Re: [galaxy-dev] Galaxy Docker and Tool Shed repository for Chinese researchers?

Hi Steven, Using Docker can simplify deployment, enhance reproducibility, and enhance security with the eventual goal of allowing users to run untrusted code on the shared Galaxy infrastructure, to name a few reasons. For details on how to set up your own tool shed, this page should help you

Re: [galaxy-dev] Custom Builds not accessible for user

Hey Ulf, Thanks for reporting this; the error handling should definitely be better here -- I'll get a fix out shortly. -Dannon On Mon, Dec 8, 2014 at 7:23 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote: Dear Galaxy Dev One of our users has managed to lock himself out of his Custom Builds.

Re: [galaxy-dev] Manage jobs interface error

Ok, found it. This was fixed in revision 14955:5454f62f54df and applied to the stable branch in 14968:cb0c2ea402e4, and an update should fix your problem. -Dannon On Tue, Dec 9, 2014 at 3:32 PM, C. Ch. tuto...@hotmail.com wrote: Hi Dannon, Sorry, forgot to add that info. The changeset is

Re: [galaxy-dev] CloudMan + Ansible + AWS

Thanks for the pointer, this is great stuff and I had not seen it before. I’ve wanted to do something similar for a while now, and it’s becoming even more important as we loop in GCE.  I’ll definitely read through and play with this and see what we might be able to use, contribute back to,

Re: [galaxy-dev] Tool Tests failing with Exception: History in error state.

Yep, the FutureWarning that that commit resolves would have caused the upload job to end up as an error; I'm betting this is what was causing Peter's issues too. On Fri Jan 30 2015 at 12:18:10 PM Nicola Soranzo nsora...@tiscali.it wrote: Hi Peter, I was also getting Exception: History in

Re: [galaxy-dev] apache proxy

Hey Thon, I'd probably recommend using a simple supervisord (http://supervisord.org/) configuration to do this. Here's a link to some great reference material that might help you out: https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay/AdminWalkthrough#Configure_supervisord -Dannon On

Re: [galaxy-dev] Galaxy server and ssl

server in single process mode while installing tools. Thanks for the link... I'll look into that and see what I can glean from it. Best regards, Scott On Wed, Feb 18, 2015 at 7:14 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Scott, What weird behavior are you seeing? Paste

Re: [galaxy-dev] History options confirmation dialog boxes

Hi Jose, I can confirm this is broken and will get a fix out. Thank you for the report! -Dannon On Thu Feb 19 2015 at 12:24:13 PM Jose Juan Almagro Armenteros jjalma...@gmail.com wrote: Hi all I have noticed that confirmation dialog boxes that appear in the history options seems to be

Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?

On Fri Jan 30 2015 at 5:36:29 AM Peter Cock https://toolshed.g2.bx.psu.edu/repository/get_functional_ test_rss?owner=peterjcstatus=all Internal Server Error ... Trello issue logged, https://trello.com/c/ZOW0NPzb/2378-main-toolshed-rss-feed- for-test-results-offline Also still

Re: [galaxy-dev] data sharing without duplication?

Bjoern's answer is a good one. Another way we commonly do this is by preparing a 'base' history published with the datasets the students need to get started -- something like https://usegalaxy.org/u/mimi31k/h/chip-seq-example-1-raw-data. Students then click a single button to import that history

Re: [galaxy-dev] S3/Swift object store cache path and `extra_dir`s

Hey Brian, Thanks for the interest in Galaxy's Swift object store! I also tested Charles' PR and it looks like a nice improvement -- I'll go ahead and get that pulled into Galaxy shortly. The HierarchicalObjectStore was written with exactly what you're trying to do in mind, so you're definitely

Re: [galaxy-dev] Question Regarding fetch_eggs c. vs pip

I believe I've fixed this in 16583:5b2f1eab2819, if you want to give it another shot. External version of pkg_resources (and not ours in lib/) is what was causing the weird egg fetching errors. Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard

Re: [galaxy-dev] cluster queue job id?

Hi Anna, This information should all be available in the admin - manage jobs interface. Clicking on the job id will display more details. Are there other things that you'd like included that aren't there? -Dannon On Wed, Jan 7, 2015 at 11:50 AM, Anna Terry iseegl...@googlemail.com wrote:

Re: [galaxy-dev] ValueError: Attribute 'fields' does not accept objects of type type 'list'

Hi Peter, Yes, this is a known recent issue that I'm actually at work fixing right now. -Dannon On Tue Feb 24 2015 at 9:53:24 AM Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm trying the (BETA 2) GitHub repository with a view to switching from hg for my Galaxy development. There

Re: [galaxy-dev] History panel error

Hi Jose, Can you review (and share, maybe) the relevant part of the logs from when you attempt to execute a job? It'd be worth it, if you still have the logs, to know what the Internal Server Error indicated in your first message was, as well. -Dannon On Fri, Apr 24, 2015 at 11:00 AM Jose Juan

Re: [galaxy-dev] InvalidRequestError: kombu.transport.sqlalchemy.Queue

Hi Asma, This is a known issue I'm still working on a permanent fix for. For right now, you can simply restart the process and it'll hopefully work fine -- we'll have a much better fix out soon. -Dannon On Thu, Apr 23, 2015 at 2:12 PM Asma Riyaz asmariya...@gmail.com wrote: Hi, I am

Re: [galaxy-dev] anybody seen this class of error before?

Hi Brad, Like Martin mentioned, this is something I've been trying to fix for a while now in various ways, but none 100% successful so far. If you have an environment where you can reliably reproduce this (and are able to test things), you could try

Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed

Like Peter mentions, we did this because historically not all tools used (still don't, I guess) exit codes correctly. If yours does, you can set exit_code tags and everything should work. On Tue, Apr 28, 2015 at 11:47 AM Ryan G ngsbioinformat...@gmail.com wrote: ok, thanks. Let me look at

Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed

Hey Ryan, Yes, this is exactly why. By default, galaxy expects that anything written to stderr means that there was a failure, though you can change this by using the error_code syntax (among other options) found here: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax -Dannon On Tue,

Re: [galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

No need, unless it becomes particularly worse after the next attempt to fix it :) On Wed, Apr 29, 2015 at 8:30 AM Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Dannon, Do you want me to send you any future TravisCI cases of this failure? Peter On Wed, Apr 29, 2015 at 1:14 PM, Dannon

Re: [galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped

Hi Peter, No need to rerun for my benefit -- it's definitely a race condition that I know about and think I have a fairly good understanding of now. We've tried a few different ideas for fixing it, (obviously none of which have worked, yet), and I've been poking at a new fix this week. -Dannon

Re: [galaxy-dev] Fwd: History panel error

of the table wrongly, so everything is okay. Sorry for inconvenience and thanks a lot for your help. Regards, Jose 2015-04-28 1:12 GMT+02:00 Dannon Baker dannon.ba...@gmail.com: Jose, Regarding the job table being empty -- how exactly are you checking this? This table should never be empty

Re: [galaxy-dev] Fwd: History panel error

help! Regards, Jose 2015-04-24 17:16 GMT+02:00 Dannon Baker dannon.ba...@gmail.com: Hi Jose, Can you review (and share, maybe) the relevant part of the logs from when you attempt to execute a job? It'd be worth it, if you still have the logs, to know what the Internal Server Error

Re: [galaxy-dev] Fwd: Failure to set attributes_type metadata for interval files / error in gff_filter_by_attribute tool

Hi Marius, It'd be great if you wanted to submit a PR for the json issue separately -- I can confirm that that's a working fix. I'll let someone else speak to the tool change. -Dannon On Thu, Apr 30, 2015 at 2:30 PM Marius van den Beek m.vandenb...@gmail.com wrote: Hello all, Not sure if

Re: [galaxy-dev] missing auth_conf.xml.sample

Thanks for catching this, we'll be updating the bitbucket release shortly to correctly include the new .sample. On Fri, May 15, 2015 at 2:05 PM Will Holtz who...@lygos.com wrote: Here is the file: https://raw.githubusercontent.com/galaxyproject/galaxy/dev/config/auth_conf.xml.sample -Will

Re: [galaxy-dev] Older galaxy I'm keeping alive by drip feed, has problem restarting when I turn debug off.

, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada From: Dannon Baker [dannon.ba...@gmail.com] ... Hi Damion, I'm suspicious of the compiled templates. Can you disable debug, then do something like find

Re: [galaxy-dev] Older galaxy I'm keeping alive by drip feed, has problem restarting when I turn debug off.

. From: Dannon Baker [dannon.ba...@gmail.com] Sent: Wednesday, April 15, 2015 2:36 PM ... Hrmm, was worth a shot. And, I *think* the logic is such that this won't change anything, but you can also (safely) wipe out that whole compiled_templates directory and see if that does anything

Re: [galaxy-dev] dat quota

Hey Charles, This was an error on our end (bug that has since been fixed), and I've recalculated your quota. You should be good to go now. Thanks for using Galaxy! -Dannon On Thu, Mar 26, 2015 at 8:21 AM, Williams, Charles Houston charles.williams...@vanderbilt.edu wrote: After reading

Re: [galaxy-dev] Galaxy admin access

that others might be able to help you as well. On Wed, Jun 17, 2015 at 12:18 PM Davenport, Aneisha adave...@gru.edu wrote: I'm typing the command in terminal Original message From: Dannon Baker dannon.ba...@gmail.com Date: 06/17/2015 12:05 PM (GMT-05:00) To: Davenport

Re: [galaxy-dev] Galaxy admin access

Hi Aneisha, When you say you cannot alter config/galaxy.ini, what do you mean? You should be able to create (if not there) and edit this file in your regular terminal on that machine. Does a different user own the file, perhaps a 'galaxy' one? If so, you could change to that user and then

Re: [galaxy-dev] default value for param type color

Hi Wolfgang, You should be able to set a default value for the color parameter by including 'value' with an appropriate color value in the tag. Something like the following would default to red, for example: param name=default_red type=color value=#ff/ -Dannon On Fri, Aug 14, 2015 at 6:43

Re: [galaxy-dev] Problems installing pbs_python from scramble.

Hi Zuzanna, You can temporarily relocate the 'pkg_resources.py' that ships with Galaxy (and delete the corresponding .pyc file) to get around this error. Let me know if this doesn't work for you, though, and I can help debug some more. We're hoping to swap to new dependency management code that

Re: [galaxy-dev] Setting up Galaxy without e-mail

Hi Raymond, Regarding activation, you mean you set user_activation_on = True, right? You can just leave 'user_activation_on = False', which is the default (and the value if left commented), which will disable any requirement of having a local SMTP server for user creation and won't validate the

Re: [galaxy-dev] Security issues

Hi Scott, Serious security problems should not be fixed via pull request - please responsibly disclose these by e-mailing them (with or without patches) to galaxy-...@lists.galaxyproject.org. The Galaxy core development team will issue patches to public servers before announcing the issue to

Re: [galaxy-dev] Slow repsonses viewing histories

Hey Christian, I used galaxy_dir/scripts/db_shell.py and something like https://gist.github.com/dannon/e71b7aa9546fcecf6e9e to reset problematic BAM metadata. Basically, it selects all the large metadata and completely strips out the new overly large optional attributes, leaving required

Re: [galaxy-dev] Switching history doesn't work with prefix

What revision are you running? I'm seeing my proxy-prefix get appended correctly in both release_15.05 and in current -dev. On Thu, Jul 23, 2015 at 5:10 AM Peter Cock p.j.a.c...@googlemail.com wrote: Hello Ping, I can confirm this bug. I noticed this some time back when the new history was

Re: [galaxy-dev] using Bioblend with external authentication

My guess is that it has to do with the prefix there. Is the Galaxy API at galaxy-dev.fmi.ch/galaxy/api or galaxy-dev.fmi.ch/api? On Thu, Oct 22, 2015 at 6:41 AM Hans-Rudolf Hotz wrote: > Hi > > We would like to start using BioBlend on our production servers (which > use external

Re: [galaxy-dev] URGENT HELP!

It looks like the Galaxy server was downgraded relative the database. Do you know how this may have happened? It also looks like this instance is probably quite a bit out of date, in any event, so I'd be hesitant to give advice recommending a major upgrade given the current state of things. I'd

Re: [galaxy-dev] email activation setting failed

Per the error message 'Temporary failure in name resolution', it sounds like your server was unable to locate smtp.gmail.com. Can you verify the server does have the ability to connect to this machine and send email? This may help:

Re: [galaxy-dev] login problem (redirection to the login page)

Hi Floreline, This sounds a lot like your cookie_path specified in galaxy.ini might be incorrect. Are you using a proxy (and the proxy_prefix) in galaxy? Can you share the following lines and settings from your galaxy.ini, including any comments (#) on the lines? They should be near the

Re: [galaxy-dev] updated eggs needed for OS X El Capitan compatibility

Hi Wolfgang, Thanks for the extensive testing! I hadn't noticed this since I was using a brew-installed python in a virtualenv, but I can confirm that this is broken with the new OSX system python. I'll build and test a few updated eggs now. -Dannon On Mon, Oct 12, 2015 at 6:18 AM Wolfgang

Re: [galaxy-dev] login problems when using a proxy and serving at a subdirectory

When I've seen similar behavior in the past, it's always that cookie_path is incorrect. On Thu, Aug 27, 2015 at 1:46 PM, John Chilton jmchil...@gmail.com wrote: Not really sure what is happening here, does your galaxy.ini file have the following sections: [filter:proxy-prefix] use =

Re: [galaxy-dev] External User Authenticaion

Hi Ryan, It may be that Galaxy is looking for a different remote user header than your proxy is setting. I believe by default we look for HTTP_REMOTE_USER, but this is configurable in galaxy.ini (so, you could set yours to HTTP_USER there). Let me know if this doesn't sort it out for you and we

Re: [galaxy-dev] External User Authenticaion

In galaxy.ini, I have > > use_remote_user = True > remote_user_header = HTTP_MAIL > > After restarting,Galaxy still gives the same error. > > On Mon, Aug 31, 2015 at 3:44 PM, Dannon Baker <dannon.ba...@gmail.com> > wrote: > >> Hi Ryan, >> >> It may be tha

Re: [galaxy-dev] Fatal Error while uploading a File with special Characters

to make sure I'm testing your situation as well. On Thu, Sep 10, 2015 at 10:14 AM, Matthias Enders < m.end...@german-seed-alliance.de> wrote: > It was the name of the File: > > > > Blühzeitpunkt.txt > > > > (for example) > > > > *Von:* Dannon Bake

Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

You're currently seeing 91% usage? I just checked again and your disk calculation should have been up to date (the recalc procedure did not change anything), and I'm seeing 50% usage on your account. On Tue, Dec 1, 2015 at 3:45 AM, Felix Mayr wrote: > The login emailaddress I

Re: [galaxy-dev] security: brute force login

Hi Amogelang, I'd recommend using a general purpose tool like fail2ban for this. Here's a quick getting started guide that might help if you're using nginx: https://www.digitalocean.com/community/tutorials/how-to-protect-an-nginx-server-with-fail2ban-on-ubuntu-14-04 -Dannon On Mon, Jan 4, 2016

Re: [galaxy-dev] Collapse tool panel and history panel

Hi Makis, We've restructured much of the client code fairly recently. Something like this should work for you now: https://gist.github.com/dannon/bd470d9c70019b07cb8b Sorry for the slow response! -Dannon On Sat, Dec 19, 2015 at 2:57 PM, Makis Ladoukakis wrote: >

Re: [galaxy-dev] INIT script for Ubuntu

Hi Mic, The name of galaxy's default configuration file changed a while back (from universe_wsgi.ini to galaxy.ini) but there is no functional difference. Edit your copy of galaxy.ini the same way you see the tutorial changing universe_wsgi.ini and you should be good to go. -Dannon On Fri, Dec

Re: [galaxy-dev] Please terminate iGeneMap cluster

Hi Laura, This is something we cannot do for you -- did you manage to get it done from your end? If not, you should be able to do so by simply going to the instance cloud console (http:///cloud, in your browser) and selecting "Terminate instance". You can always confirm that termination by

Re: [galaxy-dev] tabular file displayed without tabs

Sorry, I'm late to the thread -- one more question: How many columns are in the file? Galaxy will only display tabular datasets with fewer than 50 columns using the 'fancy' display which also loads the file incrementally and renders on demand. For very 'wide' files, Galaxy defaults to using the

Re: [galaxy-dev] AssertionError: there is no script for 130 version

Hey Bill, The only time I've seen this is when switching from (for example) tip of the 'dev' brach of Galaxy over to 16.01, 15.10, or some other stable release. Basically, sqlalchemy_migrate sees the 0130_change_pref_datatype.pyc (or some other one) and thinks a version should exist. The

Re: [galaxy-dev] quota api error

ontroller class. > I join a patch for the quota.py file with this email > I can propose a pull request if you want. > > > Best, > > -- > Fabien Mareuil | Centre d'Informatique pour la Biologie > fabien.mare...@pasteur.fr | Institut Pasteur > 25,28 rue du Docteur Roux 75015

Re: [galaxy-dev] Error attempting to display contents of library (New data library)

Hi Juan, I'm working on a few errors I've uncovered trying to track down your issue here, but my hunch is you're hitting a different one. The branch is here if you want to try it: https://github.com/dannon/galaxy/commits/library_errors Do you have any non-ascii characters in a particular field

Re: [galaxy-dev] Error installing from main toolshed

Hi Anmol, It's a known temporary issue that we're working on right now. Should be resolved shortly. -Dannon On Wed, Mar 9, 2016 at 8:49 AM, Anmol Hemrom wrote: > Hi, > > I am getting error " HTTPError: HTTP Error 500: Internal Server Error" > while installing tools from

Re: [galaxy-dev] Missing dependency issue

Scott, I'm not sure what's going on here, but maybe it'd be useful to try to run the build by hand to see what's going on here? cd /readline/6.2/iuc/package_readline_6_2/52d6f646b3b5/ ./configure On Fri, Mar 11, 2016 at 8:25 AM, Scott Szakonyi wrote: > Sorry, I

Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

I haven't seen this before but did a little googling. What version is your ansible installation? If it's a little bit older, ( https://github.com/ansible/ansible/issues/5412) might be what you're seeing. It's a bit of a long read, but it looks like reinstalling or updating your ansible (or

Re: [galaxy-dev] UnicodeDecodeError with 16.01

hanks all for your (very efficient) help! > I added this to the env, and now it works: > > export LC_ALL=en_US.UTF-8 > export LANG=en_US.UTF-8 > export LANGUAGE=en_US.UTF-8 > > It was fr_FR.UTF-8 before > > Anthony > > > On 07/03/2016 16:15, Dannon Baker wrote:

Re: [galaxy-dev] Error when executing cleanup scripts

Hi Scott, The quick fix is to source your virtualenv first and you should be good to go. -Dannon On Fri, May 20, 2016 at 9:07 AM Scott Szakonyi wrote: > Hi all, > > I'm getting an error when executing the cleanup scripts in Galaxy 16.01. > It appears the script is

Re: [galaxy-dev] galaxy.masthead.js change

Once you've changed the file, you'll need to rebuild the client. Run 'make client' from the root Galaxy directory and it should build your changes. On Tue, May 17, 2016 at 8:20 AM Mohamed Kassam wrote: > Dear Aysam Guerler, > thank you I find it, but I tried to change but I

Re: [galaxy-dev] remote user CAS invalide session

Thank you for the report! I'm able to reproduce this here on my local test install and will try to figure out what's going on and let you know when I have a fix. -Dannon On Tue, Apr 19, 2016 at 3:07 AM, Laure QUINTRIC wrote: > Hi galaxy users, > > I just installed

Re: [galaxy-dev] DOS attack launched from our Galaxy instance

Keith, Did you figure this out? I'm very curious as to what this was. Outside mass admin tool updates, or maybe wheel installation, I can't think of anything that would have triggered anything like this on the Galaxy side. -Dannon On Wed, Jul 13, 2016 at 5:31 PM Suderman Keith

Re: [galaxy-dev] Adding a download link to the "Download or Export Workflow" page with load balancing

Can you elaborate on the load balancing that you've implemented which seems to be causing the problem? This might help figure out what's going on. On Mon, Jul 25, 2016 at 8:56 AM Alex Rodriguez wrote: > Dear Galaxy developers, > I am interested in adding a download

Re: [galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled

Hey, thanks for this. I've made an issue ( https://github.com/galaxyproject/galaxy/issues/2671) and will check it out today. On Wed, Jul 27, 2016 at 12:44 PM Ryan G wrote: > Hi all - We are using a SSO system so that user's authenticate externally > from Galaxy. >

Re: [galaxy-dev] Info Page after tool execution

Hi Katherine, That'd be this method: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/controllers/dataset.py#L978 Which fills this template: https://github.com/galaxyproject/galaxy/blob/dev/templates/show_params.mako On Wed, Jul 27, 2016 at 1:20 PM Katherine Beaulieu <

Re: [galaxy-dev] workflow problems

: > I remember this issue and that it was fixed. Updating to a newer revision > should resolve it. > > On Wed, Jul 27, 2016 at 10:06 PM, Dannon Baker <dannon.ba...@gmail.com> > wrote: > >> This is indeed weird behavior. What revision is your Galaxy at? >> >>

Re: [galaxy-dev] workflow problems

This is indeed weird behavior. What revision is your Galaxy at? On Wed, Jul 27, 2016 at 9:07 PM Cristel Thomas wrote: > Hi all, > I ran into a weird behavior on my local instance of galaxy and I was > wondering if anyone had the same experience (and if so what did you

Re: [galaxy-dev] Adding a download link to the "Download or Export Workflow" page with load balancing

add: > uwsgi_read_timeout 180; > > location / { > uwsgi_pass 127.0.0.1:8080; > uwsgi_param UWSGI_SCHEME $scheme; > include uwsgi_params; > } > > = > > Any suggestions will help greatly! > > Thanks, > >

Re: [galaxy-dev] Retrieving bam index file for visualization outside of Galaxy

Hi Scott, This isn't currently exposed through the API, but I'm working on implementing it at https://github.com/galaxyproject/galaxy/pull/2741, if you'd like to test it. -Dannon On Thu, Aug 4, 2016 at 10:38 AM Ouellette, Scott < scott_ouelle...@hms.harvard.edu> wrote: > Hi all, > > I have a

Re: [galaxy-dev] activate authentication through LDAP using the auth_conf file

There's an open PR with a few build issues to build a Galaxy-side wheel for python-ldap here: https://github.com/galaxyproject/starforge/pull/97, and once that's resolved it should be automatically installed as a conditional dependency the usual Galaxy way. Until then, yeah, a workaround is to

Re: [galaxy-dev] Galaxy Workflow delete intermediate files

Hi DK, This isn't currently possible, but you're not the first person to request this feature -- it should be straightforward to implement and I'll try to bump it up my priority list a bit. -Dannon On Tue, Aug 16, 2016 at 6:25 PM, D K wrote: > Hi Galaxy-devs > > I've

Re: [galaxy-dev] Command line building

Check out https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/command_factory.py Let me know if this wasn't what you were looking for. -Dannon On Fri, Aug 5, 2016 at 10:49 AM Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > Within the galaxy app itself, does anyone

Re: [galaxy-dev] Question about Galaxy integration with external access control

Hi Simon, On Thu, Sep 29, 2016 at 11:22 AM, Simon Chang wrote: > > 1) Assuming Galaxy can read LDAP directory service information, to what > extent is access control enforced? Is it on a file system level? > The 'galaxy' user, or whichever user is running the

Re: [galaxy-dev] Upgrade to Galaxy 16.07, import dumps problem

K <danielforti...@gmail.com> wrote: >> >>> I have modified some files in my own local galaxy commit (I think only >>> the sniffers in lib/galaxy/datatypes) >>> >>> >>> >>> On Fri, Aug 26, 2016 at 9:31 AM, Dannon Baker <dannon.ba...

Re: [galaxy-dev] Upgrade to Galaxy 16.07, import dumps problem

Hey DK, The cloudlaunch controller was deprecated and should not be in 16.07. Is this a custom modification you have? -Dannon On Fri, Aug 26, 2016 at 12:30 PM, D K wrote: > Hi Galaxy-devs, > > I just tried upgrading to 16.07 from 16.01 and get this error when >

Re: [galaxy-dev] Upgrade to Galaxy 16.07, import dumps problem

), run something like ```find -name "*.pyc" -delete```. On Fri, Aug 26, 2016 at 12:35 PM, D K <danielforti...@gmail.com> wrote: > I have modified some files in my own local galaxy commit (I think only the > sniffers in lib/galaxy/datatypes) > > > > On Fri, Aug

Re: [galaxy-dev] Upgrade to Galaxy 16.07, import dumps problem

ll > there if I did a git pull (did I do this incorrectly?)? > > I did a "git log -- cloudlaunch.py" and got the following: > > commit 303597e48a8503aac09c33910aa5482a374f06a1 > Author: Dannon Baker <dannon.ba...@gmail.com> > Date: Wed Aug 12 14:17:44 2015 -0

Re: [galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used

t; I assume you'll be able to add "edit" buttons to pages pointing > at the markdown pages on GitHub? While it could be prettier, > this works pretty well for us using GitHub Pages: > > https://github.com/biopython/biopython.github.io/pull/78 > > Regards, > > Peter

Re: [galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used

Hi Peter, We're in the middle of migrating the wiki right now -- you may notice that the current wiki is in read-only mode. Going forward, the place to report (and fix) issues like that will be https://github.com/galaxyproject/galaxy-site. -Dannon On Tue, Nov 15, 2016 at 10:06 AM, Peter Cock

Re: [galaxy-dev] More problems installing Galaxy

Hernan, Sorry for the slow response here, have you made any progress? I'd be glad to help sort this out. Instead of creating an alias to a particular python in your .bashrc, I'd recommend that if you're having problems you should manually create the virtualenv with the specific python version

Re: [galaxy-dev] purge dataset at a different location

Hi Mark, I'm not sure this is something I'd encourage pursuing for most folks, but I understand that custom deployments may need special functionality. To implement this for your Galaxy instance, you'd want to look at the ObjectStore "delete" functions, here:

Re: [galaxy-dev] Dataset Cleanup

The quota usage can occasionally get out of sync with reality. If you're an admin user, go to /admin/users, select a user, and you should be able to recalculate the quota to verify it is correct. There's also a script distributed with Galaxy (/scripts/set_user_disk_usage.py) that allows you to

Re: [galaxy-dev] html with styles

Hi Wolfgang, As a security measure, we added sanitization by default of content displayed as HTML. Local galaxy administrators can use the display whitelist (left side of the admin window) to configure 'safe' applications, which will then no longer be sanitized on display. Let me know if this

Re: [galaxy-dev] html with styles

ver security: > > Why does sanitization have to care about in-document style information? > > > On 03.11.2017 17:49, Dannon Baker wrote: > >> Hi Wolfgang, >> >> As a security measure, we added sanitization by default of content >> displayed as HTML. Local

Re: [galaxy-dev] Trackster ownership issue

in a sense that they are called "course1" through "course10" > (as username and password) and all associated with the same email address... > > Could this be problematic in general? > Cheers, > Christopher > > On 05/16/2018 02:35 PM, Dannon Baker wrote: > >

Re: [galaxy-dev] Trackster ownership issue

ould see each other's files in trackster, so it's not > really an issue. > > Thanks for answering! This is the first time I did a Galaxy Course and I'm > still optimizing a bit > > Christopher > > On 05/16/2018 03:55 PM, Dannon Baker wrote: > > Oh that's interesting. It shou

Re: [galaxy-dev] Trackster ownership issue

I definitely have not seen this before, and am not able to reproduce it on my local instance. Can you provide a screenshot of what you're seeing, and the organization of the histories that are being sourced for the incorrect datasets? On Wed, May 16, 2018 at 7:25 AM Previti <

Re: [galaxy-dev] V18.01 'View all histories' doesn't work

Are you perhaps hosting at a prefix using proxy-prefix (so, instead of `/api/histories` we should be looking for `/mygalaxy/api/histories`, or the like)? I'll take a quick look, this should be an easy fix. On Tue, May 15, 2018 at 12:25 PM Ping Luo wrote: > The Galaxy log

Re: [galaxy-dev] V18.01 'View all histories' doesn't work

gt; On Tue, May 15, 2018 at 11:30 AM, Dannon Baker <dannon.ba...@gmail.com> > wrote: > >> Are you perhaps hosting at a prefix using proxy-prefix (so, instead of >> `/api/histories` we should be looking for `/mygalaxy/api/histories`, or the >> like)? I'll take a quick l

Re: [galaxy-dev] tabular data display

I'm not familiar with MetaProSIP, but how many columns *should* be in the output? Galaxy automatically displays tabular data with more than 50 columns in the 'raw' view you're seeing here, instead of using a table. The last bit of data in particular, when looking at the sample, is a ton of `0`

Re: [galaxy-dev] tabular data display

number of columns? > > What would be the Galaxy way to handle data with a larger number of > columns? > > I agree that the scidx problem is unrelated. Might be worth to open an > issue? > > Best, > Matthias > > On 01.06.2018 15:44, Dannon Baker wrote: > > I'm n

Re: [galaxy-dev] MySQL errors and warnings with a fresh install of Galaxy 18-05

Frederic, you may want to follow this issue to track a resolution here: https://github.com/galaxyproject/galaxy/issues/6401 On Thu, Jun 14, 2018 at 1:24 AM SAPET, Frederic wrote: > Hi Hans, > > We have a very nice MySQL server with a lot of RAM and associated storage > (as well as Oracle for

Re: [galaxy-dev] User Registration Error

Do you think you may have run Galaxy previously as root (using sudo?). This could potentially create these compiled template files under a different user, preventing a non-root user from overwriting them. In any event, it's safe to `rm -r database/compiled_templates`, and allow them to be

[galaxy-dev] Galaxy 18.09 Release

We are pleased to announce the *release of Galaxy 18.09 *. A few release highlights are: Extensive Workflow Enhancements Workflows got

Re: [galaxy-dev] run.sh problem

What version of Galaxy exactly is this? And, it looks like it's being run by planemo, and not a simple 'run.sh' via the command line -- is that correct? On Tue, Jan 8, 2019 at 10:04 AM Matthias Bernt wrote: > Dear all, > > a colleague tries to run.sh on a Manjaro Linux and got the following

Re: [galaxy-dev] run.sh problem

about > this command. > ERROR: Galaxy client build failed. See ./client/README.md for more > information, including how to get help. > ``` > > Best, > Matthias > > > On 08.01.19 16:09, Dannon Baker wrote: > > What version of Galaxy exactly is this? And, it looks

Re: [galaxy-dev] Update from 17.10 to 18.05

Can you look and see which resources are failing to load? That'd help me figure out what's going on here. If you have any local changes to the interface you will need to run 'make client-production' from the root of the repository (which should be safe to do in any event, and will rebuild the

[galaxy-dev] Re: new datasets appear in database/files/000/

Hi Jochen, Yes, those new directories would coincide with when you passed 100,000 datasets on your instance, so congrats! You can see the code that builds this hashed path here: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/__init__.py#L137 So, for example, dataset id `9`

[galaxy-dev] Re: King Skrupellos hack

Sorry for the delayed response here, I think this fell through the cracks while folks were engaged with GCC this year. The attachment didn't make it through, can you provide more information? For what it's worth, we've seen 'hacks' like this in the past simply be that someone uploads data with

[galaxy-dev] Re: Upgrade galaxy built from source?

This depends a bit on the installation, but general procedures (a bit dated, but these still apply) can be found here: https://galaxyproject.org/admin/maintenance/ Ideally, without any local code customizations, it's really just something like: ``` git fetch origin git checkout release_20.09 &&

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