[galaxy-dev] Public toolshed giving internal server error
Hello I'm trying to make a new repository on the public toolshed at https://toolshed.g2.bx.psu.edu/ but I keep getting the internal server error page. I was also unable to log out, or even to see the front page when trying to access it from a different browser. Is anyone else having this problem? Thanks best wishes Peter -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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] Nothing being tested on Test and main Tool Shed?
On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night. e.g. My new basic mummer tool which now has a full set of dependency packages thanks to Bjoern: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there are many unexpected failures with: Exception: History in error state. I'm sure you'll learn more once you look over the logs, Thank you, Peter Hi Dave, Any progress? All the following seem to have been tested in the last few days on the TestToolShed, but failed with Exception: History in error state. https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod https://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id That's about half of my TestToolShed repositories - most of the others report their tests passed :) I am also seeing unexpected problems with packages, e.g. https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_29 Error getting revision e78bbab7933d of repository package_blast_plus_2_2_29 owned by iuc: An entry for the repository was not found in the database. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Public toolshed giving internal server error
On Wed, Nov 19, 2014 at 9:36 AM, Peter Briggs peter.bri...@manchester.ac.uk wrote: Hello I'm trying to make a new repository on the public toolshed at https://toolshed.g2.bx.psu.edu/ but I keep getting the internal server error page. I was also unable to log out, or even to see the front page when trying to access it from a different browser. Is anyone else having this problem? Thanks best wishes Peter I just tried uploading an update on the test tool shed and got: Internal Server Error Galaxy was unable to successfully complete your request ... IOError: [Errno 28] No space left on device Perhaps a coincidence, but maybe the main ToolShed has the same issue? 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] Public toolshed giving internal server error
Getting same error, Trying to install Repository 'column_join' from here: https://toolshed.g2.bx.psu.edu/repository/view_repository?changeset_revision=6bb6c0a30c67id=e752a5a291d2d283 Click on the column_join button to reproduce error it looks like 404 error. Best, Ofer Fridman On Wed Nov 19 2014 at 11:36:14 AM Peter Briggs peter.bri...@manchester.ac.uk wrote: Hello I'm trying to make a new repository on the public toolshed at https://toolshed.g2.bx.psu.edu/ but I keep getting the internal server error page. I was also unable to log out, or even to see the front page when trying to access it from a different browser. Is anyone else having this problem? Thanks best wishes Peter -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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] Public toolshed giving internal server error
Hi Peter, can you try again? I'm able to browse the ToolShed and reset metatada for example. Cheers, Bjoern Am 19.11.2014 um 10:36 schrieb Peter Briggs: Hello I'm trying to make a new repository on the public toolshed at https://toolshed.g2.bx.psu.edu/ but I keep getting the internal server error page. I was also unable to log out, or even to see the front page when trying to access it from a different browser. Is anyone else having this problem? Thanks best wishes 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/
[galaxy-dev] Creation of a backup/migrate script for data/users
Hi, I would like to create a code to backup and migrate(*) galaxy datas, based on the api and/or with the script I did here: https://github.com/remyd1/galaxy_debug_params/blob/master/source/Templates/parameters/generate_shell_script.mako To do that, I would use the galaxy model, to retrieve everything in the old one and recreate everything in the new one. However, I would like to be able to do that without my web server running. That is to say, a cold migration to avoid any current task to write additionnal things into the database. Obviously, that is a problem for the api because this one use the web server. Could you give some advice to do that ? Should I recreate a code from 0 ? Could I use the code in the api ? Is there a way to create a code that could use the api differently (recreate a copy of the api without the web server) ? Kind regards, Remy (*) this is important; that means you could import data from an old galaxy to a recent one (or the opposite); a simple backup of files and a dump of the db is not enough. ___ 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 issue with datatypes in Galaxy version of last week
Hi,
This issue is appearing again, after the upgrade of our Galaxy on October the
23rdanyone experiencing the same?
Thanks,
Pieter.
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: vrijdag 4 april 2014 10:59
To: Bossers, Alex; Kuijt, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of
last week
Hi Alex, all
FYI - I've added the card to https://trello.com/c/ro8knsaa some time ago. Can
you please vote for it?
Thanks,
Pieter.
From: Bossers, Alex
Sent: dinsdag 25 maart 2014 16:52
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Strange issue with datatypes in Galaxy version of
last week
Pieter,
I just experienced the same with another generic tabular .tab file output. It
broke the filename at dash without any extension.
The file itself was ok, just the name.
Alex
Van:
galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Lukasse, Pieter
Verzonden: dinsdag 25 maart 2014 16:33
Aan: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] Strange issue with datatypes in Galaxy version of last
week
Hi,
Apparently a new datatypes bug has been introduced in the Galaxy version of
last week:
I have a tool that generates a csv file. Tool configuration is like this:
outputs
data name=simOut format=msclust.csv label=${tool.name} on ${on_string}
- SIM file/
The datatypes has this entry:
datatype extension=msclust.csv type=galaxy.datatypes.tabular:Tabular
mimetype=text/csv display_in_upload=true subclass=true/
At first Galaxy output seems fine:
[cid:image001.png@01D003FF.9BD73320]
But when I download the file, the downloaded file name will be :
Galaxy40-[MsClust_on_data_1_-_SIM_file]-
When I go to edit attributes and just click save, then upon downloading
again, the file name is correct...
Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .
Anyone faced this issue?
Thanks and regards,
Pieter.
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317481122; skype: pieter.lukasse.wur
http://www.pri.wur.nlhttp://www.pri.wur.nl/
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Re: [galaxy-dev] Public toolshed giving internal server error
Hello Bjoern Thanks, seems to be okay now (on the main toolshed) - I can log out, log back in, and create and populate my new repository now. Thanks, best wishes Peter On 19/11/14 10:57, Björn Grüning wrote: Hi Peter, can you try again? I'm able to browse the ToolShed and reset metatada for example. Cheers, Bjoern Am 19.11.2014 um 10:36 schrieb Peter Briggs: Hello I'm trying to make a new repository on the public toolshed at https://toolshed.g2.bx.psu.edu/ but I keep getting the internal server error page. I was also unable to log out, or even to see the front page when trying to access it from a different browser. Is anyone else having this problem? Thanks best wishes Peter -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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] Public toolshed giving internal server error
I am also having problems when using the option Search and browse toolsheds ! [cid:image001.jpg@01D0040B.AF3C7270] -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Briggs Sent: woensdag 19 november 2014 14:01 To: Björn Grüning; Galaxy Dev Subject: Re: [galaxy-dev] Public toolshed giving internal server error Hello Bjoern Thanks, seems to be okay now (on the main toolshed) - I can log out, log back in, and create and populate my new repository now. Thanks, best wishes Peter On 19/11/14 10:57, Björn Grüning wrote: Hi Peter, can you try again? I'm able to browse the ToolShed and reset metatada for example. Cheers, Bjoern Am 19.11.2014 um 10:36 schrieb Peter Briggs: Hello I'm trying to make a new repository on the public toolshed at https://toolshed.g2.bx.psu.edu/ but I keep getting the internal server error page. I was also unable to log out, or even to see the front page when trying to access it from a different browser. Is anyone else having this problem? Thanks best wishes Peter -- Peter Briggs peter.bri...@manchester.ac.ukmailto:peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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 server file upload problem
Hi Johngui, Can you specify which request is 404'ing -- the exact URL that's being attempted? And, can you provide a little more of your nginx configuration? Is galaxy being served at the root of the domain? -Dannon On Wed, Nov 19, 2014 at 2:01 AM, 홍종희 h...@syntekabio.com wrote: Hi galaxy-dev members Recently we're trying to setup the galaxy server in a production mode. Everything seems to be ok but when I tried to upload a file it shows error message like this Failed: Not found(404) I found one thread in galaxy-dev fourn about this one It says that it's because of change in proxy server configuration So I set exactly what was written in Galaxy wiki about nginx configuration related to proxy setting like below set $dst /api/tools; Should I change some oher configuration ? Any kind of suggestion would be welcomed Thanks Regards Jonghui ___ 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] Problem with LWR (input size limitation)
If you install pycurl (globally or in a Galaxy's virtualenv) and set LWR_CURL_TRANSPORT=1 in Galaxy's environment than the LWR will stream large files with CURL instead of the mmap hack. I don't understand your second question - the LWR should stream whatever data inputs are selected by the user. If you want the tool to be able to take many inputs you can use multiple=true on your data parameter or use a repeat block. (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax). Hope this helps, -John On Mon, Nov 17, 2014 at 3:04 AM, Misharl Monsoor mmons...@sb-roscoff.fr wrote: Hi everybody, In our lab, we are trying to connect our Galaxy instance to a Windows 7 64 bits server, in order to executes programs that need to be run within Windows. However we have a problem concerning the size of the input that is uploaded to the Windows server, it doesn't accept inputs with a size 1.3 Gb ? We have the following problem with mmap function: data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) error: [Errno 12] Cannot allocate memory I have another question concerning the inputs, is there a way to use several inputs that be uploaded to a Windows Server? Thank you very much in advance, Bests regards, Cheers, Misharl Monsoor ___ 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] Fwd: Bug with multiple reverse proxies
Hey Jan, Thanks for the fixes. Sorry no one responded to your earlier e-mail. I think the pull request should serve as contact point on this - it cannot be merged until this (https://github.com/bbangert/routes/pull/33) is fixed and Galaxy updated to target it right? On Thu, Nov 13, 2014 at 11:02 AM, Jan Kanis jan.c...@jankanis.nl wrote: Hi, We ran into a problem if galaxy is running behind multiple reverse proxies. Galaxy assumes that the X-Forwarded-Host header only contains a single host to which it redirects, but apache will append comma-separated components to it if it already exists, which is the case of multiple reverse proxies. The result is that galaxy sometimes (i.e. sometimes after user login, depending on browser specifics, and when installing toolshed tools) tries to redirect the browser to hostname, hostname. Apache docs I have a patch for galaxy in this pull request. That change fixes a file that makes the same assumption. The actual fix requires a change in Routes. The Routes PR is here, so actually fixing this requires an update of Routes after that pr is merged there. Jan ___ 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] Public toolshed giving internal server error
Hi all, Sorry for the service interruption. The Tool Shed should be back now, and the underlying disk usage problem has been alleviated, so it shouldn't occur again. --nate On Wed, Nov 19, 2014 at 9:15 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: I am also having problems when using the option Search and browse toolsheds ! -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Briggs Sent: woensdag 19 november 2014 14:01 To: Björn Grüning; Galaxy Dev Subject: Re: [galaxy-dev] Public toolshed giving internal server error Hello Bjoern Thanks, seems to be okay now (on the main toolshed) - I can log out, log back in, and create and populate my new repository now. Thanks, best wishes Peter On 19/11/14 10:57, Björn Grüning wrote: Hi Peter, can you try again? I'm able to browse the ToolShed and reset metatada for example. Cheers, Bjoern Am 19.11.2014 um 10:36 schrieb Peter Briggs: Hello I'm trying to make a new repository on the public toolshed at https://toolshed.g2.bx.psu.edu/ but I keep getting the internal server error page. I was also unable to log out, or even to see the front page when trying to access it from a different browser. Is anyone else having this problem? Thanks best wishes Peter -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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/ ___ 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] master_api_key currently doesn't benefit from a real admin's key?!
If you already have an admin key in the database - that is more useful than the master_api_key - I don't believe there is anything that the master API key can do that the admin API key cannot (let me know if I am wrong). I created master_api_key mostly just to bootstrap users and API keys for new installations. So my question is what are you trying to accomplish with a master API key if you already have an admin API key? I would be happy to comment on the different ideas you mentioned - but I want to understand what you are trying to accomplish. -John On Tue, Nov 18, 2014 at 8:35 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: I made the erroneous assumption that if I put my own admin user API key into the galaxy configuration master_api_key field, it would accept that and run all the api functions that needed a key connected to a user. It took fair bit of debugging to realize that the master_api_key field chops off all the user info even if it is available (i.e. has no user object), thus yielding numerous API errors for those things a user object is needed for. I can see a few dev solutions to this dilemma, and am wondering what people think - and the result could get into a Trello feature card... a) allow master_api_key to be accompanied by a master_api_email; together they trigger a user object to be associated that has the email address; and this eliminates all the API errors one currently gets. I like this solution because it doesn't depend on the UI interface for managing user keys, i.e. its rather permanent and secure. b) allow a api key called admin_api_key to be placed in the galaxy config file. This key has to be active as one user's api key (presumably power user), so that all those api errors are avoided. c) have master_api_key just have a dummy user object included, with say admin@localhost for an email address. Thoughts? Damion ___ 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] Public toolshed giving internal server error
Thanks - uploading tar-balls to the Test Tool Shed is working again :) Peter On Wed, Nov 19, 2014 at 2:34 PM, Nate Coraor n...@bx.psu.edu wrote: Hi all, Sorry for the service interruption. The Tool Shed should be back now, and the underlying disk usage problem has been alleviated, so it shouldn't occur again. --nate ___ 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 issue with datatypes in Galaxy version of last week
I have created a ticket for this issue here (https://trello.com/c/jxqT0ndZ).
When the file is in the incorrect state (extension missing from the
download) - if you close out your browser tab and reopen it in a new window
and try to download the file does it still exhibit the problem (indicating
a client-side problem instead of a server metadata/datatype issue)?
-John
On Wed, Nov 19, 2014 at 7:49 AM, Lukasse, Pieter pieter.luka...@wur.nl
wrote:
Hi,
This issue is appearing again, after the upgrade of our Galaxy on *October
the 23rd*anyone experiencing the same?
Thanks,
Pieter.
*From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto:
galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Lukasse, Pieter
*Sent:* vrijdag 4 april 2014 10:59
*To:* Bossers, Alex; Kuijt, Eric
*Cc:* galaxy-dev@lists.bx.psu.edu
*Subject:* Re: [galaxy-dev] Strange issue with datatypes in Galaxy
version of last week
Hi Alex, all
FYI – I’ve added the card to https://trello.com/c/ro8knsaa some time
ago. Can you please vote for it?
Thanks,
Pieter.
*From:* Bossers, Alex
*Sent:* dinsdag 25 maart 2014 16:52
*To:* Lukasse, Pieter
*Cc:* galaxy-dev@lists.bx.psu.edu
*Subject:* RE: [galaxy-dev] Strange issue with datatypes in Galaxy
version of last week
Pieter,
I just experienced the same with another generic tabular .tab file output.
It broke the filename at dash without any extension.
The file itself was ok, just the name.
Alex
*Van:* galaxy-dev-boun...@lists.bx.psu.edu [
mailto:galaxy-dev-boun...@lists.bx.psu.edu
galaxy-dev-boun...@lists.bx.psu.edu] *Namens *Lukasse, Pieter
*Verzonden:* dinsdag 25 maart 2014 16:33
*Aan:* galaxy-dev@lists.bx.psu.edu
*Onderwerp:* [galaxy-dev] Strange issue with datatypes in Galaxy version
of last week
Hi,
Apparently a new datatypes bug has been introduced in the Galaxy version
of last week:
I have a tool that generates a csv file. Tool configuration is like this:
outputs
data name=*simOut* format=*msclust.csv* label=*${tool.name
http://tool.name} on ${on_string} - SIM file*/
The datatypes has this entry:
datatype extension=*msclust.csv* type=
*galaxy.datatypes.tabular:Tabular* mimetype=*text/csv*
display_in_upload=*true* subclass=*true/*
At first Galaxy output seems fine:
But when I download the file, the downloaded file name will be :
Galaxy40-[MsClust_on_data_1_-_SIM_file]-
When I go to “edit attributes” and just click “save”, then upon
downloading again, the file name is correct...
Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .
Anyone faced this issue?
Thanks and regards,
Pieter.
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317481122; skype: pieter.lukasse.wur
http://www.pri.wur.nl
___
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Problem to upload data to Galaxy when using pbed file format
Hello Johan, Thanks for the bug report. I can confirm this problem - I have opened up a pull request with the fix to galaxy-central's stable branch (https://bitbucket.org/galaxy/galaxy-central/pull-request/567/stable-bugfix-composite-uploads-broken-by/diff). -John On Thu, Nov 13, 2014 at 8:29 AM, tjkarls...@uma.es wrote: Dear all, I am trying to upload data from PLINK (.bed, .bim and .fam-files) for the pbed file format using a local installation of Galaxy but it is not working. The local Galaxy installation was done yesterday, following the instructions at: https://wiki.galaxyproject.org/Admin/GetGalaxy First, I click on the Get Data tool, I then select pbed as File Format, the page reloads and I now can enter the three files (.bed, .bim, .fam). Once I click Execute the job starts but never seems to finish. If I look in the log output from Galaxy I get the following error: galaxy.tools ERROR 2014-11-13 13:24:52,226 Exception caught while attempting tool execution: Traceback (most recent call last): File /home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 2180, in handle_single_execution job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) File /home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 2738, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File /home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/actions/upload.py, line 21, in execute uploaded_datasets = upload_common.get_uploaded_datasets( trans, '', incoming, precreated_datasets, dataset_upload_inputs, history=history ) File /home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/actions/upload_common.py, line 246, in get_uploaded_datasets data.uuid = uploaded_dataset.uuid AttributeError: 'Bunch' object has no attribute 'uuid' Any idea what could be the problem? Kind regards, Johan ___ 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] Is anyone using composite datatype uploads?
Well there is at least one person using this functionality - http://dev.list.galaxyproject.org/Problem-to-upload-data-to-Galaxy-when-using-pbed-file-format-td4666000.html. Just to make this more concrete - Sam has swapped the upload file button to use the new upload widget this release cycle (targeted for December 1st). So barring negative feedback - uploading pbed or velvet report datatypes (or other similar composite datatypes) will no longer be possible via the GUI. -John On Thu, Aug 14, 2014 at 2:32 PM, Aysam Guerler aysam.guer...@gmail.com wrote: Hello everyone, We are considering to disable the deprecated upload tool form which is currently accessible through Tool panel Get Data Upload file. The new upload feature (icon at the top of the Tool panel) covers all of its functionality except uploading composite datatypes like e.g. Velvet. Please let us know if you are using the composite file upload functionality of the former tool form. Thanks, Sam ___ 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] Is anyone using composite datatype uploads?
Hi John, Sam, I've not done it yet, but was hoping to implement uploading of BLAST databases at some point - mainly for use within the test framework, rather than expecting it to be useful for the end user. Is the issue here uploading an archive (e.g. .zip or .tar.gz) or offering a way to pick multiple files to be treated together as a composite dataset? Peter On Wed, Nov 19, 2014 at 3:32 PM, John Chilton jmchil...@gmail.com wrote: Well there is at least one person using this functionality - http://dev.list.galaxyproject.org/Problem-to-upload-data-to-Galaxy-when-using-pbed-file-format-td4666000.html. Just to make this more concrete - Sam has swapped the upload file button to use the new upload widget this release cycle (targeted for December 1st). So barring negative feedback - uploading pbed or velvet report datatypes (or other similar composite datatypes) will no longer be possible via the GUI. -John On Thu, Aug 14, 2014 at 2:32 PM, Aysam Guerler aysam.guer...@gmail.com wrote: Hello everyone, We are considering to disable the deprecated upload tool form which is currently accessible through Tool panel Get Data Upload file. The new upload feature (icon at the top of the Tool panel) covers all of its functionality except uploading composite datatypes like e.g. Velvet. Please let us know if you are using the composite file upload functionality of the former tool form. Thanks, Sam ___ 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/ ___ 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] master_api_key currently doesn't benefit from a real admin's key?!
Ah! Key idea is the ease of installation/maintenance of tools that need admin level api access. I was hoping that the master api key enabled my program to do any of the api calls available (I'm using bioblend btw). I am running workflows, uploading datasets from user history to data library, linking files into data library from server. Alot of this work is done on behalf of a user - but I don't want to give such a user elevated access to the server. So yes I can hard-code an admin api key into my galaxy tool for doing this work. But I would much rather just count on a master/admin/uber api key that is defined in galaxy config for doing all this work. This way, whenever a tool is installed from toolshed that needs admin functionality, it can just start working if the uber api key has been set up. (No need to set up an admin user, copy key into config or wherever, reset galaxy etc). That's what I was thinking the master api key did - I didn't realize it doesn't work with at least a handful of the API calls because it lacks an associated user object. i had tried to put an admin api key into the master_api_key field but that failed on various needed api calls - it ignores the potential to use the admin user's user object. By the way I do use the interacting user's non-privileged api key as well, it is convenient for delineating what that user does and does not have access to in terms of data libraries/datasets and workflows. Its just the extra work I trigger on their behalf has to be admin level. The tool itself is called the Data Versioning tool, and it is listing and caching/retrieving versioned fasta (or other types of) data and regenerating blast etc. databases as requested by users as an initial step to performing their other workflows. It aims to quickly deal with datasets that are anywhere from megabytes to hundreds of gigabytes in size. Hope that helps? Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada From: John Chilton [jmchil...@gmail.com] Sent: Wednesday, November 19, 2014 6:39 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] master_api_key currently doesn't benefit from a real admin's key?! If you already have an admin key in the database - that is more useful than the master_api_key - I don't believe there is anything that the master API key can do that the admin API key cannot (let me know if I am wrong). I created master_api_key mostly just to bootstrap users and API keys for new installations. So my question is what are you trying to accomplish with a master API key if you already have an admin API key? I would be happy to comment on the different ideas you mentioned - but I want to understand what you are trying to accomplish. -John On Tue, Nov 18, 2014 at 8:35 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: I made the erroneous assumption that if I put my own admin user API key into the galaxy configuration master_api_key field, it would accept that and run all the api functions that needed a key connected to a user. It took fair bit of debugging to realize that the master_api_key field chops off all the user info even if it is available (i.e. has no user object), thus yielding numerous API errors for those things a user object is needed for. I can see a few dev solutions to this dilemma, and am wondering what people think - and the result could get into a Trello feature card... a) allow master_api_key to be accompanied by a master_api_email; together they trigger a user object to be associated that has the email address; and this eliminates all the API errors one currently gets. I like this solution because it doesn't depend on the UI interface for managing user keys, i.e. its rather permanent and secure. b) allow a api key called admin_api_key to be placed in the galaxy config file. This key has to be active as one user's api key (presumably power user), so that all those api errors are avoided. c) have master_api_key just have a dummy user object included, with say admin@localhost for an email address. Thoughts? Damion ___ 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:
Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?
Hey Peter, Dave is out this week - so I have tried to fumble around and see if I could make some progress on this. I found some bugs in a recent commit and fixed them - that might help (https://bitbucket.org/galaxy/galaxy-central/commits/b81798f94dc0fd14de1d585ed7e57f820f998fae). I also have enabled more verbose logging that might help those History in error state exceptions (https://bitbucket.org/galaxy/galaxy-central/commits/a799879a82c54c2d1afec6e33d8918479bbf2373) but I am not sure it will propagate through to the tool shed API - we will see I guess. If the install and test framework just picks up the latest central - these fixes will hopefully be reflected in the next run. -John On Wed, Nov 19, 2014 at 4:48 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night. e.g. My new basic mummer tool which now has a full set of dependency packages thanks to Bjoern: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there are many unexpected failures with: Exception: History in error state. I'm sure you'll learn more once you look over the logs, Thank you, Peter Hi Dave, Any progress? All the following seem to have been tested in the last few days on the TestToolShed, but failed with Exception: History in error state. https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod https://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id That's about half of my TestToolShed repositories - most of the others report their tests passed :) I am also seeing unexpected problems with packages, e.g. https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_29 Error getting revision e78bbab7933d of repository package_blast_plus_2_2_29 owned by iuc: An entry for the repository was not found in the database. 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/ 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] Nothing being tested on Test and main Tool Shed?
Thanks John, Fingers crossed we'll get some more detailed logs in a day or two :) Peter On Wed, Nov 19, 2014 at 5:48 PM, John Chilton jmchil...@gmail.com wrote: Hey Peter, Dave is out this week - so I have tried to fumble around and see if I could make some progress on this. I found some bugs in a recent commit and fixed them - that might help (https://bitbucket.org/galaxy/galaxy-central/commits/b81798f94dc0fd14de1d585ed7e57f820f998fae). I also have enabled more verbose logging that might help those History in error state exceptions (https://bitbucket.org/galaxy/galaxy-central/commits/a799879a82c54c2d1afec6e33d8918479bbf2373) but I am not sure it will propagate through to the tool shed API - we will see I guess. If the install and test framework just picks up the latest central - these fixes will hopefully be reflected in the next run. -John On Wed, Nov 19, 2014 at 4:48 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Dave, Any progress? All the following seem to have been tested in the last few days on the TestToolShed, but failed with Exception: History in error state. https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod https://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id That's about half of my TestToolShed repositories - most of the others report their tests passed :) I am also seeing unexpected problems with packages, e.g. https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_29 Error getting revision e78bbab7933d of repository package_blast_plus_2_2_29 owned by iuc: An entry for the repository was not found in the database. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] How to get cleanup script to run in cron job ?
Hello, I am trying to figure out how to run the cleanup scripts in a cron job. The below works on command line: python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i pysqlite=2 egg successfully loaded for sqlite dialect ## # 2014-11-19 22:07:32 - Handling stuff older than 30 days # Displaying info only ( --info_only ) Deleted 0 histories Elapsed time: 0.0684289932251 ## but if I try to do this in a cron job as follows: 55 21 * * * python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i /media/Store/galaxy/galaxy-dist/temp 21 python: can't open file 'scripts/cleanup_datasets/cleanup_datasets.py': [Errno 2] No such file or directory or if I try to do this : 00 22 * * * python /media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i /media/Store/galaxy/galaxy-dist/temp 21 Traceback (most recent call last): File /media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py, line 13, in module from galaxy import eggs ImportError: No module named galaxy Note that I am directing the output to a file only to try to find out why it's not working. Is this a problem with environment? Any suggestions what to try would be much appreciated. Regards James J P Mullan ___ 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 server file upload problem
Thanks for your reply Danon I have tried to setup local galaxy-server in production mode The error that I mentioned occurred when I tried to upload file from my pc to local galaxy server( galaxy server is also installed in same pc ) and my galaxy server is at the root of the domain ( http://127.0.0.1:8080) the attached file is screenshot of error and the other attached file is my nginx configuration file Thanks for your effort in helping me Regards Jonghui - Original Message - From:Dannon Baker [dannon.ba...@gmail.com] To:홍종희 [h...@syntekabio.com] Cc:Galaxy Dev [galaxy-dev@lists.bx.psu.edu] Sent:Wed , November 19, 2014 23:19 PM Subject:Re: [galaxy-dev] galaxy server file upload problem Hi Johngui, Can you specify which request is 404'ing -- the exact URL that's being attempted? And, can you provide a little more of your nginx configuration? Is galaxy being served at the root of the domain? -Dannon On Wed, Nov 19, 2014 at 2:01 AM, 홍종희 h...@syntekabio.com wrote: Hi galaxy-dev members Recently we're trying to setup the galaxy server in a production mode. Everything seems to be ok but when I tried to upload a file it shows error message like this Failed: Not found(404) I found one thread in galaxy-dev fourn about this one It says that it's because of change in proxy server configuration So I set exactly what was written in Galaxy wiki about nginx configuration related to proxy setting like below set $dst /api/tools; Should I change some oher configuration ? Any kind of suggestion would be welcomed Thanks Regards Jonghui ___ 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/
