February 2017 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] list of names, variables that cannot be used inside XML
by Jochen Bick 20 Feb '17

20 Feb '17

Ok ur right.... I cannot reproduce this error any more... must be a typo or I don't know, sorry guys. Cheers Jochen On 20.02.2017 14:44, John Chilton wrote: > Really, that doesn't sounds correct. Why is pmode not allowed? > > -John > > On Mon, Feb 20, 2017 at 5:22 AM, Jochen Bick <jochen.bick(a)usys.ethz.ch> wrote: >> Hi all, >> >> is there any list available of names that are not allowed to use inside >> xml code? I just found out that "pmode" is one of them. >> >> Cheers Jochen >> >> >> -- >> ETH Zurich >> *Jochen Bick* >> Animal Physiology >> Institute of Agricultural Sciences >> Postal address: Universitätstrasse 2 / LFW B 58.1 >> Office: Tannenstrasse 1 / TAN D 6.2 >> 8092 Zurich, Switzerland >> >> Phone +41 44 632 28 25 >> jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> >> www.ap.ethz.ch >> ___________________________________________________________ >> 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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list of names, variables that cannot be used inside XML
by Jochen Bick 20 Feb '17

20 Feb '17

Hi all, is there any list available of names that are not allowed to use inside xml code? I just found out that "pmode" is one of them. Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 Office: Tannenstrasse 1 / TAN D 6.2 8092 Zurich, Switzerland Phone +41 44 632 28 25 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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Problem with dataset_permissions and roles
by Lemley, Rob 17 Feb '17

17 Feb '17

Hi all, This may or may not be an actual problem, it's just something we ran into on our Galaxy instance in the past few days. The symptom was that when a user clicked the "Edit attributes" button on an item in their history, they would get an "Internal server error" message. After that their history would completely disappear from the interface. Any attempts to reload it with the "Refresh history" button would result in an error. The only way to get it back was to restart Galaxy. The error from uwsgi.log is below. After some digging in the database, I found that the "role_id" column on every entry in "dataset_permissions" had no value. Additionally, the two users who have datasets on the system had no private roles in the "roles" table. I fixed the issue by creating new private roles for those users, then manually setting "role_id" in the "dataset_permissions" table. Unfortunately my Postgres backups only go back a few days, so I can't tell if something happened to those tables somewhere along the line. We're running the release_17.01 branch plus some customizations, nothing that affects those tables though. Has anyone else seen anything like this? Thanks, -Rob galaxy.web.framework.decorators ERROR 2017-02-17 10:32:36,574 Uncaught exception in exposed API method: Traceback (most recent call last): File "/software/galaxy/app/galaxy/lib/galaxy/web/framework/decorators.py", line 295, in decorator rval = func( self, trans, *args, **kwargs ) File "/software/galaxy/app/galaxy/lib/galaxy/webapps/galaxy/api/history_contents.py", line 72, in index return self.__index_v2( trans, history_id, **kwd ) File "/software/galaxy/app/galaxy/lib/galaxy/webapps/galaxy/api/history_contents.py", line 582, in __index_v2 user=trans.user, trans=trans, view='detailed', **serialization_params ) ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/base.py", line 719, in serialize_to_view return self.serialize( item, all_keys, **context ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/hdas.py", line 362, in serialize return super( HDASerializer, self ).serialize( hda, keys, user=user, **context ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/datasets.py", line 534, in serialize serialized = super( DatasetAssociationSerializer, self ).serialize( dataset_assoc, keys, **context ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/base.py", line 632, in serialize returned[ key ] = self.serializers[ key ]( item, key, **context ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/datasets.py", line 438, in <lambda> return lambda i, k, **c: serializer( i.dataset, key or k, **c ) File "/software/galaxy/app/galaxy/lib/galaxy/managers/datasets.py", line 213, in serialize_permissions 'manage' : [ self.app.security.encode_id( perm.role.id ) for perm in management_permissions ], AttributeError: 'NoneType' object has no attribute 'id' -- Rob Lemley Systems Administrator - CIRC University of Rochester

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Re: [galaxy-dev] regarding tool dependencies
by Martin Čech 17 Feb '17

17 Feb '17

Hi Nir, there is very well maintained Docker image with fully configured Galaxy available here: http://bgruening.github.io/docker-galaxy-stable/ The documentation for Galaxy administration is linked from here: https://new.galaxyproject.org/docs/#administration - most notably the recent slide decks for administration training are available here: https://gvlproject.github.io/dagobah-training/ If you encounter any problems come to chat with us here: https://gitter.im/galaxyproject/Lobby Please let us know if you are interested in more. Martin On Fri, Feb 17, 2017 at 12:14 PM Nir Shachaf <nir.shachaf(a)weizmann.ac.il> wrote: > Dear Martin, > > I appreciate your detailed reply. On zero order, my tool, along with other > existing Galaxy "metabolomics" tools should work in-house, and therefore I > can rely on system dependencies, which might mater be resolved through some > help from the community. > > However, I would like to raise a slightly bigger issue, as at least for > me, setting up the Galaxy framework is a very intricate job, evolving > editing several configuration files which goes much beyond the setting of > package dependencies. In my opinion it would be very useful to have some > "quick start recipes", or a predefined VM which can work out of the box, > including, e.g. a per-configured demo users' DB and a linked FTP server for > uploading files, etc. At least, a tutorial on how to setup such a system on > several popular Linux configurations would be greatly appreciated! At the > moment, I have abandoned the idea of setting up Galaxy in my lab, due to > time-consuming configuration problems... hopefully, we can re-try in the > future. > > Many thanks once more, > Nir. > > ------------------------------ > *From:* Martin Čech [marten(a)bx.psu.edu] > *Sent:* Thursday, February 09, 2017 6:46 PM > *To:* Nir Shachaf; galaxy-dev(a)bx.psu.edu > *Subject:* Re: [galaxy-dev] regarding tool dependencies > > Hello Nir, > > the tool publishing process looks like this: tools for Galaxy are > contributed by developers like you to the Tool Shed > https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for > Galaxies worldwide. Any Galaxy administrator can then instal the tool. Some > tools have dependencies, yours seem to depend on R. The recommended way to > have Galaxy installed these dependencies for you is to use Conda (list of > some available R packages here: https://anaconda.org/r/repo?type=conda) > To learn more about Conda please visit > https://docs.galaxyproject.org/en/master/admin/conda_faq.html > > Alternatively, when you do not care about sharing your tool, and you do > not need to track reproducibility you can add any tool to Galaxy locally > (add the .xml wrapper and point tool_conf.xml at it and restart Galaxy). > When the tool is executed and no dependencies are found Galaxy will look > for its executable and if it is on the $PATH it will just use it. > > Please let us know if you have more questions. > > Thanks for using Galaxy, > > Martin > > > On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf <nir.shachaf(a)weizmann.ac.il> > wrote: > > Dear Galaxy-dev team, > > As a research scientist in the dept. of Plant Sciences I would like to > contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is > principally written in R, with some dependencies (namely: R>=3.x, and > several R packages). Following the documentation in: > > https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies > > https://wiki.galaxyproject.org/Admin/Config/ToolDependencies > > I admit I get confused by the numerous possibilities offered by the > framework. My main concern is to be able to link the Galaxy server to tools > already installed on my development environment, and NOT to depend on the > tools available in the tool-shed repository (as many are not there, and > there are specific versions requirements). > > Could you kindly direct me to the relevant solution, or a user's-list > post, if applicable? > > Many thanks in advance, > Nir Shachaf, > Plant Sciences Dept., > Weizmann Inst. of Science, > Rehovot, Israel. > ___________________________________________________________ > 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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Re: [galaxy-dev] Last stable galaxy Release 16.10 or 17.01 ?
by Martin Čech 17 Feb '17

17 Feb '17

Hello, 16.10 is the latest release however release of 17.01 is imminent and will probably happen early next week. The release_17.01 branch is what usegalaxy.org runs for the past few weeks without any big issues. The choice is yours but updating to release_17.01 now is alright I think as along as you keep it updated with what will be added in the future. Thanks for using Galaxy, Martin On Fri, Feb 17, 2017 at 10:49 AM NGS & Bioinformatics Platform < Bioit(a)wiv-isp.be> wrote: > Dear galaxy-dev list members, > > > > Can somebody tell us, which version of galaxy is the last official stable > release ? 16.10 branch has been merge with master but not the 17.01. > Additionally this 17.01 branch seems to have a lot of recent commit, is it > normal ? > > Is it safe to update our local galaxy repository with these 17.01 changes > or is it better to wait a little and stay with galaxy 16.10 for the > moment ? > > > > Thanks for your help. > > > > > * ------------------------------ * > > *Checked as being free of known viruses.* > > > *Scientific Institute of Public Health, Brussels, BelgiumWetenschappelijk > Instituut Volksgezondheid, Brussel, BelgiëInstitut scientifique de Santé > Publique, Bruxelles, Belgique**Visit our website: * > *http://www.wiv-isp.be* <http://www.wiv-isp.be> > * ------------------------------ **DISCLAIMER* > <http://www.iph.fgov.be/disclaimer.asp>: Please see > https://www.wiv-isp.be/EmailDisclaimer > ------------------------------ > > ___________________________________________________________ > 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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ImportError and Project life cycle
by Matthias Bernt 17 Feb '17

17 Feb '17

Dear galaxy-dev list, I'm currently trying to introduce myself to the galaxy server, i.e., learning how to use and administer a galaxy server. I have installed galaxy following this excellent tutorial: https://github.com/martenson/dagobah-training Then I tried the tool "FASTQ Quality Trimmer by sliding window" which is mentioned in NGS101-6 tutorial. I installed the tool from tool shed, but I get a python error (the Admin panel shows that all dependencies are installed): Traceback (most recent call last): File "/home/berntm/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.py", line 3, in <module> from galaxy_utils.sequence.fastq import fastqReader, fastqWriter File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py", line 7, in <module> from six import Iterator, string_types ImportError: No module named six Do you have an idea what could be wrong? I guess that this is to little information, but I did not know which kind of additional information would be helpful. Another question: At my institution quite a lot of NGS projects are carried out. After a project is finished all methods and data are stored to a long term read only tape archive. For the future the idea is to use galaxy. Which options are there to implement such a project life cycle with galaxy? A last general question: would it be better to send a separate mail to the list when I have multiple questions? Best regards, Matthias Bernt

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GalaxyAdmins meetup starting soon
by Enis Afgan 16 Feb '17

16 Feb '17

Hello again, This month's GalaxyAdmins call with start in just a bit over an hour. We will be taking a look at the all-new CloudLaunch application ( beta.launch.usegalaxy.org) with a live demo and an overview of the backend architecture. The call will be held using an online conference room <https://connect.johnshopkins.edu/gxyadmins201702/>, which will open 15 minutes before the meetup. More details about the content and access instructions are available here https://new.galaxyproject.org/community/galaxy-admins/meetups/2017-02-16/

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Bad UID exception with pbs_python on galaxy 16_10 and torque 6.02
by Vandeweyer Geert 16 Feb '17

16 Feb '17

Hi all, We've been running a galaxy server for the last few years successfully, using pbs_python for connection to our HPC. Recently, we've purchased a new system, and we're trying to install galaxy on it. However, we are having some issues. When we try to submit jobs, galaxy returns the following error: galaxy.jobs.runners.pbs WARNING 2017-02-15 16:55:22,178 (20) pbs_submit failed (try 1/5), PBS error 15025: Bad UID for job execution On the pbs_server, we see: 02/16/2017 09:14:43.631;128;PBS_Server.7156;Req;req_reject;Reject reply code=15025(Bad UID for job execution MSG=ruserok failed validating galaxyuser/galaxyuser from galaxy.uza.be), aux=0, type=QueueJob, from galaxyuser(a)galaxy.uza.be However, when we submit the generated qsub script manually, using the same user, queue and pbs_account (-A) settings, the job runs just fine. In our opinion this indicats an issue with galaxy somewhere. Running jobs locally also works. The docs state that we need to scramble a specific pbs_python version for our recent pbs version, but the mentioned files are missing in galaxy 16_10. Some information: ============= pbs_server version : 6.02 galaxy: v16_10 deprecated procedures: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster (in PBS : egss.ini and scripts/scramble.py are missing) Has anybody seen this before? Are there newer docs available on pbs_python ? Best, Geert

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GalaxyAdmins online meetup: this Thursday
by Enis Afgan 15 Feb '17

15 Feb '17

This is a reminder that we are going to have a GalaxyAdmins call really soon now! The talk will be held on Thursday Feb 16th at 11AM EST. See your local time here <http://bit.ly/2kPgfSF>. with the following topic being presented: CloudLaunch <https://beta.launch.usegalaxy.org/> is an application for launching Galaxy on the Cloud instances. In this talk, an all-new version will be presented. The new CloudLaunch (beta.launch.usegalaxy.org) allows multiple flavors of Galaxy to be deployed, Docker images or applications other than Galaxy. Each application can have its own custom user interface developed to accommodate the specific application needs, which will be demonstrated.

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Fwd: Galaxy on the Amazon cloud
by Jennifer Hillman-Jackson 15 Feb '17

15 Feb '17

---------- Forwarded message ---------- From: Матвей Спринджук <msprindzhuk(a)mail.ru> Date: Wed, Feb 15, 2017 at 1:01 AM Subject: Galaxy on the Amazon cloud Are there any guidelines and tutorials on how to tune Galaxy instance in the Amazon cloud environment? We need to know how to set up .ini and .xmls files in details. I have read all the documentation which is available. We have one fresh Galaxy instance at https://genomics.tbportal.org/galaxy/ and struggling on setting it up properly. Thank you and your Team Matvey Sprindzuk, computer/biomedical scientist, MD Belarus, Minsk, UIIP +375 29 567 10 73 <+375%2029%20567-10-73>

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