November 2013 - galaxy-dev - lists.galaxyproject.org

Active Directory
by Alexander Kurze 28 Nov '13

28 Nov '13

Hi there, I have a server set up of galaxy. I would like to have a system setup where people can login via their active directory name and then use their mounted share drive to download processed data from the galaxy server. I saw that it is possible via apache to login through the AD, but will the AD also mount the share drives? If yes, is there a wrapper that allows to download Galaxy Histories onto the shared drive? Alex

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Active Directory
by Alexander Kurze 28 Nov '13

28 Nov '13

Hi there, I have a server set up of galaxy. I would like to have a system setup where people can login via their active directory name and then use their mounted share drive to download processed data from the galaxy server. I saw that it is possible via apache to login through the AD, but will the AD also mount the share drives? If yes, is there a wrapper that allows to download Galaxy Histories onto the shared drive? Alex -- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX Tel: +44 1865-243-609 Mobile: +44 7962-425-865

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Uploading files from password protected URL's
by Nicolas Cybulski 28 Nov '13

28 Nov '13

Thanks a lot for the answer ! kind regards, Nicolas Cybulski

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Add a tool to galaxy
by sun liang 28 Nov '13

28 Nov '13

hello all, We have a transcript classification tool named CNCI, that published on NAR August 6 2013, and the title of this article is "Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts". The source code is writen by python, and can be download at : http://www.bioinfo.org/software/cnci/ . We would like to add CNCI to galaxy cloudman, and help more researchers in transcriptome analysis community . If have any question please contact me! Looking forward to hearing from you soon. Yours sincerely,

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Dynamic tool loading
by Mikel Egaña Aranguren 27 Nov '13

27 Nov '13

Hi; I have developed a tool generator that performs a SPARQL query (defined by the user) and creates new Galaxy tools depending on result. I have the basic system (i.e. it generates the tool XML files and edits the tool_conf.xml in the "traditional" way) but I would like my tool generator to be a regular Galaxy tool that is able to "inject" the new tools in the Galaxy menu without having to restart Galaxy. Is there an easy way of doing so? I have come across this thread ( http://osdir.com/ml/galaxy-development-source-control/2010-07/msg00094.html) but it is not clear for me: - If this change has been implemented in Galaxy. - If it has been implemented, what should be the output of my tool generator. Thanks Regards -- Mikel Egaña Aranguren, Ph.D. http://mikeleganaaranguren.com

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Library permission page broken
by David Hoover 27 Nov '13

27 Nov '13

After the latest update, the "Manage library permissions" page is broken. The "Roles not associated" boxes are pushed to the left of the frame, and the double arrow buttons are misplaced down the page. This occurs under Safari (5.1.10) and Chrome (31.0.1650.57) on a Mac running OS X 10.6.8. Firefox (25.0.1), however, seems ok.

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Uploading files from password protected URL's
by Nicolas Cybulski 27 Nov '13

27 Nov '13

Hi all, I am trying to upload data from a password protected website (http://ddlab.sci.univr.it/~centrogenomica/huang_no_project/) My stdout is (obviously0 "Enter username for Reserved Area at ddlab.sci.univr.it:") which is kind of normal but not what I wont of course. Is there a way around this problem ? Kind regards, Nicolas Cybulski Galaxy application manager VIB - PSB Gent

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Error while trying to extract DNA
by Alan WiIliams 27 Nov '13

27 Nov '13

Hi, I am new here. I have a interval file with the columns chr,start,end. When I run it I get 10 warnings, 1st is: Unable to fetch the sequence from '172591712' to '3209' for chrom 'chr5'. Skipped 10 invalid lines, 1st is #1, "chr5 172591712 172594921" Which doesn't make sense. Can someone help? Thanks, -- Alan Williams Life is short, art long, opportunity fleeting, experience deceptive, judgement difficult.

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Compressed data files in Galaxy? (e.g. GZIP or BGZF)
by Peter Cock 26 Nov '13

26 Nov '13

Hello all, What is the current status in Galaxy for supporting compressed files? We've talked about this before, for example in addition to FASTQ, many of us have expressed a wish to work with gzipped FASTQ. I understand that some have customized their local Galaxy installations to use gzipped FASTQ as a specific data type - I'm more interested in a general file format neutral solution. Also, I'd like to be able to used BGZF (not just GZIP) because it is better for random access - see for example http://blastedbio.blogspot.com/2011/11/bgzf-blocked-bigger-better-gzip.html - and makes it much easier to break up large datafiles for sharing over a cluster (i.e. it could be exploited in the current Galaxy code for splitting large sequence files). The 11 May 2012 Galaxy Development News Brief http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-May/009757.html mentions tabix indexing - that uses bgzip, so is there something general in place yet to allow tool wrappers to say they accept not just given file formats, but different compressed versions of file formats? Ideally I'd like to be able to write an XML tool description saying a tool produced BGZF compressed tabular data, or GZIP compressed Sanger FASTQ etc. Similarly, I'd like to specify my tool accepts FASTA or gzipped FASTA (including BGZF FASTA). While for older tools if they say they accept only uncompressed FASTA, Galaxy could automatically decompress any compressed FASTA entries in my history on demand. Peter

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Why does check_html only read first 100 lines?
by Robert Davidson 25 Nov '13

25 Nov '13

Hi all, I recently tried uploading an couple of xml files to my local Galaxy installation using the standard ‘Upload File (version 1.1.3)’ tool. For some files this produced the error: The uploaded file contains inappropriate HTML content. Given the files had been created by the same automated code and contained the same tags etc, I couldn't understand why one would produce this error and the other not. Finally tracking down the function check_html() in galaxy-dist/lib/galaxy/datatypes/checkers.py, I discovered that my use of the tag <metabolite> had flagged up as a likely <META > tag and produced the warning/failed upload. The reason this did not happen in every case is that check_html only reads the first 100 lines of the file and depending upon how many samples were in my dataset, my <metabolite> tag could appear before or after this cutoff. I've solved the problem by changing my xml tag names but my question is: a) why does check_html only read up to line 100? b) would it be possible to change the regular expressions in check_html so that e.g. <meta ...> would be found but e.g. <metaxxx ...> would not? Thanks for reading. Rob Dr Robert L Davidson NERC Metabolomics Facility School of Biosciences University of Birmingham Edgbaston, UK

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