galaxy-user September 2009

galaxy-user@lists.galaxyproject.org

24 participants
28 discussions

Synonymous and non-synonymous SNPs
by Timothy Hughes 14 Sep '09

14 Sep '09

Hi, I have been taking a look at Galaxy and playing with it a bit. I have also watched several of the great tutorials. One that was particularly relevant to what I want to do was the one on SNPs. But, in addition to finding out what type of genomic region a SNP lies in e.g. intron or exon, I also want to determine, for SNPs that are in coding regions, whether they are snynonymous or non-synonymous. Is there a way of doing this in Galaxy? I have had a really good hunt in the Tools menus but I can't find anything. Any help much appreciated. Tim. -- Tim Hughes PhD (http://digitised.info) Medical Genetics Department Oslo University Hospital Ullevål Kirkeveien 166 0407 Oslo Norway

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Upload of Large Files
by Hans Vasquez-Gross 10 Sep '09

10 Sep '09

Hello All, We have a local galaxy install at our facility that is running on a VM machine with an allocated memory of 2gigs. I have a user that has been trying to upload a ~6gig fastq file to galaxy for the past couple of days within our same subnet. She tried submitting the upload but the next day it still wasn't finished uploading, so I told her to cancel the upload and try again. The same problem occurred the second day after a day of trying. Should galaxy be able to support an upload of this size? Thanks, -Hans

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create your own importer
by Ido M. Tamir 08 Sep '09

08 Sep '09

http://idotamir.blogspot.com/2009/08/adventures-in-galaxy-pt1.html http://idotamir.blogspot.com/2009/09/adventures-in-galaxy-pt2.html hope this helps. Feel free to ask questions on the blog. best, ido

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new galaxy install hangs
by Ido M. Tamir 08 Sep '09

08 Sep '09

Hi, since two days, when trying a fresh galaxy install it hangs. I don't know if it has to do with my setup or internet connection (fc8, x86_64, Python 2.5.1). hg clone http://bitbucket.org/galaxy/galaxy-central galaxy-central cd galaxy-central after sh setup.sh it stalls at: Creating static/genetrack/plots but after some time it proceeds: One of the python eggs necessary to run Galaxy couldn't be downloaded automatically. You may want to try building it by hand with: python scripts/scramble.py Mako after ./run.sh there is no output for some time, then: Traceback (most recent call last): File "./scripts/paster.py", line 24, in <module> pkg_resources.require( "PasteScript" ) File "/home/tamir/dl/galaxy/lib/galaxy/eggs/__init__.py", line 558, in require if not egg.fetch(): File "/home/tamir/dl/galaxy/lib/galaxy/eggs/__init__.py", line 101, in fetch raise EggNotFetchable( self.name ) galaxy.eggs.EggNotFetchable: PasteScript and this is of course the end of it. best wishes, ido

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When to use metadata or dataset.blurb?
by James Casbon 03 Sep '09

03 Sep '09

So I wanted to add in the number of sequences in a file, which is something that is often requested. My initial thought was to add a tool, which I could do, but then I thought that this was metadata that should probably be added to any record based class. So I then thought that I would find the code that set up the file size information in the history column and copy that, but looking at the source, that goes in the blurb (e.g. sequence.Fasta). So here are my questions: * how can a user see the metadata, as this is distinct to the blurb/peek? * why isn't the file size implemented as a piece of metadata? thanks, James

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use of public server vs local installation
by Jian WJ Wang 01 Sep '09

01 Sep '09

Dear Galaxy team: I was recently introduced to Galaxy framework by my colleagues in Singapore. I am very impressed with it and want to start using it right away. Now the questions are whether I should use the public server or attempt a local installation. I understand this depends on how we intend to use the system. What I would like to get advice from you is the security of using public server. If I setup my login and start using the system for private data, say high throughput sequencing data, who else could possibly see my data without my knowing it? As you know, pharmaceutical companies traditionally have a tendency to setup everything if possible locally. With the recent data explosion, it is becoming more and more unrealistic to maintain internal copies of public tools and data. More importantly, I feel it could be a waste of resource and could introduce unnecessary data provenance problems. From the server maintenance standpoint, how much effort is needed to keep the framework up and running? Do you encourage pharmaceutical companies to use your public server? Have you thought about carving out a section of your server to private users for a fee? I anticipate one or two people to use the server initially for a period of time when we initially get the data and afterwards occasionally use it. I hope to avoid local installation if I possible. Best regards, -Jian _____________________________________________________________ Jian Wang, PhD Informatics Eli Lilly & Co. Phone: 317 655 3496 E-mail: jian.wang(a)lilly.com This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

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headers in tabular datatypes
by James Casbon 01 Sep '09

01 Sep '09

Deaf galaxy-user, So you can have tabular datasets, and you can add a datatype that subclasses tabular and adds column definitions. Is there a way of using tabular data with column headings without defining the datatype, i.e. getting galaxy to recognise that first line is a header and should be used as column titles? thanks, James

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What are the possible computations and what are the commands for "Compute an expression on every row"? Thanks!
by Halfdan Rydbeck 01 Sep '09

01 Sep '09

What are the possible computations and what are the commands for "Compute <http://main.g2.bx.psu.edu/tool_runner?tool_id=Add_a_column1> an expression on every row"? Thanks! Halfdan Rydbeck

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galaxy-user September 2009