March 2010 - galaxy-user - lists.galaxyproject.org

The uploaded file contains inappropriate content
by Erick Antezana 04 Jun '10

04 Jun '10

Hi, It seems there is a (serious) bug while "Adding datasets" via the "Upload directory of files" (with or without copying the data into Galaxy (3545:2590120aed68), i.e. (un)tick the 'No' box) if the files are in ZIP format. Actually the files get erased from the filesystem. In the "information" column, I get: Job error (click name for more info) Then, after clicking on the file name: Information about 2010.fastq.zip Message: Uploaded by: erick(a)mydomain.com Date uploaded: 2010-03-23 Build: ? Miscellaneous information: The uploaded file contains inappropriate content error We have no problems with adding unzipped files... thanks, Erick

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setting environment for sge scripts
by Andreas Kuntzagk 15 Apr '10

15 Apr '10

Hi, I followed the advice for multiple installed python versions to set ~galaxy/galaxy-python/python and set the environment for the galaxy user to have that in the PATH Problem is, when a job is started on GridEngine, it does not use the "-V" flag to inherit the environment. So it runs with a different python version and more important it does not set LD_LIBRARY_PATH and fails for some tools which need some special lib. (libRblas in this case) Where can I fix that? regards, Andreas

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Sending data to GBrowse
by Jelle Scholtalbers 13 Apr '10

13 Apr '10

Hi, I would like to be able to send data to my GBrowse2.0 instance. I have been trying some things based on the Epigraph tool but I can't seem to get it work. Below is a mail from Lincoln that was send to the GBrowse mailinglist about how to send data to GBrowse. If its possible, how should I configure the tool? Cheers, Jelle -------- In version 2.0 it is relatively easy. POST to the GBrowse URL (including the datasource part of the URL) with the following parameters: - action="upload_file" - file=<a multipart/form-encoded file upload> - upload_id=<any numeric id of your choosing> - id=<the id of the user that you are uploading to> Alternatively to providing the "file" argument you can provide a "data" argument with the uploaded data provided directly. The "id" argument indicates the id of the user that you are uploading for. You can get this ID by bookmarking a page -- the "id" parameter records the info. Alternatively, if you don't provide an ID, GBrowse will generate it for you and return the ID in the response cookie, in an argument called "gbrowse_sess". If you have administrator's mode enabled, then you can provide the ID of the administrator and the uploaded file will become part of the public set of tracks. Lincoln

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where are my deleted datasets?
by Erick Antezana 12 Apr '10

12 Apr '10

Hi, I managed to enable the possibility to 'Add datasets' via the 'Upload directory of files' option for non-admin users. It works fine: I can import (as admin and non-admin user) specific datasets into my history (copy and/or no-copy) so that I could launch some tools over them, etc. However, if I delete a specific dataset (as admin) that was imported as non-admin and then login again as non-admin, I can still see the imported datasets in my history pane. Where is actually located the reference to the (deleted) dataset? I was able to find the copied files at .../database/files/000/* , these will be cleaned out (if deleted) by the purge scripts eventually... I am using SQLAlchemy with mysql for the DB connection. cheers, Erick

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Sequence logo
by Erick Antezana 12 Apr '10

12 Apr '10

Hi, is there any Galaxy tool supporting the display of "sequence logos" (http://en.wikipedia.org/wiki/Sequence_logo) ? thanks, Erick

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gz files
by Keith E. Giles 31 Mar '10

31 Mar '10

I apologize for the redundancy, I sent the previous email from the wrong account. I am trying to figure out why I can't upload the .gz compressed files from the broad institute into galaxy. any suggestions?

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uploading gz files
by Keith Giles 31 Mar '10

31 Mar '10

I am unable to load the raw alignment data from the broad institute datasets available from the ucsc downloads section. the data is in the gz format. any suggestions on how to get it uploaded?

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CASAVA in Galaxy
by Glen Otero 30 Mar '10

30 Mar '10

Hello- I'm about to embark on an effort to try and roll Illumina's CASAVA pipeline software--demultiplex.pl, GERALD.pl, run.pl and other scripts, into a local Galaxy install. I'd prefer not to reinvent the wheel, so I'd like to hear from anyone that's already done part or all of what I'm going to attempt. Any advice is greatly appreciated. Alternatively, if this is something that other developers are interested in, maybe it could be considered for a coding sprint during the breakout session at the developers' conference or during one of the BEER sessions? Thanks! Glen

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New feature: reusing datasets / copying datasets to the current history
by Jeremy Goecks 30 Mar '10

30 Mar '10

Hi all, You might know that you can view all your datasets by visiting 'Datasets' under the User menu. There's now a new action that you can take from this view: You can copy any of your datasets to your current history, either individually or in bulk. This feature should make it easier for you to reuse datasets and move datasets between histories as you can search for datasets and then copy them. Let us know if you have questions. Thanks, J.

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Re: [galaxy-user] A question regarding sequence retrieval
by Guruprasad Ananda 30 Mar '10

30 Mar '10

Hi Amit, I was not able to reproduce the issue reported by you. I downloaded the BED file from the website pointed by you, and fetched sequences successfully. I'm sharing my history with you: http://main.g2.bx.psu.edu/u/guru/h/test-for-amit Please make sure that you have the correct BED file, and correct metadata settings (chr,start,end columns and genome build). Also, in future, can you please report your questions/issues to one of our mailing lists: galaxy-user(a)bx.psu.edu, galaxy-bugs(a)bx.psu.edu? Thanks, Guru. On Mar 30, 2010, at 7:43 AM, pande wrote: > Hello GURU, > I am having problems with retrieving the FASTA sequences in the genomic interval that I took from > http://dir.nhlbi.nih.gov/Papers/lmi/epigenomes/hgtcell.aspx for the CTCF binding site. > The sequence file that I am getting is empty. > > Please help. > > warm regards, > Amit. > > > Guruprasad Ananda wrote: >> Hello Amit, >> >> The genomic sequences hosted on Galaxy are from UCSC and according to their convention repeats from RepeatMasker and Tandem Repeats Finder (with a period of 12 or less) are shown in lower case and non-repeating sequence is shown in upper case. >> >> Hope this answers your question. >> Thanks for using Galaxy, >> Guru. >> >> >> On Mar 11, 2010, at 5:02 AM, pande wrote: >> >> >>> Dear Galaxy, >>> I have the results for the sequence retrieval for Insulator regions in the human genome and I am having difficulty in comprehending the upper and lower case associated with my sequences.I know it for sure that they are regions which do not in any way overlap with exons or introns and are that between any 2 genes. >>> I am attaching a small part of the sequence file for you to see and help me. >>> >>> >>> warm regards, >>> Amit. >>> >>>> hg19_chr14_100364027_100364047_+ >>>> >>> AAGGCTTCTAATTTGGGTCT >>> >>>> hg19_chr14_100364319_100364339_+ >>>> >>> TATTTTCCCAGCAGAGGATG >>> >>>> hg19_chr2_21174437_21174468_+ >>>> >>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >>> >>>> hg19_chr19_50965398_50965458_+ >>>> >>> TGTCTCAAGGGATTTAGTCACTTAAAAAAtttttttaattgatttttgat >>> tttttttttt >>> >>>> hg19_chr19_50965141_50965201_+ >>>> >>> ATCCTCTCTCCCCAGGAATCACCTTCAAACCGTTCGAGTATAAGGAGCAT >>> GACTTCCGGA >>> >>>> hg19_chr16_23597358_23597397_+ >>>> >>> acccctcagactcccgagtagctgggattataggcgtgc >>> >>>> hg19_chr11_5269210_5269281_+ >>>> >>> TCTTCCAAAACATCTGTTTCTGAGAAGTCCTGTCCTATAGAGGTCTTTCT >>> TCCCACCGGATTTCTCCTACA >>> >>>> hg19_chr11_5182745_5182816_+ >>>> >>> ggaggaccgtaagggatataaaggttttactgaatactaagagcctgaaa >>> aactgcttggctgatttgact >>> >>>> hg19_chr11_1947003_1947086_+ >>>> >>> CCAGGCCCCCTCACAGCCTTCTGCTATGAGACCCTTGAGGTGCACACAGG >>> CTGGGAGCAGATGGGAGGGCTGGGGTCCCATGC >>> >>>> hg19_chr11_1944457_1944540_+ >>>> >>> GGGCCTCGTCTTTTCCCCGAAGTGTGGCCACATGGTCCTGAGGGGCCTGC >>> AGGTCAGGCTCTGGGTCCTGTCTCTCTGCTTCT >>> >>>> hg19_chr17_38531956_38532012_+ >>>> >>> cctgggctcccacttcggtggcacttgaggagcccttcagcccaccgctg >>> cactgt >>> >>>> hg19_chr17_38531327_38531376_+ >>>> >>> gatggtaacttcccggtggttaggttgttgccatggaaaggggcggtaa >>> >>>> hg19_chr3_10181494_10181542_+ >>>> >>> taattctttcattttttatagagacaggacctcgctatgttgcccagg >>> >>>> hg19_chrX_23982287_23982341_+ >>>> >>> ATTAGTGCATTCTTTTTCAGAAATTTTTTCTGTGCAGATATACAATCTGT >>> ATAC >>> >>>> hg19_chrX_23982417_23982470_+ >>>> >>> TTAATAAACATGTCACTGCtgttgtgggtggggttgcccaggaaacagac >>> tct >>> >>>> hg19_chr11_2112020_2112170_+ >>>> >>> CACCTTGCAGGGTCCCACCAAGACCACTGCAGCCTGGAATTTCCTGCTGA >>> CACTGGACGTAGGAGGCCTGGAGGGCCTGCAGGGGTCAGCCAGCGCCTCC >>> AGGACCCTCACTCAAACCTTGTCCCACGCCTTACCACCTTGCACCTGGTC >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >>> >> >> Guruprasad Ananda >> Graduate Student >> Bioinformatics and Genomics >> The Pennsylvania State University >> >> >> >> >> > Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University

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