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Partial automation for generating those twisty R dependency tool shed installation sequences
by Ross 21 Jan '15

21 Jan '15

This may be helpful for anyone else struggling to get complex nested R package dependency installation from the tool shed sorted out. That whole can of worms. While we have setup_r_packages, the developer still has to figure out the right magical incantation and make sure the tarballs are available. https://wiki.galaxyproject.org/SetUpREnvironment has some notes I've started - contribitions welcome. It has a more or less reusable R script to generate tool_dependencies.xml boilerplate, assuming you set the constant libdir to your local git repository path where those tarballs will be downloaded from. I hope this helps someone! Could make a tool to do this if enough developers want access to it without the pain of managing yet another R script?

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problem with launching Galaxy cloud
by Gurova, Katerina 20 Jan '15

20 Jan '15

Hi, I tried to start using Galaxy today and launched new instance at AWS, but I am getting all the time this error message: [cid:image001.png@01D030C2.9F312090] Please, advise what to do. Thank you, Katerina Katerina Gurova, MD, PhD Assistant Professor Department of Cell Stress Biology Roswell Park Cancer Institute Elm and Carlton Streets Buffalo, NY, 14263 Tel: 716-845-4760 Email: Katerina.gurova(a)roswellpark.org This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

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Problem with Galaxy installation
by FRITSCH Emilie - L. Int 20 Jan '15

20 Jan '15

Dear all, I installed Galaxy last week on our server following the tutorial on Admin/GetGalaxy from the wiki. I had no problem and it was running fine. However, as one of my colleague required the localhost:8080, I had to change the port number. I followed the tutorial on the wiki « Running galaxy in a production environment ». I copied the galaxy.ini.sample, modified the port and also the additional parameters as suggested. Since then, I get an error message stating that "socket.error: [Errno 98] Address already in use ». I checked and the port is free. I copy at the end of this message part of the standard and error output, hoping this could help figuring out what the problem is. Additionally I noticed that there was another warning, right at the beginning, when running the run.sh script: /data/database/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility I have checked on previous messages to see if someone had the same problem but usually it seemed that only changing the port in config/galaxy.ini worked. Thanks a lot in advance, I am newbie and am a bit puzzled on that one, Emilie Starting server in PID 27030. Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 670, in command serve() File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 654, in serve server(app) File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in server_wrapper **context.local_conf) File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1342, in server_runner serve(wsgi_app, **kwargs) File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1291, in serve request_queue_size=request_queue_size) File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1134, in __init__ request_queue_size=request_queue_size) File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1113, in __init__ request_queue_size=request_queue_size) File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 360, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib64/python2.6/SocketServer.py", line 412, in __init__ self.server_bind() File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.6/SocketServer.py", line 423, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use

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Web/Job scaling question
by Josephine Palencia 20 Jan '15

20 Jan '15

Hello, Current setup: : have 1-2 VMs w/ 4-core each, 4GB mem mounting remote lustre shared fs : use remote job submission: cli/ssh : proxied, use remote auth login/logout I'm prepping for a scenario where there will be 60-75 users/students who will simultaneously submit several complete genomics workflows to the single VM (I actually have 3 identical VMs). Full runs can go from 30min to an hour and a half each. I have 1 of the VMs set up with the standalone paste-based with 5 job handler and 5 web server processes. Would this be enough for this scenario? (or 10/10, 20/20, more?). I have the 2nd VM being set up using the uWSGI method. Would it be worth it to proceed with the standalone paste-based or just skip it and exclusively only concentrate on the uWSGI setup (or keep both?). I'd like to automate everything (remote job submissions for full workflows) and just let it (60 test users or so) run for 1 month to check reliability, anticipate problems. I'd appreciate feedback, thoughts from those who have already gone through a similar experience. TIA

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Fasta Datatype Adjustments
by Marco Albuquerque 20 Jan '15

20 Jan '15

Hello Galaxy, I have a small dilemma regarding the fasta datatype. Currently, to my knowledge, the fasta datatype does not specify any metadata. I was curious how I should go about changing the fasta datatype if I wanted to include the .fai and .dict as metadata? Basically I want to avoid unnecessary recreating of the same file done automatically by MuTect. It seems very inefficient to have to produce these files every time a user were to call MuTect in galaxy (I.e. MuTect can't find them, so it makes them itself). I guess my question is, what are the consequences to adjusting the current implementation of the fasta datatype? Will users be able to pull this tool easily? (I.e. When one uploads a tool and that tools uses a different fasta definition, how does galaxy handle this?) Could this new fasta declaration potentially be adapted by galaxy? Should I just define a new mtfasta datatype special for MuTect purposes? Let me know if you have any advice, Marco

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GalaxyAdmins is Back!
by Dave Clements 19 Jan '15

19 Jan '15

... we just don't know exactly when, *yet.* Hi all, Except for a meetup at GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014/BoFs/GalaxyAdmins>, the GalaxyAdmins group <https://wiki.galaxyproject.org/Community/GalaxyAdmins> has been on hiatus for a while. Well, thanks to the efforts of Hans-Rudolf Hotz <https://wiki.galaxyproject.org/HansrudolfHotz> the GalaxyAdmins <https://wiki.galaxyproject.org/GalaxyAdmins> group *is back.* Starting this month, we will resume our bi-monthly conference calls. *Galaxy-Admins* is a discussion group for Galaxy community members who are responsible for large Galaxy installations. In an effort to better serve the global community we will rotate the time of the call in different months to be convenient for different parts of the world. To help us pick the best set of times for the calls, *please take a few minutes and fill out this Doodle poll <http://doodle.com/dq3bexyuihs59h3c>.* It covers every hour in a 72 hour period. *Please don't forget to select the timezone before you start filling it out.* The likely presentation for the January meetup will be a summary of the Galaxy Community Survey last fall, presented by Dave C. The survey covered both Galaxy usage and deployment. The survey results will be published online before the call. Tell us what times work for you <http://doodle.com/dq3bexyuihs59h3c> We are using this survey to pick a set of times for the whole year. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Tool param type "library_data"
by Dooley, Damion 19 Jan '15

19 Jan '15

I just discovered a scant reference to this on the ToolSyntax page, and tracked it down to something that looks like it was introduced around 2011: a "LibraryDatasetToolParameter" http://bitbucket.org/galaxy/galaxy-central/changeset/8553b02ce9ee/ changeset: 8553b02ce9ee user: kanwei date: 2011-07-19 03:56:23 summary: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well. Now I can't quite fathom the syntax around this but it appears to be broken - python error displayed: TypeError: get_initial_value() got an unexpected keyword argument 'history' Which is because in the galaxy code the def get_initial_value( self, trans, context ) function is missing a "history=None" parameter like other types have?! But is this input type essentially discontinued (no other refs to it on the web) or is it supposed to be operational? I was hoping for a tool input that would list a particular libraries datasets, so that I could obtain their file paths for use in my tool. <param name="test" type="library_data" label="test" help="test help"/> <options library="Reference Bins"> </param> Regards, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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galaxyp build for docker
by Evan Bollig PhD 19 Jan '15

19 Jan '15

Hey Bjoern, I'm playing with your docker recipes (https://github.com/bgruening/docker-recipes) today and I've been waiting for the galaxyp image build to complete for about 3 hours. For the majority of that time it has been stuck on RUN install-repository "--url http://testtoolshed.g2.bx.psu.edu/ -o bgruening --name package_openms_latest" What is the typical build time you experience? Any thoughts on how this could have gone wrong? Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Unable to connect galaxy server after upgrade to latest version
by Ping Luo 19 Jan '15

19 Jan '15

I installed the latest galaxy server and started it without any change. The server stared on port 8080 and the log file looks fine. But when I typed http://localhost:8080, I got the error "Unable to connect". I had worked with version 2014_08_11 and had no problem at all. What could have been wrong?

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GCC2015 Training Day Topic Voting is open. Please vote!
by Dave Clements 19 Jan '15

19 Jan '15

Hello all,What topics should be offered at the GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/>? Topics <http://gcc2015.tsl.ac.uk/training-day/> for the GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/> are selected by you, the Galaxy Community. There are nominated topics <http://gcc2015.tsl.ac.uk/training-day/> spanning from basic usage to advanced deployment. No matter what you do with Galaxy, there are topics for you to choose from. Your vote will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes 30 January.* The Training Day schedule, including instructors, will be published before early registration opens in February. *Vote Now <http://gcc2015.tsl.ac.uk/training-day/>* ------------------------------ *About the GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/>:* The 2015 Galaxy Community Conference (GCC2015) <http://gcc2015.tsl.ac.uk/> will start on 6 July with a Training Day <http://gcc2015.tsl.ac.uk/training-day/> featuring parallel tracks, each with several multi-hour workshops. There will be at least one complete track about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances. As always, please let us know if you have any questions. Thanks, The GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers/> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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