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

Nominate the training topics you want to see at GCC2017
by Olivier Inizan 18 Jan '17

18 Jan '17

Hello all, Training Day topics are nominated by you, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see the topic nominated in - 2016 bit.ly/gcc2016noms, - 2015 bit.ly/gcc2015vote, - 2014 bit.ly/1s6NtMN, - 2013bit.ly/1i2j1gN, - and the Galaxy Events page (new.galaxyproject.org/events/) The 2017 Galaxy Community Conference (GCC2017, gcc2017.sciencesconf.org) will be held 26-30 in Montpellier, France. It will feature two days of training: the first day will be single track focused on introducing Galaxy for bioinformatics analysis; the second day will feature multiple tracks spanning the breadth of Galaxy usage, admin, deployment, and tools. Nominated topics will be published on the GCC2017 Training page as they come in (gcc2017.sciencesconf.org/) Topic Nominations close 20 January. Topics will be compiled into a uniform list by GCC2017 organizers, and then voted on by the Galaxy Community starting one week later. You can nominate a topic now: https://t.co/DkOmqELY6h Olivier Inizan, On behalf of the GCC2017 Organizing Committee Olivier Inizan ------------------------------------------------ Merci de noter ma nouvelle adresse: olivier.inizan(a)inra.fr Unité de Recherches en Génomique-Info (UR INRA 1164), INRA, Centre de recherche de Versailles, bat.18 RD10, route de Saint Cyr 78026 Versailles Cedex, FRANCE Tél: +33 1 30 83 38 25 Fax: +33 1 30 83 38 99 http://urgi.versailles.inra.fr [urgi.versailles.inra.fr] Twitter: @OlivierInizan

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Fwd: Fwd: Usegalaxy.org Data Rsync Connection refused
by Christopher Previti 17 Jan '17

17 Jan '17

Dear all, I was wondering if anybody was able to get the rsync server datacache.g2.bx.psu.edu to work? Have there been non-documented changes? We still get following messages: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX . rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): Connection refused (111) rsync error: error in socket IO (code 10) at clientserver.c(128) [Receiver=3.1.1] My colleague Georgios Nikolis and I are working on a local Galaxy installation at the DKFZ and would really like to use the pre-built indices. Cheers, Christopher Previti -------- Weitergeleitete Nachricht -------- Betreff: Fwd: [galaxy-dev] Usegalaxy.org Data Rsync Connection refused Datum: Tue, 13 Dec 2016 13:46:48 +0100 Von: Georgios Nikolis <g.nikolis(a)dkfz-heidelberg.de> An: Christopher Previti <christopher.previti(a)dkfz-heidelberg.de> *Georgios Nikolis* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) IT Management Genomics Proteomics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany phone: +49 6221 42-4659 g.nikolis(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> logo <http://www.dkfz.de> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 -------- Forwarded Message -------- Subject: [galaxy-dev] Usegalaxy.org Data Rsync Connection refused Date: Fri, 28 Oct 2016 15:23:14 +0200 From: Georgios Nikolis <g.nikolis(a)dkfz-heidelberg.de> To: galaxy-dev(a)lists.galaxyproject.org <galaxy-dev(a)lists.galaxyproject.org> Dear all, we are currently working on setting up a new local Galaxy installation and I would like to obtain the genome reference data available on the public Galaxy instance. I am following the instructions on the Wiki page (https://wiki.galaxyproject.org/Admin/UseGalaxyRsync) but I can't seem to be able to access datacache.g2.bx.psu.edu via rsync. rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX . rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): Connection refused (111) rsync error: error in socket IO (code 10) at clientserver.c(128) [Receiver=3.1.1] Does anyone know if the URL has changed in the meantime? Is there any alternative way to access this data? Thanks in advance! Best regards, Georgios -- *Georgios Nikolis* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) IT Management Genomics Proteomics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany phone: +49 6221 42-4659 g.nikolis(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> logo <http://www.dkfz.de> Management Board: Prof. Dr. Michael Boutros (interim), Prof. Dr. Josef Puchta VAT-ID No.: DE143293537

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Python script can't can't import BioPython modules in Galaxy 16.01
by Makis Ladoukakis 17 Jan '17

17 Jan '17

Hello everyone, I've recently upgraded to Galaxy 16.01 and i have some issues with a python wrapper from a tool. When I run it via Galaxy I get the following error: Traceback (most recent call last): File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, in <module> from Bio import SeqIO ImportError: No module named Bio However when I click on the "view details" icon to copy the command from the tool and run it on my command line the tool works perfectly. In addition this issue occurs while I already have installed BioPython. When I type Python and write "from Bio import SeqIO" I get no error. Can this be an issue related to the virtual environment that is initialized each time Galaxy starts? Thank you in advance, Makis Ladoukakis

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Update Galaxy from 15.10 to 16.10
by Jochen Bick 17 Jan '17

17 Jan '17

Hi, today we tried to update from 15.10 to 16.10 which included an update of your database from 129 to 131. Do we necessary run into problem if we update from an one year old instance? How is the galaxy.ini updated? Or galaxy.ini does not know any conda yet. Thanks in advance. Cheers Jochen

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installing tool dependencies
by Jochen Bick 12 Jan '17

12 Jan '17

Hi, I installed a bunch of tools at the same time and ran into some errors. After repairing those tools some of the dependencies installations did not work. If I try to repair the tools again I also get this error message: Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. the tool I tried is called: Name: camera_annotate Description: [Metabolomics][W4M][LC-MS] CAMERA R Package - Annotation - Returns annotation results (isotope peaks, adducts and fragments) Maybe anyone has an idea how to solve this. Thanks in advance 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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Galaxy Australasia Meeting Update: Register now, Poster Abstracts, Training
by Dave Clements 11 Jan '17

11 Jan '17

Hello all, The Galaxy Australasia Meeting <https://www.embl-abr.org.au/game2017/> will bring together biomedical researchers, bioinformaticians, infrastructure providers, and data producers from across Australia and Asia. GAMe 2017 will be held 3-9 February at the University of Melbourne, in Melbourne, Australia. The schedule of events is: 3 Feb Friday: Researcher Training Day <https://www.embl-abr.org.au/game2017/training-day/>: 4 Feb Saturday: Conference Day 1: BIO Day <https://www.embl-abr.org.au/game2017/conference/#bio> 5 Feb Sunday: Conference Day 2: INFO Day <https://www.embl-abr.org.au/game2017/conference/#info> 6-9 Feb Mon-Thu: Galaxy Administrator Training <https://www.embl-abr.org.au/game2017/training-for-admin-workshop/> You can register <https://www.embl-abr.org.au/game2017/registration/> to attend any combination of these events. (Details on each event are below.) *The Conference is still accepting poster submissions <https://www.embl-abr.org.au/game2017/abstracts/>.* This is a great opportunity to share your work with other researchers facing the challenges of data intensive biology. *On-time registration <https://www.embl-abr.org.au/game2017/registration/> ends 27 January*, and registering now avoids the ~ 80% cost increase for late registrations. (Some training sessions may sell out before then, so you are encouraged to register sooner rather than later.) This is a rare opportunity for the data intensive life science research community to gather, and is the first large multi-day Galaxy event to be offered outside of Europe and North America. You are encouraged to join your fellow researchers in sunny and summery Melbourne this February. Thanks, Dave C PS: And please help spread the word by sharing and posting the attached announcement or this email. Follow us: #GAMe_2017, @GalaxyAustralia ---- *Researcher Training Day <https://www.embl-abr.org.au/game2017/training-day/>, 3 February Friday* Researcher Training Day targets life scientists working with Next-Generation Sequencing data, in particular RNA-Seq, RAD-Seq, and microbial genomes. Session instructors are experienced researchers and trainers and are prominent members of both the Galaxy and Australian training communities. If you want to learn how to do NGS analysis without also having to become a systems admin, then this is the event for you. *Conference Day 1: BIO Day <https://www.embl-abr.org.au/game2017/conference/#bio>, 4 February Saturday* *Conference Day 2: INFO Day <https://www.embl-abr.org.au/game2017/conference/#info>, 5 February Sunday* The two day conference is split into BIO and INFO days. Both days will feature keynotes by prominent community members <https://www.embl-abr.org.au/game2017/conference/#keynotespeakers> James Taylor and Björn Grüning, as well as accepted and invited talks, posters, panels, and birds-of-a-feather and other networking opportunities. Speakers from Australia, Japan, India, the United States, Germany, and Canada are on the program. If you are performing, enabling or supporting data-intensive biology then this meeting will be time well spent. *Galaxy Administrator Training <https://www.embl-abr.org.au/game2017/training-for-admin-workshop/>, 6-9 February Monday-Thursday* This 4-day workshop will be intensive and hands-on, and taught by experienced instructors from the Genomics Virtual Lab, Galaxy Project, and Galaxy Freiburg teams. Participants will learn how to install, configure, customize, and extend their own Galaxy servers. Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community. This is only the second time this workshop has been offered. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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nginx 502
by pieter coussement 11 Jan '17

11 Jan '17

hi, In installed galaxy locally on debian. I'm using nginx as webserver. However now and then I get a 502 bad gateway. refreshen fix it immediatly, but it doesn't really make it practically... This is the nginx.conf file I'm now using. Any help, tips, or suggestions are really welcome! best regards, pieter ----------------------------------------------------------------------------------- /user www-data; worker_processes 4; pid /run/nginx.pid; events { worker_connections 768; # multi_accept on; } http { # https://www.datadoghq.com/blog/nginx-502-bad-gateway-errors-php-fpm/ fastcgi_buffers 8 16k; fastcgi_buffer_size 32k; fastcgi_connect_timeout 300; fastcgi_send_timeout 300; fastcgi_read_timeout 300; ## # Basic Settings ## sendfile on; tcp_nopush on; tcp_nodelay on; keepalive_timeout 65; types_hash_max_size 2048; # server_tokens off; # server_names_hash_bucket_size 64; # server_name_in_redirect off; include /etc/nginx/mime.types; default_type application/octet-stream; ## # SSL Settings ## ssl_protocols TLSv1 TLSv1.1 TLSv1.2; # Dropping SSLv3, ref: POODLE ssl_prefer_server_ciphers on; ## # Logging Settings ## access_log /var/log/nginx/access.log; error_log /var/log/nginx/error.log; ## # Gzip Settings ## gzip on; #gzip_disable "msie6"; gzip_vary on; gzip_proxied any; gzip_comp_level 4; gzip_disable "MSIE [1-6].(?!.*SV1)"; gzip_buffers 16 8k; gzip_types text/plain text/css application/x-javascript text/xml application/xml text/javascript application/json application/javascript; gzip_http_version 1.1; # gzip_types text/plain text/css application/json application/javascript text/xml application/xml application/xml+rss text/javascript; ## # Virtual Host Configs ## include /etc/nginx/conf.d/*.conf; #include /etc/nginx/sites-enabled/*; ## # Galaxy ## upstream galaxy_app { server localhost:8080; } proxy_next_upstream off; server { client_max_body_size 10G; # ... other server stuff ... location / { proxy_pass http://galaxy_app; proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; } location /static { alias /home/galaxy/Software/galaxy/static; expires 24h; } location /static/style { alias /home/galaxy/Software/galaxy/static/style/blue; expires 24h; } location /static/scripts { alias /home/galaxy/Software/galaxy/static/scripts; } location /favicon.ico { alias /home/galaxy/Software/galaxy/static/favicon.ico; } location /robots.txt { alias /home/galaxy/Software/galaxy/static/robots.txt; } # serve static content for visualization and interactive environment plugins location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ { alias /home/galaxy/Software/galaxy/config/plugins/$plug_type/$vis_name/static/$static_file; } location /_x_accel_redirect/ { internal; alias /; } } } /---------------------------------------------------------

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Fwd: Job: CaliforniaStateU_SanMarcos.PopGenetProgrammer
by Dave Clements 10 Jan '17

10 Jan '17

Hi All, Cross posting this opening from EvolDir. This opening was also linked to from the January newsletter. Please forward this on to anyone you know who may be looking for a position. Thanks, Dave C ---------- Forwarded message ---------- From: <evoldir(a)evol.biology.mcmaster.ca> Date: Mon, Jan 9, 2017 at 11:20 PM Subject: Job: CaliforniaStateU_SanMarcos.PopGenetProgrammer To: clementsgalaxy(a)gmail.com Job Description: The Sethuraman lab of population genetics at California State University San Marcos is looking to hire a scientific research programmer. Primary responsibility will be to assist in development of a model-based population genomics pipeline, and development of a graphical front-end to be hosted in the Galaxy Project platform. This position is funded by an NSF grant to Dr. Arun Sethuraman (CSU San Marcos - www.arunsethuraman.weebly.com) and Dr. Jody Hey (Temple University - https://bio.cst.temple.edu/~hey/) and will have ample opportunities for collaborative development of statistical and evolutionary genetic applications across both labs. The position will be based out of CSUSM (San Marcos, California). This work requires experience in C/C++, Perl/Python/Shell across Unix and Windows platforms. Experience with development of applications for the Galaxy Project is desired. Experience with software programming best practices, including test automation (e.x. travis-ci, jenkins.io) and task management (e.x. Jira, waffle.io) will be an added plus. The position is funded for three years, with possibilities for continued funding. The programmer/postdoc will report directly to both PI's and also have the opportunity to train and mentor graduate and undergraduate students (2-3 per year) in scientific programming and software development. Please contact Arun (asethuraman(a)csusm.edu) with any questions regarding the position. Qualifications: A Master's degree in computer science or bioinformatics with extensive experience in scientific programming is required. Candidates with a PhD in computational biology or bioinformatics, or some allied field will also be considered. University Auxiliary and Research Services Corporation (UARSC) was founded in 1990 as a 501(c) 3 public, nonprofit corporation to support the mission of Cal State San Marcos, the 20th campus in the California State University system. CSUSM is a recipient of the Chronicle's 2014 Great College to work for. UARSC offers an excellent benefits package which includes medical, dental, vision, retirement plan, life and long term disability insurance, paid holidays, and generous vacation and paid time off leave benefits. For more information about UARSC, visit our website at www.csusm.edu/uarsc. "JEANNE CLERY ACT AND CAMPUS FIRE SAFETY RIGHT-TO-KNOW LAW" NOTIFCATION - See Police Department's website located at:http://www.csusm.edu/police/Clery.pdf Application Procedure: Please apply by clicking "Apply" on this page, and be sure to submit a cover letter and resume along with your online employment application. UARSC is an Equal Opportunity Employer and does not discriminate against persons on the basis of race, color, creed, religion, ancestry, sex, gender, gender identity, gender expression, genetic information, pregnancy, sexual orientation, age, medical condition, military service, veteran's status, marital status, national origin, physical or mental disability, or any other status protected by federal, state or local laws. For questions or if you experience any difficulties with the online application process, please contact UARSC Human Resources at (760) 750-4700. -- Thank you! Arun Arun Sethuraman, PhD Assistant Professor Department of Biological Sciences California State University San Marcos http://arunsethuraman.weebly.com/ Arun Sethuraman <asethuraman(a)csusm.edu> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Wrapper for ballgown
by Dueck, Anne 06 Jan '17

06 Jan '17

Hi everyone, I was wondering if a wrapper for the ballgown tool is under progress, since the package is out there for quite some time? I would appreciate it a lot. Or can you already do some stuff with the package (sorry for this naive question)? Best, Anne

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Dataset Cleanup
by McCully, Dwayne (NIH/NIAMS) [C] 05 Jan '17

05 Jan '17

Hello Everyone, I have datasets that go back over a year in the files/000 directory but running the following script does not delete the datasets. Also, my account says I have 59 GB used and can't figure out where it's getting that number. I have almost everything deleted in my Galaxy account. galaxy_clean.sh #!/bin/sh -x /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_userless_histories.sh /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_histories.sh /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_libraries.sh /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_folders.sh /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_datasets.sh /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_datasets.sh Exit Any information on this issue would be appreciated. Dwayne

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