March 2011 - galaxy-user - lists.galaxyproject.org

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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Problems with the Groomer
by Felix Hammer 10 Mar '11

10 Mar '11

Hi, I'm experiencing some strange problems with the fastq groomer. Trying to groom my files I get the following error: "Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 37, in if __name__ == "__main__": main() File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 18, in main for read_count, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 452, in __iter__ yield self.next() File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 448, in next rval.assert_sequence_quality_lengths() File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 142, in assert_sequence_quality_lengths assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len ) AssertionError: Invalid FASTQ file: quality score length (63) does not match sequence length (36)" I've double checked the file and it should be ok. Any ideas? thx, Felix

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Import data in RGenetics
by BAULANDE Sylvain 211527 Partnerchip 10 Mar '11

10 Mar '11

dear Galaxy users, I would like to import genotyping data in Rgenetics and I can't succeed. I have ped file and map file, I try to import them in lped format but it didn't work ... Anybody with experience can help me to solve this issue ? Many thanks in advance, Best regards, Sylvain

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Fwd: Question about FTP
by Cathy Riemer 10 Mar '11

10 Mar '11

----- Forwarded message from Noushin Ghaffari <noushin.ghaffari(a)gmail.com> ----- Date: Mon, 7 Mar 2011 09:09:13 -0600 From: Noushin Ghaffari <noushin.ghaffari(a)gmail.com> To: dbadmin(a)bio.cse.psu.edu Subject: Question about FTP Dear Galaxy team, Firstly, thank you very much for the great tools. I am working on a large dataset and need to upload it to Galaxy via FTP. I used ftp://main.g2.bx.psu.edu but I cannot login. I used my email, my public name on Galaxy and just simple my name, but none of them worked. Can you please help me to know how can I login to upload my file? Here is my inofrmation: email: noushin.ghaffari(a)gmail.com public name: me-on-galaxy I appreciate you help and time in advance. Noushin ----- End forwarded message -----

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EMBOSS programs with graphical output(s)
by Martin Senger 09 Mar '11

09 Mar '11

Hi, I am new to Galaxy (but not to EMBOSS :-)) - so I may be doing something stupid. Sorry if I do. I am referring to my own local Galaxy installation. 1) I noticed that most of the emboss graphical programs (e.g. plotorf) are executed from/by the perl interpreter, e.g.: perl /home/galaxy/galaxy-dist/tools/emboss_5/ emboss_single_outputfile_wrapper.pl plotorf -sequence ... These programs are working fine. 2) There are few other programs that could produce a graphical output (freak, hmoment, iep) but they don't because the toggle "-plot" is not used in their command line. Therefore, strictly speaking, they are also working fine (producing tables instead of graphs). 3) But there are two programs, prettyplot and pepnet, that are called without any wrapper (no perl interpreter), e.g. pepnet -sequence ... and they produce graph (as PNG), indeed, but this graphical result is not shown in Galaxy. Instead, I am getting there an image showing just the text of a URL (attached). And metadata/report on this result says: 114: prettyplot on data 1 empty format: png, database: ? Info: Created /home/galaxy/galaxy-dist/database/files/000/dataset_116.dat.1.png I do not know why there is an "empty" remark - because the PNG file is created, and it is a PNG file, it is just not shown in the Galaxy. I wonder what I have wrongly configured...? Thanks for any help, Martin -- Martin Senger email: martin.senger@gmail.com,martin.senger@kaust.edu.sa skype: martinsenger

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