isn't a known issue, no. Is that the full stack trace/error report? Which files have you edited? Thanks, Carl On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims seth.s...@gmail.com wrote: Dear Galaxy devs, I am attempting to create a style directory to match my school's look and feel. I am mainly trying to get the development environment setup to do this right now. My current problem is that when I attempt to compile the standard blue_colors.ini which comes with galaxy I am receiving a syntax error: ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:10 1 base_text=#303030 2 base_bg_top=#FF I have not edited that file at all. So the first question is, what version of lessc is being used to compile the styles for the basic installation? Also are there any pitfalls I should be aware of with this process. - Seth ___ 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/ ___ 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/
Re: [galaxy-dev] lessc compiler error on blue_colors.ini
Nice catch. Maybe an old version of bootstrap's less. I'll see what I can
do about that.
Thanks for the help.
On Mon, Aug 5, 2013 at 12:17 PM, Seth Sims seth.s...@gmail.com wrote:
Dear Carl,
lessc 1.3.3 successfully compiles the scripts. So you've got a bit of a
goldielocks situation going on. Looks like only 1.3.* versions of less are
useable with galaxy as it stands.
- Seth
On Mon, Aug 5, 2013 at 12:09 PM, Seth Sims seth.s...@gmail.com wrote:
Dear Carl,
OK, I have been casting about to find out what the problem was;
invoking lessc on the ini was just something I tried since the error from
the makefile is completely opaque. I already had PIL and pyparsing
installed, just checked again to make sure...
After fighting a bit with npm to get lessc installed I now have
lessc-1.4.2 which is giving this error:
/srv/galaxy-dist/static/style$ sudo make OUT=blue
make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
lessc -x ../base.less base.css
util.error: Use console.error instead
ParseError: Unrecognised input in
/srv/galaxy-dist/static/style/bootstrap/mixins.less on line 561, column 7:
560 .spanX (@index) when (@index 0) {
561 (~.span@{index}) { .span(@index); }
562 .spanX(@index - 1);
make[1]: *** [base.css] Error 1
make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
make: *** [all] Error 2
So now I guess i'm going to try and downgrade specifically to lessc 1.3.3
- Seth
On Mon, Aug 5, 2013 at 11:56 AM, Carl Eberhard
carlfeberh...@gmail.comwrote:
The ini file is not a .less file so it will error if you call lessc
directly with it.
It may be that you're lacking some (not obvious) dependencies. Do you
have pyparsing and PIL installed and available in your terminal (pip
install will work with both)?
You can also use npm to update/install your node modules (sudo npm
install -g less) if you have npm installed.
On Mon, Aug 5, 2013 at 11:28 AM, Seth Sims seth.s...@gmail.com wrote:
Dear Carl,
You are using a more recent version of lessc then I am so it is
probably just a versioning error. Ubuntu Precise Pangolin's repositories
are still at lessc-1.2.1. So apparently I need to manually install a more
recent version of the compiler. Here is a description of the error if
anyone else has this problem:
I have not edited anything, when attempting to compile the vanilla
blue_colors.ini from the repo I receive an error like so:
$sudo lessc blue_colors.ini
ParseError: Syntax Error on line 1 in
/srv/galaxy-dist/static/style/blue_colors.ini:1:9
1 base_text=#303030
2 base_bg_top=#FF
However the only reason I used that command is because the makefile
gives a different error:
$ sudo make OUT=blue
make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
lessc -x ../base.less base.css
TypeError: Cannot call method 'charAt' of undefined
at getLocation (/usr/lib/nodejs/less/parser.js:204:34)
at new LessError (/usr/lib/nodejs/less/parser.js:213:19)
at Object.toCSS (/usr/lib/nodejs/less/parser.js:379:31)
at /usr/bin/lessc:103:28
at /usr/lib/nodejs/less/parser.js:428:40
at /usr/lib/nodejs/less/parser.js:94:48
at /usr/lib/nodejs/less/index.js:113:15
at /usr/lib/nodejs/less/parser.js:428:40
at /usr/lib/nodejs/less/parser.js:94:48
at /usr/lib/nodejs/less/index.js:113:15
make[1]: *** [base.css] Error 2
make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
make: *** [all] Error 2
Which is apparently a bug in the version of lessc I have.
On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Hey, Seth
I'm using npm less 1.3.3. That error isn't a known issue, no.
Is that the full stack trace/error report? Which files have you edited?
Thanks,
Carl
On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims seth.s...@gmail.comwrote:
Dear Galaxy devs,
I am attempting to create a style directory to match my school's
look and feel. I am mainly trying to get the development environment
setup
to do this right now. My current problem is that when I attempt to
compile
the standard blue_colors.ini which comes with galaxy I am receiving a
syntax error:
ParseError: Syntax Error on line 1 in
/srv/galaxy-dist/static/style/blue_colors.ini:1:10
1 base_text=#303030
2 base_bg_top=#FF
I have not edited that file at all. So the first question is, what
version of lessc is being used to compile the styles for the basic
installation? Also are there any pitfalls I should be aware of with this
process.
- Seth
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Re: [galaxy-dev] plain text output format
Hello Mark, Can you post the output entry from your tool xml for that file? Thanks, Carl On Mon, Jul 15, 2013 at 5:15 PM, mark.r...@syngenta.com wrote: Hi All ** ** I’m trying to format one of the three outputs of my galaxy tool as plain text. Thus far no matter how I specify my output format in the tool xml file I have the same problem. When I click the eye icon it opens a save dialog rather that displaying the text output in the central frame. The preview shows the text output and if I follow through and save the output and open with wordpad it is fine. Also if I edit the attributes of the output and change it to “txt” (which is one of the formats I had tried specifying in the xml) it will render in the central frame but I would rather not have to do that. Both of my other outputs (a vcf and a tab-delimited file are rendered in the central frame properly). What can I do to fix this? ** ** Thanks ** ** Mark ** ** ** -- ***This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.* ___ 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/ ___ 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/
Re: [galaxy-dev] Adding files to a data library - genome option
That's both a bug (should default to 'unspecified') and a usability issue (sorting the genomes). I've added a card: https://trello.com/c/Hr1JdeGq/1007-ui-bug-genome-selection-when-adding-library-data-files On Thu, Jul 11, 2013 at 11:06 AM, Lionel Guy guy.lio...@gmail.com wrote: Hi Galaxy-devs, When adding files to a data library (as admin), I have to choose the genome corresponding to my dataset, but the drop-down list is not sorted, making it a tad annoying to scroll. In addition, by default, the homIni20 genome is selected, which seems a bit anthropocentric ;) I would suggest that the genome drop-down list has the same behavior as the one in the Upload File tool (i.e. sorted alphabetically, with unspecified as the default value). Not sure this is a bug or even worth a Trello card, so I post it here. I'd be happy to fill in a Trello card if requested. Cheers, Lionel __**_ 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/http://galaxyproject.org/search/mailinglists/ ___ 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/
Re: [galaxy-dev] Strange behaviour with galaxy history
Hello, This should be working now in stable's branch, revision: 9ebd773https://bitbucket.org/galaxy/galaxy-central/commits/9ebd7732e616492f4570587496f1b9074cb2eac7. You should be able to use the saved histories list *and* log_actions=True together. Let me know if you see any more trouble. Thanks for the reports and the help in tracking it down. Carl On Tue, Jul 16, 2013 at 4:06 PM, Carl Eberhard carlfeberh...@gmail.comwrote: Nice catch! I'll see where this leads. On Tue, Jul 16, 2013 at 7:03 AM, Groot, Philip de philip.degr...@wur.nlwrote: Hi Carl, Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem. The moment I UNCOMMENT the following line: #log_actions = True I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now! Thank you for your help! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ From: Carl Eberhard [carlfeberh...@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; ambrose.andong...@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after GET /history/list HTTP/1.1? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de philip.degr...@wur.nl mailto:philip.degr...@wur.nl wrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as /)! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786tel:%2B31-317-485786 F: +31-317-483342tel:%2B31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nlmailto: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://www.nutrigenomicsconsortium.nl/ http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ___ 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
Re: [galaxy-dev] Strange behaviour with galaxy history
Nice catch! I'll see where this leads. On Tue, Jul 16, 2013 at 7:03 AM, Groot, Philip de philip.degr...@wur.nlwrote: Hi Carl, Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem. The moment I UNCOMMENT the following line: #log_actions = True I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now! Thank you for your help! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ From: Carl Eberhard [carlfeberh...@gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev@lists.bx.psu.edu; ambrose.andong...@rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after GET /history/list HTTP/1.1? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de philip.degr...@wur.nl mailto:philip.degr...@wur.nl wrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as /)! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786tel:%2B31-317-485786 F: +31-317-483342tel:%2B31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nlmailto: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://www.nutrigenomicsconsortium.nl/ http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ___ 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/
Re: [galaxy-dev] Visualization in galaxy
Hello, Sridhar How large is the file you're trying to plot? The scatterplot visualization doesn't do well with large datasets (more than ~10,000 points). I'm working to provide some form of pagination, but it may take some time. If your file is large, filtering or splitting up your data may help in the meantime. If that doesn't help, can you provide more details as to what's happening when you click the draw button? Thanks, Carl On Thu, Jul 11, 2013 at 5:22 AM, sridhar srinivasan sridhar2bioi...@gmail.com wrote: Dear Developers, I could see the visualize icon in the History page below the output file.. Actually i am trying to plot the graph between the column 4 and 8 from the output.. I tried using the visualize option, But takes long time to and i could'nt get the plot.. Please suggest , how to get the Scatter plot your suggestions are very much appericiated.. Thanks Sridhar ___ 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/ ___ 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/
Re: [galaxy-dev] Strange behaviour with galaxy history
Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after GET /history/list HTTP/1.1? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.*sample* file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de philip.degr...@wur.nlwrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as /)! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nl Internet: http://www.nutrigenomicsconsortium.nl http://www.nutrigenomicsconsortium.nl/ http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ___ 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/
Re: [galaxy-dev] [Galaxy-gcc2013] Strange behaviour with galaxy history
Hi, Ambrose A couple of places to start: Did the javascript console (in Firefox: Tools-Web Developer-Web Console) display any errors when you reloaded the failing saved history page? What does is the output of 'hg summary' when run in a terminal from your Galaxy root directory? I believe you mentioned there were no 'ERROR' messages in the Galaxy log; is this correct? Thanks for the report. (I'm moving this to the galaxy-dev mailing list). Carl On Tue, Jul 2, 2013 at 3:50 PM, Ambrose Andongabo (RRes-Roth) ambrose.andong...@rothamsted.ac.uk wrote: Dear All, I updated my local galaxy instance yesterday and all my users cannot access their saved histories. When they click on saved histories all they get is an empty page. Checking the database, all the histories are there. I cleared the browser cache as many suggested but no luck yet. Any ideas of what can be done?? Thanks Ambrose -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. ___ Galaxy-gcc2013 mailing list galaxy-gcc2...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-gcc2013 ___ 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/
Re: [galaxy-dev] visulaization tool
Hello, Shashi
It looks like TreeViewX was written in C++ as a desktop program. In this
case, there is no way that it can be used with the display_application code
without major modification.
One option is to not use TreeViewX from within Galaxy but simply have it
installed on your users' computers and have them load their Galaxy data
into it after downloading to their local machines.
Other options may include other phylogenetic tree viewers and formatters.
There are many excellent programs and libraries available:
FigTree http://tree.bio.ed.ac.uk/software/figtree/
Archaeopteryx
https://sites.google.com/site/cmzmasek/home/software/archaeopteryx
and jsPhyloSVG (javascript) http://www.jsphylosvg.com/
If you need to produce phylogenetic trees within Galaxy, the phyloviz
visualization is the best place for you to start. In order to modify it to
get the features you'd need from it, however, you'll need to have some
experience with programming in JavaScript, python, and a web development
environment. There are many resources on the internet to help you.
We'd like to add to add functionality to phyloviz at some point (such as
saving to SVG, re-formatting the trees, etc.) so, if you're not able, we
will be working on it. However, those improvements may not be done anytime
soon.
On Thu, Jun 20, 2013 at 7:36 AM, shashi shekhar me_shash...@yahoo.co.inwrote:
Hi Ross,
i am using display application as visualization in galaxy.
display id=ucsc_interval_as_bed version=1.0.0 name=display at UCSC
link id=main name=main
urlhttp://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}amp;position=${position.qp}amp;hgt.customText=${bed_file.qp}
http://genome.ucsc.edu/cgi-bin/hgTracks?db=$%7Bqp($bed_file.dbkey)%7Dposition=$%7Bposition.qp%7Dhgt.customText=$%7Bbed_file.qp%7D/url
param type=data name=bed_file url=galaxy.bed
format=bedstrict/ !-- Galaxy allows BED files to contain non-standard
fields beyond the first 3 columns, UCSC does not: force use of converter
which will make strict BED6+ file --
param type=template name=position strip=True
what is the meaninng param type=template name=position strip=True /
and what is the use of url=galaxy.bed ?
Regards
shashi
--
*From:* Ross ross.laza...@gmail.com
*To:* shashi shekhar me_shash...@yahoo.co.in
*Cc:* galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
*Sent:* Wednesday, 19 June 2013 5:32 PM
*Subject:* Re: [galaxy-dev] visulaization tool
Shashi,
Beats me. Cloning the visualisation code would be a good start I'd
guess. It will not be trivial.
Others may have better ideas.
On Wed, Jun 19, 2013 at 9:56 PM, shashi shekhar
me_shash...@yahoo.co.inwrote:
Hi Ross,
Actually i have to add the visualization which will be interactive . it
will take dataset from galaxy .it will be in the same way as tracker
works .
in stead of tracker i want to add my own visualization tool. from wehere
should i start to replace tracker with my own visulization tool.
Regards
shashi
--
*From:* Ross ross.laza...@gmail.com
*To:* shashi shekhar me_shash...@yahoo.co.in
*Cc:* Hans-Rudolf Hotz h...@fmi.ch; galaxy-dev@lists.bx.psu.edu
galaxy-dev@lists.bx.psu.edu
*Sent:* Wednesday, 19 June 2013 5:02 PM
*Subject:* Re: [galaxy-dev] visulaization tool
Shashi,
Thanks for the additional information.
AFAIK: If it's command line driven and spews out pdf's, adapt any similar
tool that spews out pdfs like fastqc.
Galaxy tool execution is isolated from the user and from Galaxy itself, so
communication is just not possible if it's interactive - unless you hack
the tool into Galaxy itself or something. There is no documentation for
that.
On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar
me_shash...@yahoo.co.inwrote:
Hi Ross,
thanks for the reply . actually i want to use TreeView as visulaization
tool.
TreeView X is an open source and multi-platform program to display
phylogenetic trees. It can read and display NEXUS and Newick format tree
files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other
programs). It allows one to order the branches of the trees, and to export
the trees in SVG format.
i have to add treeviewx in galaxy..
Regards
shashi
--
*From:* Ross ross.laza...@gmail.com
*To:* shashi shekhar me_shash...@yahoo.co.in
*Cc:* Hans-Rudolf Hotz h...@fmi.ch; galaxy-dev@lists.bx.psu.edu
galaxy-dev@lists.bx.psu.edu
*Sent:* Wednesday, 19 June 2013 3:28 PM
*Subject:* Re: [galaxy-dev] visulaization tool
Shashi,
Hans made a brave guess based on your vague question, but you'll probably
get better answers if you do us all a favour and make an effort to provide
unambiguous detail about exactly what you want to achieve.
If there is a working Galaxy tool that does what you need but using a
different visualisation program (whatever you mean by that vague term),
Re: [galaxy-dev] BWA installation
Hello, מירב It looks like the indexing system/format in 'bwa index' has changed and we haven't updated the wiki to reflect the changes. The reverse index (which includes the .r* files) are now part of the forward index. You should be fine to proceed. I'll update the wiki to reflect this. From https://github.com/lh3/bwa/blob/master/NEWS : Release 0.5.10 and 0.6.0 (12 November, 2011) The 0.6.0 release comes with two major changes. Firstly, the index data structure has been changed to support genomes longer than 4GB. The forward and reverse backward genome is now integrated in one index. On Thu, May 30, 2013 at 8:03 AM, מירב . mer...@gmail.com wrote: Hello all, I am trying to install BWA , I used the command: bwa index -a bwtsw /global_data/hg18full.fa and I got only 5 files insted of 8 The missing files are - rbwt - rpac - .rsa I didn't recieve any error message while running. thanks for your help merav ___ 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/ ___ 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/
Re: [galaxy-dev] History page not opening
Thanks. Let's try and diagnose this from the client side first. Can you: - open the history panel in it's own frame and use firebug's net tab to get the request and response headers? - open the about:config tab of firefox, search for the network.http.accept-encoding entry, and let me know what it's set to? Carl On Tue, May 14, 2013 at 12:01 AM, sridhar srinivasan sridhar2bioi...@gmail.com wrote: Hi Carl, I am using firefox 3.6.18 and linux Red Hat/3.6-1.el5_6.. Thanks Sridhar On Mon, May 13, 2013 at 8:31 PM, Carl Eberhard carlfeberh...@gmail.comwrote: Hello, Sridhar. Can you tell me the browser and operating system you're using? Thanks, Carl On Mon, May 13, 2013 at 6:50 AM, sridhar srinivasan sridhar2bioi...@gmail.com wrote: Hi after installing galaxy, i could'nt see the history page in right end of galaxy web. it shows Content Encoding Error The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression. * Please contact the website owners to inform them of this problem. Please help me to solve the issue.. sridhar ___ 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/ ___ 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/
Re: [galaxy-dev] History page not opening
Hello, Sridhar. Can you tell me the browser and operating system you're using? Thanks, Carl On Mon, May 13, 2013 at 6:50 AM, sridhar srinivasan sridhar2bioi...@gmail.com wrote: Hi after installing galaxy, i could'nt see the history page in right end of galaxy web. it shows Content Encoding Error The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression. * Please contact the website owners to inform them of this problem. Please help me to solve the issue.. sridhar ___ 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/ ___ 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/
Re: [galaxy-dev] negative user data usage
Thanks much for the information, Geert. I've created a card for this bug in Trello: https://trello.com/c/KLmH1nag. On Wed, Apr 3, 2013 at 5:39 AM, Geert Vandeweyer geert.vandewey...@ua.ac.be wrote: Hi, In case anybody is wondering, the set_user_disk_usage.py script corrects this. Best, Geert On 03/28/2013 11:04 AM, Geert Vandeweyer wrote: Hi, Today, I found out that one user in our local galaxy installation (the administrator user) has a negative disk usage. - Reports shows : -72780720701 bytes - Galaxy history shows: -1% Does anybody have suggestions on what might be causing this and how to solve it? There is about 660 Gb of data in the histories of that user, but it was more before. I believe it happened after some histories were deleted and there was a message of one of them being shared. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/**cognitivegenetics http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/**geert-vandeweyer/26/457/726http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 __**_ 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/http://galaxyproject.org/search/mailinglists/ ___ 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/
Re: [galaxy-dev] heatmap capabilities!
Hello, Hakeem Although I've never used it, you might try the java_genomics_toolkit available as a tool shed repository (or have your installation's admin install it). It contains a tool called 'Align values in a matrix' which may work for your needs. Thanks, Carl On Tue, Apr 2, 2013 at 12:51 PM, Hakeem Almabrazi halmabr...@idtdna.comwrote: Hi, ** ** Is there a heatmap tool for Galaxy? If so can someone send me a link to how to integrate it to a local galaxy? ** ** I appreciate your help. ** ** ** ** ** ** ** ** ___ 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/ ___ 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/
Re: [galaxy-dev] History periodically disappears in AWS Cloudman installation
Hello, Greg, If I understand correctly, this may be an error with the server or panel loading the previously-used/most-current history. How many histories are displayed when you use the 'history-options-button' (the gear at the top of the history panel) and click 'Saved Histories'? As a side question, which browser are you using or most commonly using? Thanks for looking, Carl On Fri, Mar 22, 2013 at 8:46 PM, Greg Edwards gedwar...@gmail.com wrote: Hi, We're running a private Cloudman Galaxy on AWS for small-scale proteomics work. Lately the whole History of the main user id we use has occasionally disappeared, ie. on login the History is empty. The datasets aren't hiding in Deleted Datasets. They appear to still be there in /mnt/galaxyData/files/000. They're not in the Anonymous (not logged in ) id. They're not in another id. The data doesn't come back later. We reload the latest datasets in use and the numbering in the history restarts from 1. We're running the most basic config, with the simple single-threaded database. Nothing of interest seems to be in the various Cloudman logs. I've searched the archives for lost/deleted/disappeared datasets/history etc but nothing useful turned up. This is our rev status .. UBUNTU /mnt/galaxyTools/galaxy-central $ hg summary parent: 8116:ecd131b136d0 tip libraries: fix in query for 'datasets_are_public' branch: default commit: 2 modified, 268 unknown update: (current) This is a poor fault report but .. appreciate any pointers here. Many thanks ... -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ ___ 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/
Re: [galaxy-dev] customtrack visualisation
Hello, Shaun Which revision of galaxy-central or galaxy-dist are you using in your local install? Thanks, Carl On Wed, Mar 20, 2013 at 12:52 PM, Shaun Webb swe...@staffmail.ed.ac.ukwrote: Hi Jen, I should have said this is in my own install. It works fine at the main server. I only noticed this as I was running a tutorial I created last year. So I can only say that something has changed in the last year.. I was wondering where in the configuration files or scripts galaxy is told to provide this link for this type of dataset, perhaps there is something I need to reconfigure. Thanks Shaun Quoting Jennifer Jackson j...@bx.psu.edu on Wed, 20 Mar 2013 07:08:13 -0700: Hi Shaun. Is this still an issue for you this morning, on the public Main Galaxy server at https://main.g2.bx.psu.edu/? I am unable to reproduce with a test dataset: - bed custom track - datatype = customtrack - database = hg18 display at UCSC main is functional, and it is the only external display (this is expected). If you want to share a history with me, please send a link and note the dataset with the problem. Thanks, Jen Galaxy team On 3/19/13 2:44 AM, Shaun Webb wrote: Hi, I have lost my view in UCSC link on my customtrack datatypes, I'm not sure when this happened. External display links are still working ok for other datatypes. I have set the genome database to hg18. Any idea what I will need to edit to get this back? Thanks Shaun webb -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __**_ 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/ ___ 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/
Re: [galaxy-dev] Displaying track into UCSC (update)
Hello, Stephanie and Julien What revision are you using IGBMC? Can you clarify what you mean by a private dataset? Are non-owners importing into a history via a shared history, or are they being passed a direct link to the UCSC display viewer from the owner? Thanks for the information, Carl On Tue, Mar 19, 2013 at 1:27 PM, Stephanie LE GRAS sleg...@igbmc.fr wrote: Hi all, Here is an update regarding the problem we are facing with Julien with our local instance of Galaxy. As Julien said we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) We have worked for hours on it today and we have identified that datasets that can be uploaded to UCSC are actually public datasets and that Julien can upload all his datasets to UCSC because they are all public by default. What is interesting now is that we've seen that the path to the data in the UCSC error message is : http://www.galaxy-igbmc.fr/display_application/f1cb3a6ff6a93c01/ucsc_interv al_as_bed/main/bea5029fce8b957e/data/galaxy.bed: While it should be : http://www.galaxy-igbmc.fr/display_at(Š)/galaxy.bed Because the right function to use in order to check whether the dataset can be uploaded to UCSC should be display_at but not display_application. Any ideas of what could cause Galaxy not to use the right function? Thank you in advance, Stephanie -- Stephanie Le Gras Bioinformatics engineer High throughput sequencing platform IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73 Tel. Solexa : +33 (0)3 88 65 32 97 Le 18/03/13 19:20, « Julien SEILER » seil...@igbmc.fr a écrit : Hi all, We have installed a local galaxy server and we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) Curiously, it works fine with my personal account but it doesn't for all other users. It also works for displaying tracks based on a public dataset for all users. Could anybody explain us what's happening ? Thanks in advance for any help, Julien ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Displaying track into UCSC
Hello, Julien Please see my reply and questions to Stephanie in her latest update. Thanks, Carl On Mon, Mar 18, 2013 at 2:20 PM, Julien SEILER seil...@igbmc.fr wrote: Hi all, We have installed a local galaxy server and we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) Curiously, it works fine with my personal account but it doesn't for all other users. It also works for displaying tracks based on a public dataset for all users. Could anybody explain us what's happening ? Thanks in advance for any help, Julien ___ 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/ ___ 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/
Re: [galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset
1 2: Very interesting then. I'll do some more digging as to why a query
would succeed (with the wrong record) with those ids.
3: Good!
4.1: That first line is just the beginning of the diff/patch file and not
something you have to enter. It records the command used to generate the
diff file. That revision was the revision I was updated to when generating
the patch and, since I was using a development version more recently
updated than your machine, your hg can't find it. There's no need to run
that line, tho (see 4.2).
4.2: If you want to import a patch in the future, I've had good luck with 'hg
import --no-commit mypatchfile.patch'. This will make the changes in the
patch file without committing them ('--no-commit'). If you want to remove
the changes later (and assuming you haven't made any other changes you want
to keep in that file) you can use 'hg revert thefilethatwaschanged.py'
and that will return the file to the previous state. Keep in mind, of
course, that patches (like any changes) may make updating, and/or merging
your instance later more difficult.
A question I forgot to ask: what database backend are you using
(postgresql, mysql, etc.)?
Carl
On Mon, Mar 11, 2013 at 12:34 PM, Jean-Francois Payotte
jean-francois.payo...@dnalandmarks.ca wrote:
Dear Dannon, John and Carl,
Thank you for your answers and for taking the time to help me solve this
issue.
Here are my answers to your questions:
1. I don't think our number of HDAs is large enough to cause an
overflow. From what I can see, the HDAs number in our two faulty galaxy
instances are:
galaxy_prod : 263,163 HDAs
galaxy_dev : 14,119 HDAs
2. Here is a list of hashed IDs for HDAs where I'm seeing this
behaviour:
(None of them are of 16-digit integers)
3. I've also tried applying John's patch on our development Galaxy
instance and so far, *it seems to do the trick*.
I've run my test tool (wich output a message to stderr) about 50
times, and the bug report always displayed the correct dataset. Yay!!
4. I would have two question though before applying the patch to our
production Galaxy instance:
1. If I run the below hg diff -r f25f3fee4da7
lib/galaxy/webapps/galaxy/controllers/dataset.py command, I receive the
following error:
*abort: unknown revision 'f25f3fee4da7'!*
Is this a normal behaviour? Are we missing something important?
2. Also, out of curiosity, is there a particular way to apply a
patch (like the one you sent me), or if I simply have to manually edit
the
file? (That's what I did.)
Thanks again for your help! This is greatly appreciated!
*Jean-Francois*
From:Carl Eberhard carlfeberh...@gmail.com
To:John Chilton chil...@msi.umn.edu
Cc:Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca,
galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Date:08/03/2013 06:07 PM
Subject:Re: [galaxy-dev] Strange issue where the dataset reported
in the bug report doesn't correspond to the current dataset
--
Hello,
We explored this for quite a while this afternoon and believe John is
correct about the location as well as the design decision.
It may be that the hashes generated in some instances will correctly parse
as 16 digit integers and, since an integer lookup is tried first (and you
may either have an extraordinary large number of HDAs or there is some
integer roll over/overflow - at a guess), the incorrect dataset is being
returned without attempting to decode the hash into the proper dataset.
This may also explain why it is consistent but intermittent.
I would be curious to see the hashed ids of the HDAs where you're seeing
this behavior. Can you provide some?
If the hash produces fully integer strings as we're (tentatively)
guessing, the if not str( id ).isdigit() may still branch improperly
unfortunately.
In any event and to John's last point, from what we can tell,
dataset.errors is only called from the new history panel and only encoded
ids are used there - so the backwards compatibility may not be needed at
this point.*
I will thoroughly check that that controller method isn't called elsewhere
with a raw id, but, in the meantime: Jean-Francois, can you apply the patch
below (and attached) to your more updated installation and (when
convenient) see if that helps?
*PS. if user's are still using the older history panel - please, do not
apply this patch as it relies on the older, raw ids for this function.
diff -r f25f3fee4da7 lib/galaxy/webapps/galaxy/controllers/dataset.py
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py Fri Mar 08 16:01:25
2013 -0500
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py Fri Mar 08 17:41:46
2013 -0500
@@ -171,14 +171,17 @@
@web.expose
def errors( self, trans, id ):
+hda = None
try
Re: [galaxy-dev] Error Report contains STDERR from different job
Glad to hear it's working, Carl On Tue, Mar 12, 2013 at 11:47 AM, Eric Enns eric.e...@phac-aspc.gc.cawrote: Hey, My bad I didn't see the patch and thought you had wanted me to revert to the Sept 12 release for that function. I now applied the patch, and am seeing the correct error when clicking the bug button. If I encounter any issue I will post back. -Eric -Carl Eberhard carlfeberh...@gmail.com wrote: - To: Eric Enns eric.e...@phac-aspc.gc.ca From: Carl Eberhard carlfeberh...@gmail.com Date: 03/12/2013 10:15AM Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca Subject: Re: [galaxy-dev] Error Report contains STDERR from different job Thanks, Eric Since the HDA is None, the if statement should be sending you the trans.show_error_message. Just to make sure we're on the same page, could you please attach or post the errors method from the dataset controller in your installation. It can be found at lib/galaxy/webapps/galaxy/controllers/dataset.py? Carl On Tue, Mar 12, 2013 at 10:59 AM, Eric Enns eric.e...@phac-aspc.gc.cawrote: The following is the stack trace I got when I applied the patch and clicked the bug icon. GET /dataset/errors?id=c39bc73d0eae67dd HTTP/1.0 500 - http://galaxy/history; Error - type 'exceptions.AttributeError': 'NoneType' object has no attribute 'hid' URL: http://galaxy/dataset/errors?id=c39bc73d0eae67dd File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call_ _ app_iter = self.application(environ, start_response) File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 in handle_request body = method( trans, **kwargs ) File '/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 175 in errors return trans.fill_template( dataset/errors.mako, hda=hda ) File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 848 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 859 in fill_template_mako return template.render( **data ) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec _template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable _(context, *args, **kwargs) File '/galaxy-dist/database/compiled_templates/dataset/errors.mako.py', line 27 in render_body __M_writer(unicode(hda.hid)) AttributeError: 'NoneType' object has no attribute 'hid' -Carl Eberhard carlfeberh...@gmail.com wrote: - To: Eric Enns eric.e...@phac-aspc.gc.ca From: Carl Eberhard carlfeberh...@gmail.com Date: 03/12/2013 09:47AM Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca Subject: Re: [galaxy-dev] Error Report contains STDERR from different job Can you post the stack trace from the error, please? Thanks for the info, Carl On Tue, Mar 12, 2013 at 10:37 AM, Eric Enns eric.e...@phac-aspc.gc.cawrote: Hey, I applied the patch and it does not help, instead I received a server error since hda was none. If it helps at all I am using mysql as my backend. -Eric -Carl Eberhard carlfeberh...@gmail.com wrote: - To: Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca From: Carl Eberhard carlfeberh...@gmail.com Date: 03/08/2013 05:10PM Cc: eric.e...@phac-aspc.gc.ca, galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error Report contains STDERR from different job Hello, Does applying the patch from [galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset help? If not, we can diagnose further. Thanks, Carl On Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca wrote: Dear Eric, I'm glad to know that I am not the only one having this bug. (Even though I would prefer if neither of us would have it). ;) I've already written twice to the galaxy mailing-list, but I didn't receive any answers so far. Let's hope someone will be able to help us solve this issue. You can see
Re: [galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset
Hello, We explored this for quite a while this afternoon and believe John is correct about the location as well as the design decision. It may be that the hashes generated in some instances will correctly parse as 16 digit integers and, since an integer lookup is tried first (and you may either have an extraordinary large number of HDAs or there is some integer roll over/overflow - at a guess), the incorrect dataset is being returned without attempting to decode the hash into the proper dataset. This may also explain why it is consistent but intermittent. I would be curious to see the hashed ids of the HDAs where you're seeing this behavior. Can you provide some? If the hash produces fully integer strings as we're (tentatively) guessing, the if not str( id ).isdigit() may still branch improperly unfortunately. In any event and to John's last point, from what we can tell, dataset.errors is only called from the new history panel and only encoded ids are used there - so the backwards compatibility may not be needed at this point.* I will thoroughly check that that controller method isn't called elsewhere with a raw id, but, in the meantime: Jean-Francois, can you apply the patch below (and attached) to your more updated installation and (when convenient) see if that helps? *PS. if user's are still using the older history panel - please, do not apply this patch as it relies on the older, raw ids for this function. diff -r f25f3fee4da7 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py Fri Mar 08 16:01:25 2013 -0500 +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py Fri Mar 08 17:41:46 2013 -0500 @@ -171,14 +171,17 @@ @web.expose def errors( self, trans, id ): +hda = None try: -hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) -except: -hda = None -if not hda: -hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( trans.security.decode_id( id ) ) +# only sent from the history panel (which uses encoded ids) +decoded_id = trans.security.decode_id( id ) +hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( decoded_id ) +except Exception, exc: +log.error( 'Could not retrieve hda with id %s: %s', id, str( exc ), exc_info=True ) + if not hda or not self._can_access_dataset( trans, hda ): -return trans.show_error_message( Either this dataset does not exist or you do not have permission to access it. ) +return trans.show_error_message( Either this dataset does not exist + + or you do not have permission to access it. ) return trans.fill_template( dataset/errors.mako, hda=hda ) @web.expose On Fri, Mar 8, 2013 at 3:49 PM, John Chilton chil...@msi.umn.edu wrote: Does rewriting this: def errors( self, trans, id ): try: hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) except: hda = None if not hda: hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( trans.security.decode_id( id ) ) if not hda or not self._can_access_dataset( trans, hda ): return trans.show_error_message( Either this dataset does not exist or you do not have permission to access it. ) return trans.fill_template( dataset/errors.mako, hda=hda ) to say this: def errors( self, trans, id ): if not str(id).isdigit(): id = trans.security.decode_id( id ) hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) if not hda or not self._can_access_dataset( trans, hda ): return trans.show_error_message( Either this dataset does not exist or you do not have permission to access it. ) return trans.fill_template( dataset/errors.mako, hda=hda ) help the problem? Neither of these are particularly good design decisions. errors should either take in an id or an encoded id, or at least take them in as different parameters. -John -John On Tue, Mar 5, 2013 at 12:38 PM, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca wrote: Dear Galaxy mailing-list, I did some more tests in order to find out what might be causing this issue and it appears that we are facing this problem on two of our local Galaxy instances, which makes me think of a possible Galaxy bug rather than a database issue (both Galaxy instances using a different database). Does anybody else is facing this issue? As a reminder, the issue we are currently facing is the Dataset generation error page displaying the wrong information (the information related to a completely different dataset) when clicking on the bug icon. (This is happening about half the time a tool ends in error). Note that
Re: [galaxy-dev] Error Report contains STDERR from different job
Hello, Does applying the patch from [galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset help? If not, we can diagnose further. Thanks, Carl On Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca wrote: Dear Eric, I'm glad to know that I am not the only one having this bug. (Even though I would prefer if neither of us would have it). ;) I've already written twice to the galaxy mailing-list, but I didn't receive any answers so far. Let's hope someone will be able to help us solve this issue. You can see my mail thread here: http://dev.list.galaxyproject.org/Strange-issue-where-the-dataset-reported-in-the-bug-report-doesn-t-correspond-to-the-current-dataset-td4658707.html Best regards, *Jean-Francois* From:Eric Enns eric.e...@phac-aspc.gc.ca To:galaxy-...@bx.psu.edu Date:08/03/2013 03:14 PM Subject:[galaxy-dev] Error Report contains STDERR from different job Sent by:galaxy-dev-boun...@lists.bx.psu.edu -- Hey, When clicking the View or report this error button the error message shown occasionally is from a different job. If you go into the info for the job you can select stderr and see the correct error. If the user submits the error to admins they receive the wrong error message and a link to the wrong history. -Eric___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] API - Status 403 Forbidden
Hello, all Thanks to you both for reporting this. John, in the steps to reproduce you mention, is step 4 going through the browser? If using curl/wget with an api key, they should of course, allow you to retrieve all histories (logged in or not). If through the browser, where you able to retrieve all your histories or just the most recent? If only the most recent, it may be that (although you were an anonymous user after logging out) it's functioning as intended. Anonymous users must be able to query the most recent (and only) histories for the history panel to work for them. This is done by using trans.galaxy_session.current_history. If there are more than your most recent history returned by that API call through the browser, let me know and I can work on that. Also, in addition to curl/wget you might want to look at the scripts/api/ directory in your installation which provides some python equivalents to these along with JSON decoding/encoding. Thanks for the additional info, Carl On Fri, Mar 8, 2013 at 9:55 AM, Rob Leclerc robert.lecl...@gmail.comwrote: Hi John, Thanks! I restarted the server, regenerated the API key, and can confirm that it's now working. As you mentioned, it's possible that I was missing a value on the end of the API key and was caught by the bug which allowed me to check find histories when I was logged out. Cheers! Rob On Fri, Mar 8, 2013 at 9:33 AM, John Chilton chil0...@umn.edu wrote: I can confirm this is a Galaxy bug. Steps to reproduce: - Log into clean galaxy. - Create an API key. - Logout - Got to localhost:8080/api/histories You should get a 403 and don't. This doesn't explain why the API isn't working for you, my best guess would be the key is off by a character or you created a new one and overwrote that one maybe. I think your instinct to try to diagnose this outside of blend4j is a good one, if you can get the API working without a browser session (perhaps from wget or curl) then I am confident the blend4j part will work (or at least we can get it to). -John On Thu, Mar 7, 2013 at 9:09 PM, Rob Leclerc robert.lecl...@gmail.com wrote: I'm trying to use the blend4j to access the Galaxy API, but I'm getting a 403 error, however when I pass the same request string through my browser I get a json response (Status 200). //Here is the URL string being passed in both cases: http://localhost:8080/api/histories?key=c5954f0e726e52da297cdad5ad4aa249 //Below are the Galaxy logs emitted on my localhost: 127.0.0.1 - - [07/Mar/2013:21:12:01 -0400] GET /api/histories?key=c5954f0e726e52da297cdad5ad4aa249 HTTP/1.1 200 - - Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.22 (KHTML, like Gecko) Chrome/25.0.1364.155 Safari/537.22 127.0.0.1 - - [07/Mar/2013:21:12:24 -0400] GET /api/histories?key=c5954f0e726e52da297cdad5ad4aa249 HTTP/1.1 403 - - Java/1.6.0_41 I'm not sure if this is related or not, because I can logout in my browser and still hit the local server without getting a 403, but how do I login (and logout) through the API to set up a session because I assume that the API key is only valid for the logged in user? Is there an API request for the login? Cheers, Rob ___ 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/ -- Rob Leclerc, PhD http://www.linkedin.com/in/robleclerchttps://twitter.com/#!/robleclerc P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-5469 Personal Email: rob.lecl...@aya.yale.edu ___ 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/ ___ 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/
Re: [galaxy-dev] upload of local file ends up with a broken pipe.
Hello, Jason,
The broken pipe can happen when a client stops listening to the servers
response (e.g. when a user closes a tab). In general it won't cause any
long term problems. I'm glad that the uploads are working now, however.
Let us know if you see any further problems,
Carl
On Thu, Mar 7, 2013 at 4:31 PM, Jason Evans jason.j.ev...@gmail.com wrote:
Greetings Carl,
Thanks for your response. I pulled and updated and the broken pipe error
still occurs. I am using revision 9fd7fe0c5712 .
The error was regular, but now seems intermittent. I've been trying to
reproduce it and could only see it cause an error once.
I don't think it was doing this before, but the upload completes properly
now. It still gives an error in the output, but finishes and the data is
there.
thanks again,
Jason
Jason Evans
jason.j.ev...@gmail.com
On Mar 7, 2013, at 9:52 AM, Carl Eberhard carlfeberh...@gmail.com wrote:
Hello, Jason
At which revision of galaxy-central or galaxy-dist is your installation?
Does this happen intermittently or regularly (with every upload)?
Thanks,
Carl
On Mon, Feb 25, 2013 at 1:49 PM, Jason Evans jason.j.ev...@gmail.comwrote:
I am having difficulties with my local instance of Galaxy on Mac OS X.
Upon using the local file upload tool I get an error resultant of a broken
pipe in python.
The command-line output is as follows.
127.0.0.1 - - [25/Feb/2013:12:36:32 -0400] GET /history HTTP/1.1 500 -
http://localhost:8080/tool_runner/upload_async_message; Mozilla/5.0
(Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like
Gecko) Version/6.0.2 Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 50438)
Traceback (most recent call last):
File
/Users/jjevans/Work/Tools/Galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py,
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 641, in __init__
self.finish()
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 694, in finish
self.wfile.flush()
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py,
line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
127.0.0.1 - - [25/Feb/2013:12:36:34 -0400] GET
/api/histories/2a56795cad3c7db3 HTTP/1.1 200 -
http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
galaxy.jobs.manager DEBUG 2013-02-25 12:36:35,289 (77) Job assigned to
handler 'upload_handler'
My instance has worked for this task in the past, but I'm not sure if it
has been since my last Galaxy update or perhaps something with my
configuration changed.
thanks for your help,
Jason
___
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and other Galaxy lists, please use the interface at:
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___
Please keep all replies on the list by using reply all
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and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hello, Ross makes an important point: if this installation is for more than one user, you should install a more complete database system. This page may help with your decisions there: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=Admin%2FConfig%2FPerformance To your first question Is all the data in datacache.g2.bx.psu.edu/indexes needed?, I would say you should only need the data specific to the subject of your analyses and the tools you plan to use. To your second question can all of these needed data be downloaded (via rsync)? - perhaps you can clarify, please? We don't have any restriction on the amount you rsync from there and you're free to download all the data. If a problem or topic isn't covered in that wiki page, this mailing list is a good place to ask questions related to data set up. Thanks, Carl On Wed, Feb 27, 2013 at 5:44 AM, Ross ross.laza...@gmail.com wrote: Hi, shenwiyn I'd also add: Fourth, replace distributed default sqlite with postgresql to your list if it's for any serious use. Sqlite is ok for testing. On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn shenw...@gmail.com wrote: ** **Hello Carl, Thank you very much for your help.I have some thoughts about installing my local galaxy : First,download the latest source of galaxy from https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer. Second,install dependencies tools mentioned in http://wiki.galaxyproject.org/Admin/Data%20Integration successfully. Third ,install the needed data and configure the .loc files from the following help of wiki page http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. Finally ,our installation of local galaxy overs and it works in the mass.Is it right ? And I also have some confusions: First ,How large the total needed data is ?Is all the data in datacache.g2.bx.psu.edu/indexes needed ? Second, can all of these needed data be downloaded (via rsync) by the help of http://wiki.galaxyproject.org/Admin/Data%20Integration? These are the most important questions I concerned about now.I am so thankful for some of you advice. Thank you very much. -- shenwiyn *From:* Carl Eberhard carlfeberh...@gmail.com *Date:* 2013-02-23 02:42 *To:* shenwiyn shenw...@foxmail.com *CC:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: ** Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/ AaegL1.fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/ AgamP3.fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/ anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/ apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/ apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/ aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2 .fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/ bx.psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn -- *From:* Carl Eberhard carlfeberh...@gmail.com *Date:* 2013-02-22 01:20 *To:* shenwiyn shenw...@gmail.com *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn shenw...@gmail.com wrote: ** Hi all, Are all the data files in .loc files needed to download and put to the right directory when we install our local galaxy? thaks shenwiyn -- ___ Please keep all replies
Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: ** Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1. fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3. fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/ anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/ apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/ apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/ aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2. fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx. psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn -- *From:* Carl Eberhard carlfeberh...@gmail.com *Date:* 2013-02-22 01:20 *To:* shenwiyn shenw...@gmail.com *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn shenw...@gmail.com wrote: ** Hi all, Are all the data files in .loc files needed to download and put to the right directory when we install our local galaxy? thaks shenwiyn -- shenwiyn ___ 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/ ___ 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/
Re: [galaxy-dev] Problem to upload files to Galaxy
Hello, Roy There was a recent fix for this. Is this problem still occurring for you? Thanks, Carl On Thu, Jan 31, 2013 at 10:17 PM, Blum, Roy roy.b...@nyumc.org wrote: Dear Galaxy support, In the last 24 hours we are unable to load files to the Galaxy server. We tried doing so as guest and by login as users but failed. We try to load a small file (about 1M) but so far no success. Has the Galaxy server been experienced problems recently? Thanks a lot, Roy *___* *Roy Blum, Ph.D. * New York University School of Medicine, Cancer Institute, Smilow Research Building, 11th Floor, Room 1106 552 First Ave. New York, NY, 10016 Mob: +1 (646) 716-2875 Lab:+1 (212) 263-6169 *http://blumroy.googlepages.com* ___ 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/ ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
Hello, Dan.
I'm glad you updated.
I noticed another error in your log:
127.0.0.1 - - [04/Feb/2013:09:50:43 -0700] POST
/tool_runner/upload_async_create HTTP/1.1 500 - http://localhost:8080/;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML,
like Gecko) Chrome/24.0.1312.57 Safari/537.17
Debug at: http://localhost:8080/_debug/view/136104
Two things -
1. Can you restart your daemon and make sure you're using a fresh history
before the upload?
2. If you're upload fails this time, would you search your paster.log for
something close to Debug at: http://localhost:8080/_debug/view/;... and
navigate there with your browser? It should show that error in more depth
and allow you to post that here.
Thanks for the help,
C
On Mon, Feb 4, 2013 at 12:55 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi Carl,
On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Here you go. I notice a couple of stack traces.
Thanks!
Dan
I noticed that another user on the list seemed to have a similar
problem and I saw that that problem was possibly addressed in a new
commit. I updated to 8531:3299529e0fe8 and I still have the same
problem, but perhaps different output.
I tried logging in and the UI does not seem to recognize that I have
logged in. Then I tried to upload a file and it failed, with a
traceback in the console:
127.0.0.1 - - [04/Feb/2013:09:45:13 -0700] GET /history HTTP/1.1 200
- http://localhost:8080/tool_runner/index; Mozilla/5.0 (Macintosh;
Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko)
Chrome/24.0.1312.57 Safari/537.17
127.0.0.1 - - [04/Feb/2013:09:45:12 -0700] GET /history HTTP/1.1 200
- http://localhost:8080/tool_runner/upload_async_message;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17
(KHTML, like Gecko) Chrome/24.0.1312.57 Safari/537.17
Exception happened during processing of request from ('127.0.0.1', 49617)
Traceback (most recent call last):
File
/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py,
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 641, in __init__
self.finish()
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 694, in finish
self.wfile.flush()
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py,
line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
Then I started a daemon session in order to be able to send you the
full output, but, although the upload still fails, I don't get this
same traceback in the paster.log. I attach it anyway.
Thanks,
Dan
On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Ok - interesting!
Can you send me the paster.log from a daemon session where you try an
upload?
Steps for that are:
1. from the directory of your galaxy installation: sh run.sh --daemon
(you
should see 'Entering daemon mode')
2. Wait a minute, then load localhost:8080 in your browser, login, and
try
an upload
3. When that fails, you can shut down: (from the galaxy installation
again)
sh run.sh --stop-daemon
The file 'paster.log' should be in that same directory.
Let me know if there are any problems,
C
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Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
Just to be clear, Dan - this solved the login issue and not the upload issue (in which case I'd owe Carlos a six-pack), correct? C On Mon, Feb 4, 2013 at 4:04 PM, Carl Eberhard carlfeberh...@gmail.comwrote: Thanks much, Carlos - I owe you a beer! On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as your email' in the 'User' menu at the top? No. I think I'm not actually being logged in. All I see under the User menu is Login and Register. I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case. This behavior is something I have seen often with Chrome in particular and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this thread. I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine. Indeed, it works with Firefox. And it works with Chrome after I delete my cookies. Thanks very much! Dan Hope it helps, Carlos ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
Even better - thanks again, Carlos - and thanks for the help in tracking this down, Dan. On Mon, Feb 4, 2013 at 4:46 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard carlfeberh...@gmail.com wrote: Just to be clear, Dan - this solved the login issue and not the upload issue (in which case I'd owe Carlos a six-pack), correct? Sorry...this solved both issues. Dan C On Mon, Feb 4, 2013 at 4:04 PM, Carl Eberhard carlfeberh...@gmail.com wrote: Thanks much, Carlos - I owe you a beer! On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as your email' in the 'User' menu at the top? No. I think I'm not actually being logged in. All I see under the User menu is Login and Register. I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case. This behavior is something I have seen often with Chrome in particular and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this thread. I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine. Indeed, it works with Firefox. And it works with Chrome after I delete my cookies. Thanks very much! Dan Hope it helps, Carlos ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
Thanks much, Carlos - I owe you a beer! On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as your email' in the 'User' menu at the top? No. I think I'm not actually being logged in. All I see under the User menu is Login and Register. I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case. This behavior is something I have seen often with Chrome in particular and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this thread. I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine. Indeed, it works with Firefox. And it works with Chrome after I delete my cookies. Thanks very much! Dan Hope it helps, Carlos ___ 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/
Re: [galaxy-dev] How to use the API when using a proxy server
I'm glad that worked, Thon. Let us know if you run into any other problems with the API in a proxy set up. Carl On Thu, Jan 31, 2013 at 7:58 PM, Anthonius deBoer thondeb...@me.com wrote: Hi Carl, I am using the submit and get functions from the scripts/api/common.py I actually found that I just need to add authentication to the calls, so I added this code def authenticate(url, u, p): auth_handler = urllib2.HTTPBasicAuthHandler() auth_handler.add_password(realm='GALAXY@GHI. Please log in with your Windows account', uri=url, user=u, passwd=p) opener = urllib2.build_opener(auth_handler) # ...and install it globally so it can be used with urlopen. urllib2.install_opener(opener) def make_url( api_key, url, args=None ): # Adds the API Key to the URL if it's not already there. if args is None: args = [] argsep = '' if '?' not in url: argsep = '?' if '?key=' not in url and 'key=' not in url: args.insert( 0, ( 'key', api_key ) ) return url + argsep + ''.join( [ '='.join( t ) for t in args ] ) def get( api_key, url, user, pw ): # Do the actual GET. url = make_url( api_key, url ) authenticate(url, user, pw) try: return simplejson.loads( urllib2.urlopen( url ).read() ) except simplejson.decoder.JSONDecodeError, e: print URL did not return JSON data sys.exit(1) . . . /code This will authenticate for each call and it seems to work nicely (if you add the authenticate step to each of the functions, like I did here for get Thon On Jan 31, 2013, at 11:44 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Hello Anthonius, Can you elaborate on how you're invoking the API? How are you calling it? Thanks, Carl On Wed, Jan 30, 2013 at 6:30 PM, Anthonius deBoer thondeb...@me.comwrote: Hi, I am trying to use the API with my galaxy server running behind a proxy server. How do I pass username/password information to the API so it can actually run? If I use the regular API calls I get a access denied... Thanks Thon ___ 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/ ___ 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/
Re: [galaxy-dev] History not updating automatically
Joachim, is your history panel still not updating or did you find a
solution from the info in this thread?
If not, can you post the contents of the alert/popup message?
Thanks,
Carl
On Tue, Jan 29, 2013 at 5:26 AM, Joachim Jacob |VIB|
joachim.ja...@vib.bewrote:
Hi,
I have a similar - but not identical issue. The history panel is not being
updated: I have to restart Galaxy to see the updated panel.
It appears only to happen after an error relating to the history API of
Galaxy (it's a popup error, and I have closed it).
My apache config (thanks for any hints and tweaks to improve my setup).
[galaxy@galaxy conf.d]$ cat galaxy_web.conf
NameVirtualHost 157.193.230.103:80
VirtualHost 157.193.230.103:80
ServerName galaxy.bits.vib.be
Proxy balancer://galaxy
BalancerMember http://localhost:8080
BalancerMember http://localhost:8081
BalancerMember http://localhost:8082
BalancerMember http://localhost:8083
BalancerMember http://localhost:8084
BalancerMember http://localhost:8085
BalancerMember http://localhost:8086
BalancerMember http://localhost:8087
BalancerMember http://localhost:8088
BalancerMember http://localhost:8089
BalancerMember http://localhost:8090
BalancerMember http://localhost:8091
BalancerMember http://localhost:8092
/Proxy
RewriteEngine on
RewriteLog /tmp/apacheGalaxy.log
### LDAP authentication will be implemented later
# Location /
# AuthType Basic
# AuthBasicProvider ldap
# AuthLDAPURL
ldap://smeagol.vib.be:389/DC=**vib,DC=local?sAMAccountNamehttp://smeagol.vib.be:389/DC=vib,DC=local?sAMAccountName
# AuthLDAPBindDN vib\administrator
# AuthLDAPBindPassword tofillin
# AuthzLDAPAuthoritative off
# Require valid-user
# # Set the REMOTE_USER header to the contents of the LDAP query
response's uid attribute
# RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}
# /Location
RewriteRule ^/static/style/(.*)
/home/galaxy/galaxy-dist/**static/june_2007_style/blue/$1
[L]
RewriteRule ^/static/scripts/(.*)
/home/galaxy/galaxy-dist/**static/scripts/packed/$1
[L]
RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/**static/$1 [L]
RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/**static/favicon.ico
[L]
RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/**static/robots.txt [L]
RewriteRule ^(.*) balancer://galaxy$1 [P]
/VirtualHost
Cheers,
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 01/28/2013 09:02 PM, Langhorst, Brad wrote:
Nate:
I used the config from the wiki directly…
Location /
…
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}**e
...
/Location
but I also had a section like this below it...
# Location /api
# Satisfy Any
# Allow from all
# /Location
I thought that the /api location would inherit the auth and headers stuff
of it's container, but that's not true.
Commenting the api location fixes the problem form e.
Brad
On Jan 28, 2013, at 2:35 PM, Nate Coraor n...@bx.psu.edu
wrote:
Hi Brad and Sajoscha,
Is there any chance that your proxy configurations are not passing the
username in the REMOTE_USER header when the request is to an /api path?
Could you provide the relevant portions of your proxy server configs?
Thanks,
--nate
On Jan 28, 2013, at 7:12 AM, Langhorst, Brad wrote:
Hi Sajoscha:
I have exactly the same problem… it started about a month ago.
Also with external ldap auth.
I have not yet investigated in detail, since it's not crippling - just
annoying.
Brad
On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de
wrote:
Hi list,
I have a weird problem after updating to the latest version.
After doing the update as usual, the history panel is not updating
automatically anymore. And when I press refresh, I get an javascript popup
saying:
Error getting history updates from the server.
Forbidden
Also, in the log I see the following:
galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as
'(null)' externally, but has a cookie as 'sa...@embl.de' invalidating
session
We are using LDAP to connect to Galaxy, but I don't know if this has
something to do with the problem. As I said, it was working perfectly fine
before the update.
Does someone know the problem or has any ideas?
Thanks for your help,
Sajoscha
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--
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langho...@neb.com
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Re: [galaxy-dev] How to use the API when using a proxy server
Hello Anthonius, Can you elaborate on how you're invoking the API? How are you calling it? Thanks, Carl On Wed, Jan 30, 2013 at 6:30 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I am trying to use the API with my galaxy server running behind a proxy server. How do I pass username/password information to the API so it can actually run? If I use the regular API calls I get a access denied... Thanks Thon ___ 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/ ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
I was incorrect in stating that the changes in the next galaxy-dist will
help in this case, unfortunately. From the stack trace you posted, there is
a deeper error with your instance that the client-side changes won't help.
Can you post the size, type, and name of the file you're trying to upload?
On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Another thing you might try is to upload the file to our test server:
https://test.g2.bx.psu.edu/ and see if that works.
Thanks, that does work.
Setting up an FTP server on my local installation seems pretty
complex. All I really want to do is work around this issue and fool
Galaxy into thinking that I have uploaded a file using the
uploader...since this is a local installation I can put a file
anywhere on my system, I don't have to actually upload it, just place
it in a directory.
If there is no such workaround, I'll wait for the fix, I guess. Thanks
very much for working on this!
Dan
On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
If this is happening consistently and a refresh on the history isn't
doing
anything, you might try ftp upload:
http://wiki.galaxyproject.org/FTPUpload
or if you have permissions or are an admin you can try uploading to a
data
library:
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
On Wed, Jan 23, 2013 at 5:44 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
What sort of database are you using on your local instance?
The default (sqlite I guess). It's a completely vanilla instance, I
have not touched the config files.
Dan
On Wed, Jan 23, 2013 at 5:37 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
Thanks, Dan. That helps and I'll start looking into this.
We will be pushing out a new galaxy-dist revision sometime this
week
if
all
goes well. This revision includes some code for the history panel
that
may
help handle this situation a bit better. I'd recommend updating to
that
revision when it comes out.
Thanks! Is there a workaround to upload a file or add it to my
history
in the meantime? Command-line is ok. If there isn't one, that's ok
too
Dan
I'll let you know what I can find.
Carl
On Wed, Jan 23, 2013 at 5:18 PM, Dan Tenenbaum
dtene...@fhcrc.org
wrote:
Hi Carl,
On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
Heya, Dan.
Sorry for the trouble.
When you get that error again look for a line like you have
above:
Debug at: http://localhost:8080/_debug/view/1358978130
If you open a new tab or window in your browser and go to the
address
('http://localhost:8080/_debug ...'), you should see a more
informative
error message - complete with a list of function calls that led
to
the
error
(a stack trace).
Can you post that stack trace when you see it?
Thanks for the quick response. Here it is:
URL: http://localhost:8080/tool_runner/upload_async_create
File
'/Users/dtenenba/dev/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File
'/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/base.py',
line 160 in __call__
body = method( trans, **kwargs )
File
'/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 73 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )
File
'/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 317 in upload_async_create
datasets.append( create_dataset( name ) )
File
'/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
If you go to your galaxy root in a terminal and then cd to eggs, what is
the version listed for SQLAlchemy?
Do you have SQLAlchemy installed already on that machine (apart from the
one in Galaxy's eggs)?
On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
I was incorrect in stating that the changes in the next galaxy-dist will
help in this case, unfortunately. From the stack trace you posted, there
is
a deeper error with your instance that the client-side changes won't
help.
Can you post the size, type, and name of the file you're trying to
upload?
I can reproduce this by just typing hello, world into the
URL/Text: box on the Upload File page. Any file of any type seems
to trigger this problem.
Thanks,
Dan
On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Another thing you might try is to upload the file to our test server:
https://test.g2.bx.psu.edu/ and see if that works.
Thanks, that does work.
Setting up an FTP server on my local installation seems pretty
complex. All I really want to do is work around this issue and fool
Galaxy into thinking that I have uploaded a file using the
uploader...since this is a local installation I can put a file
anywhere on my system, I don't have to actually upload it, just place
it in a directory.
If there is no such workaround, I'll wait for the fix, I guess. Thanks
very much for working on this!
Dan
On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
If this is happening consistently and a refresh on the history isn't
doing
anything, you might try ftp upload:
http://wiki.galaxyproject.org/FTPUpload
or if you have permissions or are an admin you can try uploading to a
data
library:
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
On Wed, Jan 23, 2013 at 5:44 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
What sort of database are you using on your local instance?
The default (sqlite I guess). It's a completely vanilla instance, I
have not touched the config files.
Dan
On Wed, Jan 23, 2013 at 5:37 PM, Dan Tenenbaum
dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
Thanks, Dan. That helps and I'll start looking into this.
We will be pushing out a new galaxy-dist revision sometime this
week
if
all
goes well. This revision includes some code for the history
panel
that
may
help handle this situation a bit better. I'd recommend updating
to
that
revision when it comes out.
Thanks! Is there a workaround to upload a file or add it to my
history
in the meantime? Command-line is ok. If there isn't one, that's
ok
too
Dan
I'll let you know what I can find.
Carl
On Wed, Jan 23, 2013 at 5:18 PM, Dan Tenenbaum
dtene...@fhcrc.org
wrote:
Hi Carl,
On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
Heya, Dan.
Sorry for the trouble.
When you get that error again look for a line like you have
above:
Debug at: http://localhost:8080/_debug/view/1358978130
If you open a new tab or window in your browser and go to
the
address
('http://localhost:8080/_debug ...'), you should see a more
informative
error message - complete with a list of function calls that
led
to
the
error
(a stack trace).
Can you post that stack trace when you see it?
Thanks for the quick response. Here it is:
URL: http://localhost:8080/tool_runner/upload_async_create
File
'/Users/dtenenba/dev/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs
Re: [galaxy-dev] Blank history panel / Error in history API at listing contents
They likely shouldn't say 'Error' and do increase the noise to signal in the logs. The web transactions have a convenience function for getting the most current history for that transaction's user (get_history). If I understand correctly, these messages occur the transaction can't get or create a history ( when no user is currently logged in - or other situations where such as web crawlers). You can also see these messages in the day-to-day logs of your server, local instance, or the Galaxy main or test servers. As far as I know, they're harmless. C On Fri, Jan 25, 2013 at 5:41 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Tue, Jan 22, 2013 at 4:43 PM, Carl Eberhard carlfeberh...@gmail.com wrote: Short form: Both the API and client side should handle single datasets error-ing more gracefully than they did and the history panel should be more resilient and useful during and after a server error (at least of this kind). Please let me know if you see more problems, C I'm seeing some (apparently harmless) errors in the output during the 'upload' step when running Galaxy unit tests - in this case for one of my tools: functional_tests.py INFO 2013-01-25 10:37:19,810 Functional tests will be run against localhost:9500 nose.plugins.manager DEBUG 2013-01-25 10:37:19,865 DefaultPluginManager load plugin sqlalchemy = sqlalchemy.test.noseplugin:NoseSQLAlchemy nose.plugins.manager DEBUG 2013-01-25 10:37:19,986 DefaultPluginManager load plugin nosetestdiff = nosetestdiff.plugin:NoseTestDiff nose.plugins.manager DEBUG 2013-01-25 10:37:19,989 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML TMHMM 2.0 ( tmhmm2 ) Test-1 ... galaxy.web.framework DEBUG 2013-01-25 10:37:20,366 Error: this request returned None from get_history(): http://localhost:9500/ galaxy.web.framework DEBUG 2013-01-25 10:37:20,425 Error: this request returned None from get_history(): http://localhost:9500/ galaxy.web.framework DEBUG 2013-01-25 10:37:20,676 Error: this request returned None from get_history(): http://localhost:9500/user/logout galaxy.web.framework DEBUG 2013-01-25 10:37:20,731 Error: this request returned None from get_history(): http://localhost:9500/ galaxy.tools.actions.upload_common INFO 2013-01-25 10:37:24,312 tool upload1 created job id 1 galaxy.jobs.manager DEBUG 2013-01-25 10:37:27,460 (1) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-01-25 10:37:32,755 (1) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/1 galaxy.jobs.handler DEBUG 2013-01-25 10:37:32,755 dispatching job 1 to local runner galaxy.jobs.handler INFO 2013-01-25 10:37:33,041 (1) Job dispatched galaxy.jobs.runners.local DEBUG 2013-01-25 10:37:33,153 Local runner: starting job 1 galaxy.jobs.runners.local DEBUG 2013-01-25 10:37:33,712 executing: ... Are these lines just false positives? Error: this request returned None from get_history(): http://localhost:9500/ Error: this request returned None from get_history(): http://localhost:9500/user/logout Error: this request returned None from get_history(): http://localhost:9500/ Thanks, Peter ___ 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/
Re: [galaxy-dev] UCSC Data Browser
Hello, Robert When they mention the UCSC browser, is your user using the 'Get Data - UCSC Main table browser' tool or are they trying the 'display at UCSC main' link within a dataset in the history panel (which leads to the UCSC genome browser display application)? Does this problem still happen or happen in a reproducible way? If you've seen it happen, could you use firebug (if you use firefox) or the chrome developer tools (if using chrome) to see if there are any browser/client-side errors? If you have access to the channing server logs (for galaxy), can you see any errors around the time this happens? Thanks for letting us know and for the extra information, Carl On Wed, Jan 16, 2013 at 5:03 PM, Robert Chase re...@channing.harvard.eduwrote: Hello, Is anyone having trouble with the UCSC data browser? I got the following from one of my users: Hi guys, I try to fetch data from UCSC browser. A summary of my query shows that I am getting what I ask for, but when I Send the data to Galaxy I am returned to the channing galaxy home page and the data never appears in the history. When I use public instance, it all works. Not sure where the disconnect is. Thanks Any help would be appreciated. -Rob ___ 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/ ___ 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/
Re: [galaxy-dev] missing eye icon on running jobs…
The display icon has been re-enabled in revision 8634:b9d44cf4b68e. Thanks for the catch/feedback. On Wed, Jan 9, 2013 at 12:00 PM, Langhorst, Brad langho...@neb.com wrote: In some cases (e.g. mira) it's nice to be able to follow what's going on in the log file… Does anybody else miss being able to view files as they're running? brad -- Brad Langhorst langho...@neb.com ___ 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/ ___ 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/
Re: [galaxy-dev] JAVAscript error after initiating tool
Hi, Joachim If you have access to your server logs, do you see any log messages containing 'Error in history API' around the time those happen? Is there a situation where this happens more often (or a way to reliably reproduce)? I'm unable to reproduce this locally so far. The error definitely can be handled better on the javascript side, but I'd like to track down the API error as well before I change the javascript. Thanks for the help, C On Wed, Jan 16, 2013 at 7:57 AM, Joachim Jacob joachim.ja...@vib.be wrote: Hi all, For who is interested. Occasionally I get this strange Javascript error, just after clicking 'run' on a tool. ERROR updating hdas from api history contents:e47699a32b93ce7f The tool gets running, but the history panel is not updated. I click 'analyse data' to see the updated history. Cheers, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib __**_ 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/ ___ 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/
Re: [galaxy-dev] Where is the eye icon for datasets in error state?
Hi Sascha and Ted, The history panel is undergoing some major revisions and the omission of the display icon was part of that. It will be re-added today. Information from a jobs stdout and stderr are still be available using the 'i'nformation icon within each history item's display (You'll see a 'Show details' bit of help text when you hover your mouse over the icon; clicking on it will bring up a page with links to display both stdout and stderr). We'll definitely consider a more extensive error dataset but it may not be feasible at the moment. Thanks, Carl On Tue, Nov 20, 2012 at 1:59 PM, Ted Goldstein t...@soe.ucsc.edu wrote: Let me echo Sascha. I've been thinking about this problem. I suggest that we need an Error Document dataset type that contains two kinds information: 1. which will help the end user correct the problem (E.g. Please be sure to use MAF files not BAM files etc). 2. which will help tool developers collect a bunch of log files.. Error Documents could be aggregated (especially useful in a cluster computation). Then the report a bug button would aggregate the log file document and send it to the tool developer. Before sending, the end user would be able to see the contents and be sure that they were not posting confidential information offsite. Thanks Ted On Nov 20, 2012, at 8:02 AM, MSc. Sascha Kastens wrote: Hey devs! It seems that many things related to history datasets has changed since I have updated my local Galaxy instance and the current version. Unfortunately it seems that one cannot Display data in browser (eye icon) if the dataset is in error state. Where can I get that feature back? Some of my tools write logging information to a separate logfile which will be in error state if the tool fails but contain useful information. Thanks, Sascha ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] History will not refresh after workflow submission via the API
Hi Sascha, This may be due to the recent history panel changes. Can you update to the latest revision and see if the error still occurs? Thanks, Carl On Tue, Nov 20, 2012 at 2:22 AM, MSc. Sascha Kastens s.kast...@gatc-biotech.com wrote: Hi devs! After updating my local instance to changeset 19cbbaf566216cb46ecc6a6d17e0f1e0ab52978e my tool which submits a workflow via the API and set force_history_refresh to TRUE does not refresh the history anymore. The job is submit via DRMAA to SGE. Unfortunately the job seems to run forever because it is still in yellow state (even after SGE tells Galaxy that the job has finished. As soon as I refresh the history manually the according history entries get green and all entries for the submitted workflow are shown. I have no idea where I can have a look at. If you need any further information let me know! Thanks for your help in advance! Cheers, Sascha ___ 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/ ___ 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/
Re: [galaxy-dev] Where is the eye icon for datasets in error state?
Sascha, As of the latest revision, the display button has been re-added for datasets in the error state. The 'edit attributes' button has been re-added for error'd datasets as well. Let me know if you see any other problems with the history panel and thanks, Carl On Wed, Nov 21, 2012 at 11:03 AM, Carl Eberhard carlfeberh...@gmail.comwrote: Hi Sascha and Ted, The history panel is undergoing some major revisions and the omission of the display icon was part of that. It will be re-added today. Information from a jobs stdout and stderr are still be available using the 'i'nformation icon within each history item's display (You'll see a 'Show details' bit of help text when you hover your mouse over the icon; clicking on it will bring up a page with links to display both stdout and stderr). We'll definitely consider a more extensive error dataset but it may not be feasible at the moment. Thanks, Carl On Tue, Nov 20, 2012 at 1:59 PM, Ted Goldstein t...@soe.ucsc.edu wrote: Let me echo Sascha. I've been thinking about this problem. I suggest that we need an Error Document dataset type that contains two kinds information: 1. which will help the end user correct the problem (E.g. Please be sure to use MAF files not BAM files etc). 2. which will help tool developers collect a bunch of log files.. Error Documents could be aggregated (especially useful in a cluster computation). Then the report a bug button would aggregate the log file document and send it to the tool developer. Before sending, the end user would be able to see the contents and be sure that they were not posting confidential information offsite. Thanks Ted On Nov 20, 2012, at 8:02 AM, MSc. Sascha Kastens wrote: Hey devs! It seems that many things related to history datasets has changed since I have updated my local Galaxy instance and the current version. Unfortunately it seems that one cannot Display data in browser (eye icon) if the dataset is in error state. Where can I get that feature back? Some of my tools write logging information to a separate logfile which will be in error state if the tool fails but contain useful information. Thanks, Sascha ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Scatter plot integration in pages
I'd also like to add in a way for the user to save/download the svg from our visualizations that use it. Unfortunately, there's no clean/straightforward way to do this. I've seen some solutions that are better than nothing and it's on the list as well. On Thu, Nov 15, 2012 at 2:45 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Scatterplots will behave just as Trackster does: you'll be able to save scatterplots and embed them in Pages. Looking forward, the Galaxy team is in the process of developing a plug-in framework for visualizations that will allow for arbitrary Web visualizations to work with Galaxy. With this framework in place, all visualizations integrated into Galaxy will have the same save/embed functionality. J. On Nov 15, 2012, at 4:06 AM, Joachim Jacob wrote: Dear devs, How will the scatterplot in the future be integrated in Galaxy, e.g, for saving and displaying a scatterplot in pages? Kind regards Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Galaxy, Apache, WSGI and mod_wsgi
Hi, Paul I would like to know if mod_wsgi has been considered for the deployment of Galaxy at all, and whether anyone has any positive or negative experiences with it. I can only speak for the second part of your question: I've had some experience with Apache 2 + mod_wsgi, but within a Django stack. There was a somewhat complex set up/configuration (not horrible, just tedious) - that may have been particular to our situation and/or Django. It might be easier in your Galaxy situation. After set up, I found it pretty easy to work with: - Very rarely had to deal with bugs/workarounds or modification in general. - His/Their documentation for the mod is excellent - which is an often understated positive. - I found no problems with logging, debugging, or the mod 'getting in the way' of normal Apache features. - If I recall correctly, there was a good user base out there (~2-3 years ago). Carl On Mon, Oct 22, 2012 at 9:26 AM, Paul Boddie paul.bod...@biotek.uio.nowrote: Hello, I have recently had the opportunity to look at the deployment of Galaxy together with Apache, and I saw that the recommendation is to run the Galaxy Web server behind Apache with the latter acting as a proxy: http://wiki.g2.bx.psu.edu/**Admin/Config/Apache%20Proxyhttp://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy Other than convenience - one can just put Apache in front of an existing server - is there any particular reason for doing things this way? It seems that Galaxy uses the built-in Web server provided by the Paste framework, which in turn is based on the Python standard library BaseHTTPServer framework, and although paste.httpserver seems to add capabilities to the underlying framework, each such server must still be constrained to running in a single process. I imagine that this then leads to the use of load balancing as described on the following page: http://wiki.g2.bx.psu.edu/**Admin/Config/Performance/Web%** 20Application%20Scalinghttp://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling Given that Apache is an acceptable part of a large-scale solution, I would like to know if mod_wsgi has been considered for the deployment of Galaxy at all, and whether anyone has any positive or negative experiences with it. It seems to me that mod_rewrite is often something that should only be brought into play where other, typically more elegant, solutions cannot be used. Many Python-based Web applications have mod_wsgi as a recommended deployment option once their users look beyond CGI, and I wondered why this isn't the case with Galaxy. Paul __**_ 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/ ___ 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/
