galaxy-user October 2012

galaxy-user@lists.galaxyproject.org

63 participants
82 discussions

Re: [galaxy-user] Galaxy in cloud (not Amazon)
by Enis Afgan 04 Oct '12

04 Oct '12

Hi Anatoliy, If you're going to keep that cluster alive continuously, just set it up as per the page whose link you provided and you should be ok. If you plan on having multiple users have their own cloud clusters with Galaxy, you'll probably want to do what I suggested in my previous email. Good luck, Enis On Thu, Oct 4, 2012 at 6:10 PM, Anatoliy Pandorin <pandorinpan(a)gmail.com>wrote: > Hi. > Thanks for your help! > > At the moment, we have organized a system like this: > In the cloud OpenStack running several virtual machines (on them built > virtual cluster torqui (with scheduler maui)) and the Galaxy set for > cluster(http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster). > > We need Galaxy for large biological data quickly (faster than a stand > alone machine). > > Maybe we do not understand something? > > Best regards, > Anatoly > > 2012/10/3 Enis Afgan <eafgan(a)emory.edu> > >> Yes there is, the setup is just not documented very well at this point... >> >> Also, are you familiar with the cloud concepts or just looking to use >> Galaxy? >> >> The basic approach is to setup a CloudMan (usecloudman.org) machine >> image on the local cloud (using the image building process from >> https://github.com/chapmanb/cloudbiolinux is the recommended method). >> Install Galaxy as well as all of its tools, dependencies, and reference >> data on the appropriate block storage volumes and turn those into snapshots >> (see this paper for the architecture overview >> http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full and then >> Galaxy's wiki (http://wiki.g2.bx.psu.edu/Admin) for the details on how >> to set everything up). Beyond that, it's a matter of making sure it all >> works as desired on your setup. You'll probably also want to use a version >> of the code similar to https://github.com/chapmanb/biocloudcentral to >> launch instances because for the non-amazon case, the user data ( >> http://wiki.g2.bx.psu.edu/CloudMan/UserData) required by an instance is >> a bit tedious to compose by hand (the user data link just explains what the >> user data is but the full set of user data fields required for non-amazon >> clouds is not yet documented - I'll do that soon). >> >> Hope this helps. I'm also CCing the galaxy-dev mailing list because >> others may be interested in this topic as well. >> Enis >> >> On Tue, Oct 2, 2012 at 9:37 PM, <pandorinpan(a)gmail.com> wrote: >> >>> Hi Enis! >>> In our institute we process biological data. And we have cloud, based on >>> OpenStack. >>> We want to use the Galaxy in the cloud (OpenStack). Are there any >>> solutions for this? (or just Amazon) >>> >>> Thank you so much for the Galaxy! :) And sorry for my English. >>> >> >> >

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GeneTrack server error
by Doo Yang 03 Oct '12

03 Oct '12

Hi, I can't connect the GeneTrack server. This is the error message. I tried this a couple times in different days but keeps failing. Firefox can't establish a connection to the server at genetrack.g2.bx.psu.edu. Thank you,

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Performing operations on tab delimited text files
by Lanelle Oni Edwards 03 Oct '12

03 Oct '12

Hi, My name is Lanelle Edwards. I am a new galaxy user. I uploaded a tab delimited text file to my history. However, the first column of the data I imported is solely chromosome number and start and end position (ALL IN ONE COLUMN) in the format chrI:1000000-2000000. My question is: How can I filter out these values into separate columns using galaxy tools? For example: Having a separate column for chromosome number, column for start position, column for end position. I would really appreciate the help. Thanks, Lanelle Edwards Lab Manger University of Maryland

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blast tools on free public server
by John DeFilippo 03 Oct '12

03 Oct '12

We're using the free public Galaxy server (main.g2.bx. psu.edu). We uploaded a genome FASTA sequence via ftp, and want to do BLAST searches (e.g., tblastn) against protein sequences that we've also uploaded to Galaxy, as well as on NCBI. BLAST tools don't show in the tools column, or when entered in the search box. Google searches on 'BLAST in Galaxy' bring up pages on 'wrappers' and xml, and we're but humble biologists. Can anyone please explain (simply, presuming no knowledge of wrappers, perl, python, java, scripts, xml, etc. on our part) how we can do this? Thank you. John D

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Cannot find upload options
by Matina Fragkogianni 03 Oct '12

03 Oct '12

Hello, I have an instance of Galaxy locally and I'm trying to upload a dataset. I have administrator privileges and I have already created a data library. The problem is that I want to upload a directory of files into Galaxy but in the drop-down menu (Upload option:) I have only two options 1) upload files (where i can upload only one file at a time) 2) import dataset from current history. I don't have the other options show on the wiki. Do you have any idea what the problem might be? I've downloaded the latest version as instructed using this command. ( hg clone https://bitbucket.org/galaxy/galaxy-dist/) Kind Regards, Matina

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Installing Galaxy on SGE Cluster - Questions
by greg 03 Oct '12

03 Oct '12

Hi guys, I'm following the instructions here to install Galaxy on our SGE cluster. http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster (I'm aiming for the unified install) Here are a couple of questions I'm hoping someone could clear up for me: How exactly do I use virtual env to make Galaxy install all the Python libraries there instead of on the system? How will Galaxy know to use the virtualenv to run and to use it for grid jobs? Do I need to install all of the dependencies listed on this page: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies If so what's a good way to make sure they're contained in the galaxy-dist directory and make sure Galaxy and all of the jobs know to find these tools there? Thanks, Greg

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Cuffdiff no without replicates
by i b 03 Oct '12

03 Oct '12

Dear all, how reliable is running Cuffdiff without replicates? e.g.one samples agains another one? Is it statistically makign any difference when using replicates? Thanks, ib

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Galaxy download
by Lizex Husselmann 02 Oct '12

02 Oct '12

Hi all I downloaded galaxy om my Mac OS 10.6.8 and have followed the following steps: Install Galaxy on MacBook Pro OS10.7.4 (08-10-2012) • Install Mercurial http://mercurial.selenic.com/wiki/ • Open Applications/Utilities/Terminal.app • Confirm Mercurial installation by pasting in "hg version", no quotes and hit return response = version 2.3+20120807 • Check Python version by pasting in "python -V", no quotes and hit return response = Python 2.7.1 • Go to your home directory by pasting in "cd", no quotes and hit return • Get Galaxy by pasting in "hg clone http://bitbucket.org/galaxy/galaxy-dist/", no quotes and hit return • Go to the Galaxy directory by pasting in "cd galaxy-dist", no quotes and hit return • Start up Galaxy by pasting in "sh run.sh", no quotes and hit return • Open web browser and paste in “http://localhost:8080”, no quotes and hit return I started galaxy by pasting sh run.sh and it fetched everything and updated whats needed. Upon pasting http://localhost:8080 in my browser GoogleChrome and Safari respectively, it didn't work. I even changed the host setting in the universe_wsgi.ini to 0.0.0.0 and still didn't open. Any suggestions? Kind regards Lizex Husselmann This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:Servicedesk@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 000 604 Fax number : 0800 00 7788 Email address : arc(a)tip-offs.com Please Call me : 32840 Website: www.tip-offs.com For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.

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FTP Upload Error
by Amanda Jones 01 Oct '12

01 Oct '12

I'm having trouble uploading via FTP to my Galaxy account. I've been receiving the following error message: 503 Sorry, the maximum number of clients(3) for this user are already connected. I've ensured that I'm only using a single connection to upload. Any clue what's going on? I still have available space in my Galaxy account for the upload and I've previously uploaded similarly sized files with no problems.

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October 2012 Galaxy Update
by Dave Clements 01 Oct '12

01 Oct '12

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galaxy-user October 2012