- galaxy-dev - lists.galaxyproject.org

using nginx instead of paste as Galaxy web server
by Dean Snyder 02 Nov '11

02 Nov '11

I switched from using the default Python Paste web server for my local Galaxy installation to nginx. I have verified that it works fine so far, but shouldn't the following option in the universe_wsgi.ini file be changed? (I don't see anything in the documentation about this.) # The internal HTTP server to use. Currently only Paste is provided. This # option is required. use = egg:Paste#http Dean A. Snyder Senior Programmer/Analyst Johns Hopkins University, School of Medicine Center for Inherited Disease Research (CIDR) 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 cell:717 668-3048 office:410-550-4629 www.cidr.jhmi.edu

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Re: [galaxy-dev] [galaxy-user] Cannot get rid of custom build error
by Jeremy Goecks 02 Nov '11

02 Nov '11

Hi Jim, You'll need to update your datatypes_conf.xml file to get custom builds + converters to work. This file is located in the root of your galaxy directory. If you haven't modified your datatypes_conf.xml file previously, you can just copy datatypes_conf.xml.sample to datatypes_conf.xml If you have modifed this file, please add the following lines to your datatypes_conf.xml: (a) <converter file="fasta_to_2bit.xml" target_datatype="twobit"/> <converter file="fasta_to_len.xml" target_datatype="len"/> to the fasta definition and (b) <converter file="len_to_linecount.xml" target_datatype="linecount"/> to the len definition See datatypes_conf.xml.sample for examples. Also, you'll need to download and add the UCSC program fastaToTwoBit to your path as well. You can find UCSC executables here: hgwdev.cse.ucsc.edu/~kent/exe/ Good luck, J. > Hello, > > I've tried to create a custom build (starting from the trackster page) > and clearly made some mistake. I get a NoConverterException error > which is almost certainly my fault putting something wrong in. > However, now the Custom Builds page shows this error and I cannot make > it go away. > > I have a local install, have killed and restarted, logged in and out, > but still this error stays. I cannot try to enter another custom build > because there is nothing on the page except this error. Does anyone > kow how to get rid of this? Any help in getting around this error are > appreciated. > > Jim > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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Providing Data to Galaxy Users
by Ostell, Jim (NIH/NLM/NCBI) [E] 02 Nov '11

02 Nov '11

Hello Galaxy Folks, NCBI has received a few requests to provide a mechanism for people browsing the NCBI databases to download the data they have selected into Galaxy, so we are looking into it. I know some other sites have done this, it looks like through a URL based callback mechanism. However, I know things can change over time, and I'd like to be sure that we are assessing an approach that reflects your current best thinking, whether it turns out to be something well established you are happy with, or if you might be considering moving toward something new, we'd like you to tell us what you think would work best for your users in your environment. If you can just point me at a URL with the appropriate documentation, that's great. If you'd prefer to dialog a little, we're happy to talk. If there is a particular person we should be talking to, let me know. Thanks for your help. Regards, Jim Ostell James M. Ostell, Ph.D. Chief, Information Engineering Branch National Center for Biotechnology Information, NLM, NIH Bldg 45, Rm 5AN.44A 45 Center Drive Bethesda, MD 20892-6510

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data set import into current history
by Oren Livne 02 Nov '11

02 Nov '11

Dear All, Is there an API call for importing data sets into the current history (or a new history)? This feature exists in the web UI. Thanks so much, Oren

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Appropriate method of coalescing tool output (not workflow)
by Jesse Erdmann 01 Nov '11

01 Nov '11

I have an in-house Perl tool that generates a double digit number of outputs that we'd like the user to have access to, but don't necessarily need to be in the history. A complicating factor is that the exact number is determined at run time as user input can add any number of outputs that can't be determined in the scope of the tools' XML processing. Ideally, the end result would be that executing the tool would produce a single output in the history with the other files either being hidden or in the extra_files path. The visible file should be an HTML file that can be used to describe and link to the other outputs as well as providing the option to either unhide or add the hidden outputs to the history for use in subsequent analysis. I've looked at composite datatypes, but as far as I can tell the documentation and examples don't cover how to produce a composite datatype with a variable number of outputs. I briefly tried to use the deprecated <code> tag to iterate over the results with the other outputs added as hidden extra files to the index after execution, but wasn't really excited about using a deprecated feature and couldn't get it working quickly, regardless. Any other suggestions? -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123

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Running galaxy on external hard drive
by Alessia D 01 Nov '11

01 Nov '11

Hi, I am very new to Galaxy and so far have only used the online interface. However, I have an old Unix-running computer and I was hoping to run Galaxy as a local instance. However, the computer has a very small hard drive, that is already half full, so I was wondering if there is any way I can run Galaxy by installing it on an external hard drive. I tried already, and was able to install it properly and connect, but I get errors when I try to upload data. Any help would be greatly appreciated. I don't have a lot of experience with Unix systems, so it might be something easy to solve or impossible to do, I have no idea. Thanks! Alessia

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Can I contribute my Chinese locale files to the galaxy?
by Hanfei Sun 01 Nov '11

01 Nov '11

Hi, all I'm from China and was interested in the i18n of galaxy. I wrote 4 locale files such as ginga.po/mo and tools.po/mo ,tried them on my server and it worked well. I want to contribute it to the galaxy repository but don't know how to do that because I don't have the permission to push it to bitbucket. Could anyone tell me how to contribute them ? Thanks~ Best wishes, Hanfei Sun

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Upcoming Galaxy Events
by Dave Clements 31 Oct '11

31 Oct '11

Hello all There are several Galaxy related events going on at Cold Spring Harbor Laboratory in November, but if you aren't already registered for those it is now too late to get in. However, there are several deadlines in November and events in the coming months. See the Events<http://wiki.g2.bx.psu.edu/Events>page ( http://wiki.g2.bx.psu.edu/Events) for a full listing of upcoming events. If you have a Galaxy related event please send it to outreach(a)galaxyproject.organd we will help you get the word out. Date Topic/Event Venue/Location Contact November 2-5 Best practices for variant discovery through Galaxy: Oscillating evolution within dual coding genes <http://meetings.cshl.edu/meetings/info11.shtml> Genome Informatics 2011 <http://meetings.cshl.edu/meetings/info11.shtml>, Cold Spring Harbor, New York, United States Dan Blankenberg <http://wiki.g2.bx.psu.edu/dan> November 8-21 Advanced Sequencing Technologies & Applications Course<http://meetings.cshl.edu/courses/c-seqtech11.shtml> Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> November 9-15 Compuational & Comparative Genomics Course<http://meetings.cshl.edu/courses/c-ecg11.shtml> Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 8-21 2012 2012 Workshop on Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kruml…> Features Galaxy and much more. *Application deadline is November 1.* Český Krumlov, Czech Republic James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 14-18 2012 Galaxy Session @ GMOD Workshop PAG 2012 <http://www.intlpag.org/>, San Diego, California, United States Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> January 17 2012 Reproducible workflows for next generation sequencing analysis<http://www.nowgen.org.uk/facilities/events/event.php?id=30> Nowgen <http://www.nowgen.org.uk/>, University of Manchester<http://www.manchester.ac.uk/>, United Kingdom Tom Hancocks <training(a)nowgen.org.uk> Thanks, Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Integrating a new display tool with bigwig format
by Jeremy Villalobos 31 Oct '11

31 Oct '11

Hello: I am trying to add a display tool to a local galaxy instance. However, I don't understand the scripts used. In the tutorial at: http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20T… The script for "Basic Topics" uses variables that are not traceable. Is there a reference for the "global" variables for galaxy?. I imagine this is like the "global" variables one uses when creating html pages with javascript. Where can I find the log files for galaxy ?. If the scripts don't work, I imagine information about a possible errors must be printed in some log somewhere. Do I need to restart the portal after I perform changes to the display_applications directory and datatypes_conf.xml ? Thanks for any help Jeremy Villalobos

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Re: [galaxy-dev] Importing existing data into Galaxy
by Greg Von Kuster 28 Oct '11

28 Oct '11

The files are not touched - metadata is generated for the files, but the content of the files themselves is not changed. On Oct 28, 2011, at 3:21 PM, Oren Livne wrote: > Dear Greg, > Great, thanks! Just one more question: if I uncheck the "copy data files" option, does Galaxy change the original day files in any way when it loads them into a data library (e.g., prepend them with some metadata header), or does it leave them intact and stores the metadata separately? > Thanks, > Oren > > On 10/28/2011 1:44 PM, Greg Von Kuster wrote: >> Hello Oren, >> >> We use a sort of informal approach to implementing new Galaxy API features (they're implemented when the need arises), so unfortunately it doesn't look like the features you are looking for exist yet. If you'd like to contribute them, the community would certainly appreciate it! >> >> Greg Von Kuster >> >> On Oct 28, 2011, at 12:45 PM, Oren Livne wrote: >> >>> Dear Greg, >>> >>> Thank you so much, this is exactly what I need. I will use the API access (scripts/api/*.py) to create the new data library. I have two more questions: >>> - Is there an API function for deleting a library? >>> - Is there an API function to make a library accessible only to the user whose API key is passed in? >>> >>> Oren >>> >>> On 10/27/2011 7:55 PM, Greg Von Kuster wrote: >>>> Oren, >>>> >>>> The best way to do this would be to use galaxy data libraries, uploading files from file system paths and not copying the files into the Galaxy file location. >>>> >>>> The following provides all of the details about data libraries: >>>> >>>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries >>>> >>>> >>>> The following provides specific details about the various options for uploading files to data libraries. >>>> >>>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files >>>> >>>> Let us know if you encounter any issues. >>>> >>>> Greg Von Kuster >>>> >>>> >>>> On Oct 27, 2011, at 4:31 PM, Oren Livne wrote: >>>> >>>>> Dear All, >>>>> >>>>> We have a large collection of large data files on our shared file system. We would like to make a subset of them available to a galaxy user session (based on user privileges; different subsets for different users). We want to leave files in their original locations and point galaxy to their paths without copying them. What is the best option for implementing this bridge? Remote data source/data library uploaded on the fly/other? >>>>> >>>>> Thanks, >>>>> Oren >>>>> ___________________________________________________________ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> >>>>> http://lists.bx.psu.edu/ >>>> Greg Von Kuster >>>> Galaxy Development Team >>>> greg(a)bx.psu.edu >>>> >>>> >>>> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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