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

Create a new datatype svg
by Jochen Bick 09 Feb '17

09 Feb '17

Hi all, I'm working on a tool that will have svg as an output file. Is this data type already established? If not how do I start? Cheers Jochen

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Pulsar Metadata
by Joseph Brent Greer 07 Feb '17

07 Feb '17

Hi All, We've been using Pulsar to send jobs to our cluster on campus. Generally we send a dataset list of files over. We're wondering if there is a way to get the metadata for the files after they've been sent to the cluster. We're specifically trying to find the filepaths of the files before they were through Pulsar to the cluster. Any guidance would be great. Thanks, Joe

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GalaxyAdmins Feb online meetup (Enis Afgan)
by David Kovalic 07 Feb '17

07 Feb '17

Enis, Could you send the call-in information please? David On Tue, Feb 7, 2017 11:00 AM, galaxy-dev-request(a)lists.galaxyproject.org wrote: Send galaxy-dev mailing list submissions to galaxy-dev(a)lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request(a)lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-owner(a)lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.Today's Topics: 1. Re: Request more details from Nikolaos Tur about pyBamTools & pyBamParser dependency packages message (Peter Briggs) 2. GalaxyAdmins Feb online meetup (Enis Afgan) 3. Create a new datatype svg (Jochen Bick) 4. Re: Create a new datatype svg (Björn Grüning) 5. Re: Create a new datatype svg (Jochen Bick) 6. Re: Request more details from Nikolaos Tur about pyBamTools & pyBamParser dependency packages message (Jennifer Hsieh) 7. SLURM configuration problem (Leonor Palmeira) 8. Re: Issue when using xsendfile with galaxy release_16.07 (SAPET, Frederic) _______________________________________________ galaxy-dev mailing list galaxy-dev(a)lists.galaxyproject.org https://lists.galaxyproject.org/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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Vote for the Training you would like to see at GCC2017
by Dave Clements 07 Feb '17

07 Feb '17

Hello potential GCC2017 Attendees! The 2017 Galaxy Community Conference (GCC2017) <https://gcc2017.sciencesconf.org/> will be held 26-30 June, in Montpellier, France. GCC2017 training <https://gcc2017.sciencesconf.org/> will be held 27-28 June. *We need your vote to determine what to offer at GCC2017 training.* If there is even a remote chance that you will attend GCC2017 (it's in the South of France; it will be summer; don't let that influence your decision), then *please vote on which of the **34 nominated topics you would like to see offered at GCC2017.* *Vote Now! <https://docs.google.com/forms/d/e/1FAIpQLSdpkLoRuCGZOO3_T6dgRwFeDxVjb_zW-tl…>* 27 June will be single track and focus on how to use Galaxy for research. 28 June will have multiple tracks, and offer the full spectrum of Galaxy training. Vote for as many topics as you like, but please note that the more topics you vote for, the less your vote for each single topic will count. *Voting closes on 8 February.* Once that happens the organisers will scramble to confirm instructors and set a schedule. The training schedule will be posted before registration opens in February. The nominated topics this year are: - *Using Galaxy Topic Nominations <https://gcc2017.sciencesconf.org/resource/page/id/8#using>* 1. Galaxy 101 - A gentle introduction to Galaxy <https://gcc2017.sciencesconf.org/resource/page/id/8#galaxy_101> 2. Galaxy at scale <https://gcc2017.sciencesconf.org/resource/page/id/8#galaxy_at_scale> 3. Visualisation of BIG DATA in Galaxy <https://gcc2017.sciencesconf.org/resource/page/id/8#visualisation_of_big_da…> 4. GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome <https://gcc2017.sciencesconf.org/resource/page/id/8#gsuite_hyperbrowser> 5. ChIPseq analysis using DeepTools and MACS <https://gcc2017.sciencesconf.org/resource/page/id/8#chipseq> 6. RADseq Data Analysis Through STACKS on Galaxy <https://gcc2017.sciencesconf.org/resource/page/id/8#radseq> 7. RNAseq analysis in Galaxy <https://gcc2017.sciencesconf.org/resource/page/id/8#rnaseq> 8. Flow Cytometry Analysis with ImmPort Galaxy <https://gcc2017.sciencesconf.org/resource/page/id/8#flow_cytometry> 9. Metabolomics Analysis with Galaxy on W4M infrastructure <https://gcc2017.sciencesconf.org/resource/page/id/8#metabolomics> 10. How to analyze metagenomic and amplicon data in Galaxy? <https://gcc2017.sciencesconf.org/resource/page/id/8#metagenomics> 11. Galaxy for Proteomics <https://gcc2017.sciencesconf.org/resource/page/id/8#proteomics> 12. Processing and Analysis of Hi-C data using HiCExplorer <https://gcc2017.sciencesconf.org/resource/page/id/8#hic> 13. SNP analysis and GWAS using SNiPlay <https://gcc2017.sciencesconf.org/resource/page/id/8#snp> 14. Small genome de novo assembly using Galaxy <https://gcc2017.sciencesconf.org/resource/page/id/8#assembly> 15. Scripting Galaxy using the API and BioBlend <https://gcc2017.sciencesconf.org/resource/page/id/8#scripting> - *Deploying, Administering, and Extending Galaxy Topics <https://gcc2017.sciencesconf.org/resource/page/id/8#admin>* 1. Introduction to Galaxy admin: Setting up a Galaxy instance as a service <https://gcc2017.sciencesconf.org/resource/page/id/8#intro_admin> 2. Advanced customisation of a Galaxy instance <https://gcc2017.sciencesconf.org/resource/page/id/8#custom> 3. Advanced accelerated Galaxy admin <https://gcc2017.sciencesconf.org/resource/page/id/8#aaga> 4. How to use Galaxy Ansible Playbooks <https://gcc2017.sciencesconf.org/resource/page/id/8#ansible> 5. Testing Galaxy <https://gcc2017.sciencesconf.org/resource/page/id/8#testing> 6. Using and deploying your application to the cloud <https://gcc2017.sciencesconf.org/resource/page/id/8#cloud> 7. Galaxy Architecture <https://gcc2017.sciencesconf.org/resource/page/id/8#arch> 8. Writing & Publishing Galaxy Tools <https://gcc2017.sciencesconf.org/resource/page/id/8#tools_basic> 9. Advanced Topics in Galaxy Tool Development <https://gcc2017.sciencesconf.org/resource/page/id/8#tools_advanced> 10. Visualisation Development in Galaxy <https://gcc2017.sciencesconf.org/resource/page/id/8#viz_dep> 11. Adding support for new external sources <https://gcc2017.sciencesconf.org/resource/page/id/8#data_sources> 12. Conda and Containers for Tool Dependencies - A Developers Perspective <https://gcc2017.sciencesconf.org/resource/page/id/8#conda_dev> 13. Conda and Containers for Tool Dependencies - A Deployers Perspective <https://gcc2017.sciencesconf.org/resource/page/id/8#conda_dep> 14. Introduction to Galaxy Interactive Environments <https://gcc2017.sciencesconf.org/resource/page/id/8#ie_intro> 15. Advanced topics in Galaxy Interactive Environments <https://gcc2017.sciencesconf.org/resource/page/id/8#ie_adv> 16. Galaxy and Tripal - coupling Galaxy to a community database <https://gcc2017.sciencesconf.org/resource/page/id/8#tripal> 17. The Galaxy Genome Annotation project: Dockerized genome annotation environment based on Galaxy and GMOD tools <https://gcc2017.sciencesconf.org/resource/page/id/8#gap> 18. Using Hadoop with Galaxy <https://gcc2017.sciencesconf.org/resource/page/id/8#hadoop> - *Trainer Training Topics <https://gcc2017.sciencesconf.org/resource/page/id/8#trainer_training>* 1. Galaxy for Training and Education <https://gcc2017.sciencesconf.org/resource/page/id/8#galaxy_for_training> Please vote <https://docs.google.com/forms/d/e/1FAIpQLSdpkLoRuCGZOO3_T6dgRwFeDxVjb_zW-tl…>! Your participation helps make Galaxy Community Conferences the successful and community focused events that they are. And, thanks to everyone who nominated topics and/or contributed topic descriptions. Hope to see you in Montpellier! Dave Clements, on behalf of the GCC2017 Organising Committee -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Request more details from Nikolaos Tur about pyBamTools & pyBamParser dependency packages message
by Jennifer Hsieh 07 Feb '17

07 Feb '17

Hi, I've installed a local instance of Galaxy (on Ubuntu 16.04, python 2.7.12) and have run in to this exact problem (posted by Nikolaos Tur https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg03955.ht… ) while trying to add naive_variant_caller tool. Naive_variant_caller can't install because these two dependency packages can't be installed. I basically get exactly the same error message that ends with "IOError: Could not build the egg." Unfortunately I'm very new to both Galaxy and Python (Taking Coursera Galaxy course at the moment) and I don't really understand the solution Nikolaos described about modifying the setup.py to use "setuptools" instead of "distribute". I don't even know where to find setup.py... Can anyone help me with step-by-step details as to how to solve this dependency problem? Much Thanks! -- Jennifer Hsieh PhD Neuroscience (student) Department of Psychiatry and Mental Health University of Cape Town Tell: +27 21 447 3157 Cell: +27 74 841 4761

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GalaxyAdmins Feb online meetup
by Enis Afgan 06 Feb '17

06 Feb '17

Hello everyone, We are going to have a GalaxyAdmins call this month! This is a wonderful venue to get an update on what's going on in the Galaxy community as mostly relevant to people managing Galaxy instance(s). The talk will be held at the 'standard' GalaxyAdmins time: on Feb 16th at 11AM EST. Here is a short description of the topic that will be presented: CloudLaunch 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. The call will be held online, using an online meetup room with Adobe Connect. The online conference room will open 15 minutes before the meetup. The call will use Johns Hopkins' Adobe Connect server, which in turn uses Adobe Flash. You are encouraged to connect a few minutes early to work out any unexpected bumps.

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AD/LDAP Integration
by Yip, Miu ki 06 Feb '17

06 Feb '17

Hi all, After setting up AD/LDAP in Galaxy, we noticed that for some reason, some users are able to log in but others were not. We don’t think that it has anything to do with the set up of LDAP or AD at our institute and we’ve tried to find common threads between the users who can log in but we have not found anything interesting. Could someone explain what exactly Galaxy looks for when signing users in with AD/LDAP? We found the source code here: ./lib/galaxy/auth/providers/ldap_ad.py but all the code seems to be functioning properly. Here is one of the error outputs in the log when somebody tries to log in for the first time, but cannot: galaxy.auth.providers.ldap_ad DEBUG 2017-02-01 17:16:17,954 LDAP authenticate: whoami is u:SCIEDU\chess galaxy.auth.providers.ldap_ad DEBUG 2017-02-01 17:16:17,954 LDAP authentication successful server ip - - [01/Feb/2017:17:16:12 -0400] "POST /galaxy/user/login?use_panels=False HTTP/1.0" 200 - “http:/galaxyurl.edu/galaxy/user/login?use_panels=False<http://galaxy/user/login?use_panels=False>" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.95 Safari/537.36" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 55724) Traceback (most recent call last): File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib64/python2.7/SocketServer.py", line 651, in __init__ self.finish() File "/usr/lib64/python2.7/SocketServer.py", line 710, in finish self.wfile.close() File "/usr/lib64/python2.7/socket.py", line 279, in close self.flush() File "/usr/lib64/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe Any insight would be appreciated. Thanks!

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Question about Data Managers
by Carlos Lijeron 03 Feb '17

03 Feb '17

Everyone, I’m trying to setup various data managers to automatically download and index reference indices. However, I can’t figure out where to change the default location where these are saved. As you can see in the attached image, the default location for the indexes is the … /tool-data/dbkey/index_name However, I would like to save them in /projects/reference_datasets which is a shared location that has a lot of space available. Please advise. Thank you all ! Carlos. [cid:image001.png@01D25B9D.4F483110]

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Ampliocn Sequencing
by Abebe Fola 03 Feb '17

03 Feb '17

Dear Galaxy Community, I am a Ph.D. student working on Plasmodium Genome. My project mainly focuses on short Amplicon sequence using Miseq platform and I have a total of 200 primers designed for targeted 200 loci on 14 chromosomes. I would like to ask you which pipeline would be better to do demultiplex 200 primers/ sample for 96 samples (output from MiSeq), quality filter, mapping reads and variant calling simultaneously. Since the majority of current pipelines (GATK and others) are designed for large reads and diploid organism like human. Any suggestion or comment highly appreciated for my data (short millions of multiplexed reads for a haploid organism)... With Regards, Abe

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How to include local tools with Docker image of Galaxy ?
by Md. Rezaul Karim 02 Feb '17

02 Feb '17

Dear All, I'm a new user of Galaxy. I have been exploring the things and trying to use the Docker image of Galaxy. Eventually, I am planning to run the docker container on our local Cluster. I was wondering if there's any way to include local tools with the Dockerfile. For example using the Docker image of Galaxy at https://github.com/bgruening/docker-galaxy-stable it shows how to include the tools to the Docker image of Galaxy from the Galaxy tool shed as follows: RUN install-repository \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_numpy_1_7" \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_perl_pdf_api2_2_023" \ This command will pull the tools from the Galaxy tool shed and install inside the docker container. But, is there's any similar way to include my own local tools? Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc PhD Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html>

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