- galaxy-dev - lists.galaxyproject.org

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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January 2017 News of the Galaxy: Register now for GAMe 2017!
by Dave Clements 04 Jan '17

04 Jan '17

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wrapper for tool with multiple outputs
by Jochen Bick 04 Jan '17

04 Jan '17

Hi, I have a tool that produces multiple output files a log file, two bam files. (https://github.com/nugentechnologies/nudup) The tool it self provides an option called --out to specify a path to a directory with a prefix that will be added to the output files: --out /tmp/out this will produce 3 files: /tmp/out_dup_log.txt /tmp/out.sorted.dedup.bam /tmp/out.sorted.markdup.bam so my question is if this out prefix will give me problems overwriting next output files coming from this tool? Cheers Jochen

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installation error on venv dependencies.xml
by Bakker, Linda 04 Jan '17

04 Jan '17

Hi All, I posted my question before the holidays but i got not reply. Can someone please point me in the right direction? I am having some problems with my tool dependencies to setup a python venv. Dependencies.xml looks like this: [X] [X][cid:7b48a44d-07dd-4838-8f90-5024d9d22593] When i install my tool from the toolshed, it fails to install the venv dependency with this error message: [X][cid:0f2c174a-5011-423f-9eaf-ef2ed88c353d] I am not sure what the problem exactly seems to be. os.py should be a default python package right or do i need to specify it in the dependencies file? Together with our system administrator, we have been trying to solve the issue, but no luck so far. Is my dependencies.xml file ok? Thanks & a happy new year! with regards , Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker(a)wur.nl<mailto:linda.bakker@wur.nl>

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GalaxyAdmins Online Meetup 15 December
by Dave Clements 04 Jan '17

04 Jan '17

Hello all, The next GalaxyAdmins online meetup <https://new.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_12_15/> is this Thursday, 15 December at [see your local time <http://bit.ly/2h2QOsT>]. The meetup will feature two presentations: - Galaxy Training Materials: Community creation, curation, and use, by Björn Grüning and Bérénice Batut, University of Freiburg - The new Galaxy Hub: Community creation, curation, and use, by Dannon Baker, Johns Hopkins University. The call will last around an hour, and will include discussion. Hope to see you there, Dave C & HAns-Rudolf -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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