July 2016 - galaxy-dev - lists.galaxyproject.org

dataset collection datatype
by Cristel Thomas 29 Jul '16

29 Jul '16

Hello galaxy developers, how do you set the format for datasets in output dataset collections? I looked at some xmls from John Chilton, and tried using format_source="input", or inherit_format="true". Those unfortunately do not work. I also naively tried format="txt" to no avail. I can't find anything in the documentation. Can someone point me in the right direction? Thanks much, Cris

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Recommended Hardware for Galaxy
by Durdevic, Marija 29 Jul '16

29 Jul '16

Dear all, In our Center for Medical Research we installed Galaxy server for our researchers. We are running Galaxy on login node (Virtual Machine) and job execution is on cluster configured using SLURM. In Galaxy configuration we are using Supervisor-uWSGI-Nginx and two handlers. We are facing low performance problem and very slow Galaxy response. Our Virtual Machine has 4 cores and 16GB of RAM memory. Is there any recommended hardware configuration for Galaxy? Thanks in advance, Marija

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Galaxy in Docker and nginx
by Yip, Miu ki 29 Jul '16

29 Jul '16

Hi Galaxy Team, I'm currently trying to use Galaxy in Docker, and I wanted to know if there are special actions that I have to do in Galaxy for nginx. I'm trying to set up a reserve proxy and have url forwarding. Do I need to inform Galaxy in Docker that nginx is being use? Thanks, Miuki

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August Galaxy News
by Dave Clements 29 Jul '16

29 Jul '16

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Fwd: Storing data in the user session
by Katherine Beaulieu 28 Jul '16

28 Jul '16

---------- Forwarded message ---------- From: Katherine Beaulieu <katherine.beaulieu014(a)gmail.com> Date: Thu, Jul 28, 2016 at 4:32 PM Subject: Re: [galaxy-dev] Storing data in the user session To: Björn Grüning <bjoern.gruening(a)gmail.com> Hi Bjoern, Do you think you could contact me to discuss what you've done so far? I indeed did talk to Eric today but if you have already implemented some of the back-end stuff, I wouldn't want to be repeating your work and I could potentially work with you on the user interface for this? Thanks, Katherine On Thu, Jul 28, 2016 at 3:17 PM, Björn Grüning <bjoern.gruening(a)gmail.com> wrote: > Hi Eric, > > I think they are. What you described is more the user-facing part. > My current proof-of-concept does not have a tool-user-interface, it just > stores the credentials in the framework and makes it accessible through > the user-object. Which should be enough for dynamic job destinations. > A dedicated user-interface for tools is a nice idea and we can put this > ontop I think very easily! > > Thanks for sharing! > Bjoern > > Am 28.07.2016 um 21:09 schrieb Eric Rasche: > > Hey Björn, > > > > I talked a bit about this with Katherine today, her group is quite > > interested in working on this as well. > > > > I know we had discussed this a bit at GCC, and I posted a message today, > > outlining my plans which were formulated when I was at PSU the other > > month. Were those suggestions compatible with the existing work you'd > > done on generic KV store stuff? > > > > Cheers, > > Eric > > > > On 28. juli 2016 18:59, Björn Grüning wrote: > >> Hi Steve & Mohammed, > >> > >> I'm working on a user-profile extension to get credentials for a user, > >> but this will take a few more weeks sorry. > >> > >> In the meantime can you look at the following idea: > >> > >> my_programm.py --credentials $USER_CREDENTIALS --arguments > >> > >> The variable $USER_CREDENTIALS is set during job execution with dynamic > >> destination mappings > >> > https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping > >> > >> What do you think, would this work for you? > >> This assumes you as admin can pass along the user credentials if you > >> know the username. > >> > >> If not please get in touch and I will tell you about my plans to extend > >> the user-preferences maybe you can help me with this to speed things up. > >> > >> Ciao, > >> Bjoern > >> > >> > >>> Hi Bjorn, > >>> sure, I don’t want to have the credentials stored in the tool but the > tool > >>> needs to act on behalf of the user to retrieve data from the > repository, so > >>> it needs access to credentials. This could for example be a token > generated > >>> via an OAuth2 exchange - basically something that is sent along with > every > >>> http request to the remote resource to authenticate the user. > >>> > >>> My thought is that this could be stored in the user profile if this > can be made > >>> available to the tool in the same way that __user_email__ is now. > >>> > >>> When you say ‘on the framework level’ do you mean by Galaxy? > >>> > >>> Steve > >>> — > >>> Department of Computing, Macquarie University > >>> http://web.science.mq.edu.au/~cassidy > >>> > >>>> On 28 Jul 2016, at 5:23 PM, Björn Grüning <bjoern.gruening(a)gmail.com> > wrote: > >>>> > >>>> Hi Steve, > >>>> > >>>> can you explain the larger use-case behind it. Imho you should not > >>>> populate a tool with credentials, this should be handled on the > >>>> framework level. > >>>> > >>>> Hope you are fine, > >>>> Bjoern > >>>> > >>>> Am 28.07.2016 um 03:15 schrieb Steve Cassidy: > >>>>> Hi again, > >>>>> I’m looking for the right way to store some user credentials in the > >>>>> galaxy session so that tools can work on behalf of the user with our > >>>>> repository. > >>>>> > >>>>> Currently users have an API key and they need to upload it as a data > >>>>> item to that is then passed to each tool that needs it as input. > This > >>>>> doesn’t seem like the right solution since the API key becomes part > of > >>>>> the history and so would be shared if the history were shared. > >>>>> > >>>>> What would be better would be a way of storing the API key in the > user > >>>>> session and then being able to pass that into a tool. > >>>>> > >>>>> I note that there are a few user session variables available in the > tool > >>>>> xml file: __user__, __user_email__, __user_name__ and __user_id__. > >>>>> There is also a user preferences page where they can fill out a few > >>>>> details. However, I can’t see a mechanism to extend this in any way > and > >>>>> have extra properties in the preferences pane that would then be > >>>>> available to tools via the template file. > >>>>> > >>>>> I can see that the standard practice for the data sources on > >>>>> usegalaxy.org <http://usegalaxy.org> is to send the user off to a > >>>>> repository website to find data that is then posted back to the > galaxy > >>>>> server. This isn’t appropriate for us since the interaction with the > >>>>> repository is not just for downloading a single dataset - tools will > >>>>> query the repository, download various kinds of data and possibly > upload > >>>>> new data, so we need to store user credentials in some way. > >>>>> > >>>>> Is there already a good way to achieve this or is this an > enhancement to > >>>>> Galaxy? > >>>>> > >>>>> Thanks, > >>>>> > >>>>> Steve > >>>>> > >>>>> > >>>>> — > >>>>> Department of Computing, Macquarie University > >>>>> http://web.science.mq.edu.au/~cassidy > >>>>> <http://web.science.mq.edu.au/%7Ecassidy> > >>>>> > >>>>> > >>>>> > >>>>> ___________________________________________________________ > >>>>> 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: > >>>>> https://lists.galaxyproject.org/ > >>>>> > >>>>> 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: > >> https://lists.galaxyproject.org/ > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/mailinglists/ > > > > -- > > > > Eric Rasche > > Programmer II > > > > Center for Phage Technology > > Rm 312A, BioBio > > Texas A&M University > > College Station, TX 77843 > > 404-692-2048 <tel:404-692-2048> > > esr(a)tamu.edu <mailto:esr@tamu.edu> > > Not responding quickly enough? > > < > https://calendar.google.com/calendar/embed?src=esr%40tamu.edu&ctz=America/C… > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >

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Information about SparkGalaxy
by Léo Biscassi 28 Jul '16

28 Jul '16

Hi folks, I recently saw this tweet [1] about SparkGalaxy. I'm working in one project which uses spark to process protein-ligand docking data and would like try use this workflow in my project, can anyone give me more information, e.g. where I can download it or if it's built in galaxy implementation, about? I'm pretty excited, this is a great job! [1] https://twitter.com/galaxyproject/status/758727733643874304 Thanks for your attention! -- Best regards, *Léo Biscassi*

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possible bug found - unable to log out of impersonated user when external authentication enabled
by Ryan G 28 Jul '16

28 Jul '16

Hi all - We are using a SSO system so that user's authenticate externally from Galaxy. when I impersonate a user then try to log out as that user, I'm unable to. I get the page " Access to Galaxy user controls is disabled User controls are disabled when Galaxy is configured for external authentication." If I close the browser down, and restart, I get my SSO log in page, but when I get to Galaxy, I'm still impersonating the user.

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Trying to understand python dependencies
by Tony Schreiner 28 Jul '16

28 Jul '16

I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5. I was in the process of adding matplotlib from the toolchest. It has a dependency on package_python_2_7. Before proceeding, I'd like to understand a bit how that works. Does that install a whole new python, and how then does it get invoked? Tony Schreiner

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Password Parameter Opinions
by Katherine Beaulieu 28 Jul '16

28 Jul '16

Hi Everyone, I know this is sort of a controversial topic so I will try to tread lightly. It seems that for a couple of years the idea of a password parameter for Galaxy tools has come up a lot but has also been rejected a lot although I believe there is a lot of merit to it. I have found at least two other times where people have tried to implement this and it was rejected, but there must have been a reason why they needed that parameter. My situation currently is that I have created two tools in Galaxy which communicate with another software called iRODS which needs authentication from the user. In my own department, there is another tool that was created which needed authentication from the user but the developer had to create some other workaround for this problem. In terms of the work I have done for this so far, I have been working off the latest release version of Galaxy. I have implemented the field so that it is obfuscated in the tool form view as well as on the tool info page. I will next be looking into storing the parameter in an environment variable so it doesn't get passed through the command line and encrypting the password before it enters the database. Speaking with a co-worker of mine, we discussed the possibility of implementing two option, irreversible encryption of the password as it gets entered into the database but then making the tool not workflow compatible, or using regular encryption and making the tool workflow compatible. I look forward to hearing your opinions and ideas. Katherine

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TestToolShed down?
by Peter Cock 28 Jul '16

28 Jul '16

Hello all, The main Tool Shed seems fine, but the Test Tool Shed is not: https://testtoolshed.g2.bx.psu.edu/ > Galaxy > > The Tool Shed could not be reached > > You are seeing this message because a request to the > Tool Shed timed out or was refused. This may be a temporary > issue which could be resolved by retrying the operation you > were performing. If you receive this message repeatedly or > for an extended amount of time, please report it to the > Galaxy Team at galaxy-bugs(a)bx.psu.edu with details on > what you were trying to do and the URL in the address bar. > More information on the current state of Galaxy services > may be available on the Galaxy status page or the > @galaxyproject Twitter feed. The https://status.galaxyproject.org/ page reports it should be operational. It responds to ping (same server name and IP address as the main Tool Shed): $ ping -c 4 testtoolshed.g2.bx.psu.edu PING radegast.galaxyproject.org (128.118.250.5) 56(84) bytes of data. 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=1 ttl=45 time=130 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=2 ttl=45 time=129 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=3 ttl=45 time=129 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=4 ttl=45 time=129 ms --- radegast.galaxyproject.org ping statistics --- 4 packets transmitted, 4 received, 0% packet loss, time 3133ms rtt min/avg/max/mdev = 129.744/129.955/130.358/0.348 ms $ ping -c 4 toolshed.g2.bx.psu.edu PING radegast.galaxyproject.org (128.118.250.5) 56(84) bytes of data. 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=1 ttl=45 time=130 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=2 ttl=45 time=129 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=3 ttl=45 time=129 ms 64 bytes from radegast.galaxyproject.org (128.118.250.5): icmp_seq=4 ttl=45 time=130 ms --- radegast.galaxyproject.org ping statistics --- 4 packets transmitted, 4 received, 0% packet loss, time 3135ms rtt min/avg/max/mdev = 129.785/129.977/130.196/0.179 ms Peter

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