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

You’ll probably get a more informative error message if you check the logs. Sent from my iPhone > On 15. May 2018, at 17:45, Ping Luo wrote: > > I just installed Galaxy V18.01. I got an error when clicking 'View all > histories' in the history tool bar > > The error

Re: [galaxy-dev] extract extra info (logs) from history

d them... > > But maybe I can use the flagstat tool for now. > > Cheers Jochen > > >> On 02.05.2018 16:34, Devon Ryan wrote: >> By default the logs are just to stdout. You need to use one of the >> options (under "Summary Options" on the vers

Re: [galaxy-dev] extract extra info (logs) from history

By default the logs are just to stdout. You need to use one of the options (under "Summary Options" on the version on our instance) if you want things saved as a history item. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Imm

Re: [galaxy-dev] extract extra info (logs) from history

There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're under "Summary Options". Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and E

Re: [galaxy-dev] Problem with dependencies: Conda/freebayes

This is presumably the same question elsewhere: https://biostar.usegalaxy.org/p/26197/ -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Thu, Jan 11, 2018 at 9:44 AM, Björn

Re: [galaxy-dev] MACS2 Error

That doesn't change anything, I also using Galaxy within docker. On 10/18/2017 06:27 PM, Deepak Tanwar wrote: I am using Galaxy via Docker. On Oct 18, 2017, at 11:51 AM, Devon Ryan <dprya...@gmail.com <mailto:dprya...@gmail.com>> wrote: Assuming you don't have galaxy set to

Re: [galaxy-dev] MACS2 Error

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Re: [galaxy-dev] Job output not returned from Cluster Error

Presuming SGE runs this on a remote node, it's likely the file hasn't been flushed to disk. Have you checked to see if the files eventually show up? Sent from my iPhone > On 17. Aug 2017, at 17:49, Yip, Miu ki wrote: > > Hi, > > We’re having a bit of an error where the GUI

Re: [galaxy-dev] Creating a tool dependency packages

In general, see if the new package is available in conda-forge or bioconda. If so, you just need to mention it in the requirements section of the tool XML. -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51

Re: [galaxy-dev] Creating a tool dependency packages

use conda as a dependency resolver then you can skip creating a tool dependency package. This saves a LOT of hassle, in my experience. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freibu

Re: [galaxy-dev] Moving Shared Data Library Folders

quot; table). Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Thu, Jul 6, 2017 at 8:30 AM, D K <danielforti...@gmail.com> wrote: > Is it possible to move the

Re: [galaxy-dev] DeepTools python dependency issues?

Try installing libbz2-dev (or whatever that's called on your system), since it's not in the normal conda channels. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Wed

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

This is likely an issue with using active vs. passive FTP. Unfortunately since you're not using `--net=host` you can't use passive ftp (at least it's never worked for me). Perhaps sftp on port 8022 will work better. -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

If your user is an admin then yes. Each user can use their normal login credentials. -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Fri, Jun 23, 2017 at 11:45 AM, Md. Rezaul

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

You should be able to login with the email address and password that you use for Galaxy then. That works for my instances at least. -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

Are you using galaxy-docker-stable from Björn (https://github.com/bgruening/docker-galaxy-stable) or did you make your own dockerized-Galaxy version? Björn's runs proFTPd by default, so if you're using it then ensure that's running in the container. Devon -- Devon Ryan, Ph.D. Email: dpr

[galaxy-dev] "Execute" button does nothing in the CrossMap tool?

l note that the user that reported this has tried multiple browsers (firefox and safari) with the same result (nothing happening) in both. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79

Re: [galaxy-dev] DeepTools installation error

wrote: Hi Devon, I'm also experiencing similar issues. Could you please briefly explain how to use Condo with Galaxy? Is there any other versions where Conda is integrated apart from the regular Galaxy distributions? On Mar 8, 2017 7:38 PM, "Devon Ryan" <dprya...@gmail.com

Re: [galaxy-dev] DeepTools installation error

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/ -- De

Re: [galaxy-dev] Shared Data Library, large number of files

l the end of the month. For what it's worth, opening the same library via "shared data" takes ~100 msec. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Thu, Mar 2, 20

Re: [galaxy-dev] wrapper for tool with multiple outputs

Hi Jochen, Don't have it use /tmp, but rather the current working directory and then everything will work. Galaxy jobs are run in individual working directories, so you can exploit that to ensure that files aren't overwritten. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager

Re: [galaxy-dev] building indexes

roject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email: dprya...

Re: [galaxy-dev] Parameters out

Hi Katherine, That one's beyond me, sorry. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Tue, Aug 30, 2016 at 2:46 PM, Katherine Beaulieu <katherine.beaul

Re: [galaxy-dev] Parameters out

Hi Katherine, Check the 'job_parameter' table, though you'll need to find the correct job ID from the 'job' table. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Tue