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

Adding Reference genome of Chicken and Duck in Tophat
by Vijay Kumar 09 May '16

09 May '16

Dear sir, Kindly add reference Genome of Chicken (Gallus gallus) and Duck (Anas platyrhynchos) in Tophat Reference genome section. *Regards,* *Dr. P. Vijayakumar,* *Assistant Professor,* *Instructional Livestock Farm Complex, * *Veterinary College and Research Institute,* *Orathanadu, **Thanjavur,* *Tamil Nadu,* *India- 614625*

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Proper Galaxy Installation
by Durdevic, Marija 09 May '16

09 May '16

Dear all, I am currently working on Galaxy installation at our Center for Medical Research. As a login server, we are using VM based on SLES-12. We are planning to extend it on a Cluster later and we would like to use SLURM as DRM. Is there any recommendation or "step-by-step" recipe how to setup Galaxy in a proper way to avoid future issues? Are they any recommendation regarding the filesystem of directory management system that I should care about in advance? Any advice from experienced developers will be more than helpful. Thank you in advance. Regards, Mag. Marija Đurđević Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.djurdjevic(a)medunigraz.at Email: marija.djurdjevic(a)klinikum-graz.at Web: https://zmf.medunigraz.at/

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Fwd: Error when uploading files (using Pulsar)
by Marius van den Beek 09 May '16

09 May '16

Ah, and if you want to figure out the ID of a tool, you can click the small info button of a dataset produced by the tool, so in the case of the upload tool it reads: Galaxy Tool ID: upload1 On 9 May 2016 at 12:25, Marius van den Beek <m.vandenbeek(a)gmail.com> wrote: > Puhh, you're right, and somewhere in the undepths of the wiki (I think) > this is documented, > but admittedly I didn't find it when searching for it. > If you want you could add a sample of your config to > https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample… > , > I believe this is something that the galaxy devteam carefully keeps up to > date. > You would definitely have my +1 for a Pull Request. If you don't have the > time I can also do this for you. > > Marius > > On 9 May 2016 at 12:02, Tiziano Flati <tiziano.flati(a)gmail.com> wrote: > >> Thank you very much, Marius, that worked! >> >> But how should I have known about the exact ID of the upload tool (i.e., >> upload1)? I think this is an extremely common pattern (upload data and >> execute jobs on a cluster) >> >> 2016-05-09 11:38 GMT+02:00 Marius van den Beek <m.vandenbeek(a)gmail.com>: >> >>> Hi Tiziano, >>> >>> I think you are correct in your assumption. >>> If you do not need to have uploads run on pulsar, you should be able to >>> specify a local destination for uploads (the upload tool id is upload1) >>> in your job_conf.xml. >>> There are some examples described here: >>> >>> https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample… >>> If you can place a copy of galaxy and a virtualenv on your pulsar >>> server, you could also set this up as in >>> >>> https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample… >>> >>> Note that I haven't tried this yet, but I think this is a good start. >>> Let us know if that works. >>> >>> Cheers, >>> Marius >>> >>> >>> On 9 May 2016 at 10:42, Tiziano Flati <tiziano.flati(a)gmail.com> wrote: >>> >>>> Hi all, >>>> >>>> I have succesfully setup a Galaxy-Pulsar architecture and I am able to >>>> run jobs over datasets* already uploaded on a history*. >>>> >>>> When I try to upload a new file to the history, though, the upload job >>>> fails with the following error: >>>> >>>> Traceback (most recent call last): >>>>> File "/home/flati/pulsar/files/staging/80/tool_files/upload.py", >>>>> line 18, in <module> >>>>> import galaxy.model # noqa >>>>> ImportError: No module named model >>>> >>>> >>>> Note: in job_conf.xml, Pulsar is the default destination: >>>> >>>> <destinations default="win_pulsar"> >>>> >>>> >>>> Does someone know what the problem is? >>>> I suspect that setting pulsar as the default destination causes the >>>> upload tool to run on Pulsar's side which, however, does not have access to >>>> Galaxy's lib directory (which contains the galaxy model module). >>>> >>>> Any help is very appreciated, >>>> Tiziano >>>> >>>> ___________________________________________________________ >>>> 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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Error when uploading files (using Pulsar)
by Tiziano Flati 09 May '16

09 May '16

Hi all, I have succesfully setup a Galaxy-Pulsar architecture and I am able to run jobs over datasets* already uploaded on a history*. When I try to upload a new file to the history, though, the upload job fails with the following error: Traceback (most recent call last): > File "/home/flati/pulsar/files/staging/80/tool_files/upload.py", line > 18, in <module> > import galaxy.model # noqa > ImportError: No module named model Note: in job_conf.xml, Pulsar is the default destination: <destinations default="win_pulsar"> Does someone know what the problem is? I suspect that setting pulsar as the default destination causes the upload tool to run on Pulsar's side which, however, does not have access to Galaxy's lib directory (which contains the galaxy model module). Any help is very appreciated, Tiziano

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Planemo inside of Conda
by D K 06 May '16

06 May '16

Hi Galaxy-Devs I would like to have a single python / planemo environment that is portable across computers where I can use planemo test (which instantiates an instance of Galaxy). Currently, we're using conda on our current network. That way we have shared environments where the version of python and associated modules is consistent across network computers/users. This way, any user (including the galaxy system) can use exactly the same python version and modules which greatly simplifies management. I guess it's possible to manage dependencies through toolsheds, but we didn't want to do that. Although probably not optimal, what we do is to start a conda environment between the <command> tags in a tool's xml for python scripts, e.g.: <command> source activate pythonEnv; python Script.py $input1 > $output1 </command> The problem is that planemo is also installed in this environment, and since one cannot start a galaxy instance within a conda environment, planemo test now fails (since the environment doesn't get loaded correctly). I can get this to work in planemo 0.14, but not in the newer versions. Is there a workaround for this, a better setup, or must I stay with planemo 0.14? Thanks!

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file format of individual files within collections
by emanuele lapponi 06 May '16

06 May '16

Dear all, I am currently developing a tool that outputs an arbitrary number of files, using collections as described in the excellent tutorial by Steve Cassidy at https://web.science.mq.edu.au/~cassidy/2015/10/21/galaxy-tool-generating-da… . I am having a hard time figuring out how to make galaxy aware of the format of the individual files in the collection, as the two relevant admin help pages I found do not mention this ( https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax and https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files) I tried adding a format attribute to the collection tag in the tool description, similarly to ``normal'' single data outputs: <outputs> <collection type="list" format="foo"> <discover_datasets pattern="(?P<name>.*)" directory="bar" /> </collection> </outputs> ... but to no avail. I would be grateful for any helpful pointers! :) Best, Emanuele Lapponi

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Position Vacant - Galaxy and Language Research in Sydney
by Steve Cassidy 06 May '16

06 May '16

Hi all, I’d like to draw your attention to the following vacancy on our project in Sydney, Australia: https://goo.gl/6NcY3g This is on the Alveo project and I’m posting here because part of the platform is a Galaxy server with tools developed to work on language data (text and speech). The role would suit someone with knowledge of Galaxy and some exposure to general eResearch problems; knowledge of language research methods would obviously be a bonus. The ad mentions a part-time role for 6 months but in practice we have funding for longer than this and for a full time role for the right candidate. Please get in touch if you are interested in finding out about the post. International candidates are welcome to apply. Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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Parallelism (job splitting) for ncbi_blast_plus running through CloudMan
by David Kovalic 05 May '16

05 May '16

Hello, We would like to split fasta query files and run multiple concurrent jobs to minimize our processing wall clock time for large jobs. After chatting with folks at GCC 2015 I understand this is possible, my problem is I cant find instructions on hos to configure CloudMan/ncbi_blast_plus to do this. For those of you who know me it probably goes without saying that I can't figure it out myself ;) Peter/Enis/others, can you help us out with this question? Thanks, David

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Changing temporary directory for planemo
by D K 05 May '16

05 May '16

Hi Galaxy-Devs, Is it possible to change the temporary directory used by planemo test? The reason is that one of my xml tools uses ssh to connect to a machine specifically due to licensing requirements e.g.: <command> ssh address.com 'sh runCommand.sh $input' > $output </command> Unfortunately, when executing a planemo test, the input is copied into a local temporary directory (/tmp) which is of course different from the /tmp directory on the computer where the bash script is being executed. I've tried changing the TMP and TEMP environment variables to a location that is available to both machines but that hasn't worked. Is there a workaround? Thanks!

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Kallisto tool wrapper?
by Lance Parsons 02 May '16

02 May '16

I've had requests from users to install Kallisto as Galaxy tool. I didn't see any wrappers or evidence of wrappers in my searching, but I thought I'd ask here to see if anyone is working on or interested in working on such a thing. -- Lance Parsons - Scientific Programmer Carl C. Icahn Laboratory - Room 136 Lewis-Sigler Institute for Integrative Genomics Princeton University

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