- galaxy-user - lists.galaxyproject.org

Galaxy on Cloud not recognizing .txt files as fastq
by karlerhard＠berkeley.edu 16 Mar '11

16 Mar '11

Hello, I have been able to get Galaxy to instantiate on our Cloud account, and would like to use the NGS tools to trim and map Illumina libraries. However, when I tried to import .txt files (the data contained in these files are in fastq format) located in an S3 bucket, Galaxy did not recognize them as fastq data. I tried to import the files via the URL of the S3 bucket, and Galaxy just imported the actual name of the URL rather than the file itself. Do I need to change the extension of these .txt files to .fastq? Or have I gotten something wrong with respect to the location of the data in the S3 bucket? thanks for any help! karl

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Postdoc position
by Abderrahman Khila, Dr 15 Mar '11

15 Mar '11

Dear Galaxy users, I am hoping if you could please take note and distribute the attached Postdoc ad among people who might be interested. My lab is looking for someone who can lead a genome/transcriptome assembly and annotation project. The candidate will also have the possibility of combining their Bioinfo skill with the lab’s expertise in studying gene function and evolution. Thank you in advance for your help. Best whishes. A Khila ------ Group Leader Institute of functional genomics Lyon, France

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Error on Indel Analysis Tool
by Evan Schwab 15 Mar '11

15 Mar '11

Hi, I am receiving the following error when I try to run the Indel Analysis tool on a sam file. I kept the Frequency threshold at the default 0.015. Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py", line 227, in if __name__=="__main__": __main__() File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py", line 84, in __main__ add_to_mis_matches( mis_matches[ chrom ], pos, bases ) File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py", line 34, in add_to_mis_matches mis_matches[ pos + j ] = { base: 1 } MemoryError Prior to that I tried with Frequency threshold 0.0 and it ran for days on end without any results. And I've tried Frequency threshold of 0.10 and it gave and error that said "Killed" with no explaination. Is there an error with the tool? Thanks Evan -- Evan Schwab Research Associate Megason Lab Department of Systems Biology Harvard Medical School 200 Longwood Ave Boston, MA 02115 908-938-3779

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library features
by Belinda M. Giardine 15 Mar '11

15 Mar '11

I have been working with the libraries and found some features that would make things much easier. Sometimes files get loaded into the wrong folder, it would be nice to be able to move the file to another folder rather than delete and reload it. Also the option of importing data into the library from a history is not available when updating a file. The work around is to load the new and delete the old, but you lose the history of the file changes that way. Thanks, Belinda

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Export data to filesystem
by James Lindsay 15 Mar '11

15 Mar '11

Hello, I was wondering if there was a way to export a dataset to the file system? Basically I think it would be advantageous if someone could copy a dataset to an "export" folder, they could then FTP this data away or work with it locally? Thanks for the help, James

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Re: [galaxy-user] local directory
by Peter Cock 12 Mar '11

12 Mar '11

On Fri, Mar 11, 2011 at 10:07 PM, Albert Ayoub <albert.ayoub(a)yale.edu> wrote: > I installed Galaxy on my own linux machine. I would like to perform analysis > on local RNAseq files since they are too big to upload. How do we add files > from a local directory or a network share? > Providing you are a Galaxy admin, and the import from file system feature is enabled in universe.ini then you can do this as a shared data library. See e.g. https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFil… https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibrarySecur… Peter

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Re: [galaxy-user] integrating external Data Sources while running behind a firewall
by Jelle Scholtalbers 12 Mar '11

12 Mar '11

Hi Martin, Your galaxy instance does not have to be accessible from outside. The GALAXY_URL is send to the external datasource to create a new url that your browser understands and that galaxy will use to retrieve the data prepared by the service. E.g. http://localhost/galaxy/tool_id=1?url=http://externaldata/dat1.txt. You only have to make sure that galaxy is able to reach the external service. Cheers, Jelle On Mar 12, 2011 1:08 PM, "Martin Senger" <martin.senger(a)gmail.com> wrote:

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integrating external Data Sources while running behind a firewall
by Martin Senger 12 Mar '11

12 Mar '11

Hi, I am not sure if I understand correctly how the external data sources (i.e. BioMart) are integrated into Galaxy. However, I believe that the Galaxy sends an HTTP request to the external data source with the parameter GALAXY_URL - and this URL is used later by the external data source to send parameters for a subsequent request resubmission. Without going to further details (about sync and async method), it seems to me that in any case the URL given in GALAXY_URL must be a publicly available URL (available from/by the external source). 1) But what if I am running my own Galaxy behind a firewall that does not allow access from the outside? 2) If I cannot make our firewall open, is there a way (perhaps in the Galaxy configuration) to change the host name that Galaxy is using when creating its GALAXY_URL parameter? That would allow me have a "third-party" URL where Galaxy and external data sources can communicate together. Many thanks for any help, Martin -- Martin Senger email: martin.senger@gmail.com,martin.senger@kaust.edu.sa skype: martinsenger

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local directory
by Albert Ayoub 11 Mar '11

11 Mar '11

I installed Galaxy on my own linux machine. I would like to perform analysis on local RNAseq files since they are too big to upload. How do we add files from a local directory or a network share? A L B E R T

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Cleaning of fastq files
by Felix Hammer 10 Mar '11

10 Mar '11

Hi, is there a way to clean fastq files (filter Poly-A etc.) with Galaxy? Haven't found anything so far. Also if you generally know good tools plz answer. Have seen lots of stuff for fasta and qual files but not for fastq. Thx, Felix

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