April 2011 - galaxy-dev - lists.galaxyproject.org

substitute or replace a value?
by David Hoover 26 Apr '11

26 Apr '11

Is there a tool for doing a global or column-based substitution in a text or tabular file? For example, replace all instances of the number 2 in a column to a number 1? David Hoover Helix Systems Staff http://helix.nih.gov

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MarkupSafe egg cannot be fetched
by Edward Kirton 25 Apr '11

25 Apr '11

hello, after pulling the latest changes from galaxy-central, i get the following error: WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched $ python scripts/fetch_eggs.py Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched

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DB access and passowrd field
by Bossers, Alex 25 Apr '11

25 Apr '11

Hi All, I have some tools that generate some tabular output. The next step is to aggregate the data for some filtering and analysis. In my view the best way to do by using a DB (MySQL in my case). Tools and cmd line wrappers can easily connect to this DB (another database than galaxy is using of course) when providing the details for access like address:port, username and password. Is there any way to embed a text field for a galaxy tool that is of type password or blinded? Don't want to share user specific login details when sharing histories or galaxy pages.Or is this a bad thing to pursue anyway? Thanks for any directions. Alex

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Re: [galaxy-dev] Could anyone body tell me why our C program do not work in galaxy
by Peter Cock 25 Apr '11

25 Apr '11

2011/4/25 liyanhui607 <liyanhui607(a)163.com>: > Thank you very much! > After I have added it to the path, it can work now. > Best Wishes! > Yan-Hui Li Oh good. Peter P.S. Please keep the mailing list on replies.

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Could anyone body tell me why our C program do not work in galaxy
by liyanhui607 22 Apr '11

22 Apr '11

Dear Sir, We have a program writen in C lanuage. It can run nomally in linux environment. We plan to add it to galaxy, but it did not work. The C file after complie named "shortest-path" The shortest-path.xml is as follow: Could anybody tell me what is wrong ? why it does not work? Thank you very much! Best Wishes! Yan-Hui Li <tool id="shortest_path_1" name="shortest_path"> <command interpreter="C">./shortest_path $infile1 $output </command> <inputs> <param format="text" name="infile1" type="data" label=" expressed_genes_20101024.hprd8_biogrid-2.0.58.adj_matrix.txt "/> </inputs> <outputs> <data format="tabular" name="output" /> </outputs> <tests> <test> <param name="input" value="1"/> <param name="input" value="../GEO_dataset/expressed_genes_u133a.6k_u133p2.8k_20101024.txt"/> <param name="input" value="../ppi/hprd8_biogrid-2.0.58.ppi.txt"/> <output name="out_file1" file="expressed_genes_20101024.hprd8_biogrid-2.0.58.ppi.txt"/> </test> </tests> </tool>

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NLStradamus wrapper (for nuclear localization signals)
by Peter Cock 22 Apr '11

22 Apr '11

Hi all, I just wanted to mention (to avoid duplicate work) that I have a working Galaxy wrapper for NLStradamus v1.6, a tool for prediction of nuclear localization signals (NLSs) from a protein FASTA file. The wrapper does a little reformatting of the output to get a clean tabular file for use in Galaxy. I would release this to the Galaxy Tool Shed now, but the tool's author Alex Nguyen Ba tells me he hopes to have an update released fairly soon which should include a native tabular output - probably with a richer column structure. So rather than having to change the tool output and potentially break workflows, I plan to wait till then. However, if anyone wants the wrapper before then, drop me an email. Regards, Peter References: A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics. 2009 Jun 29;10(1):202. http://www.moseslab.csb.utoronto.ca/NLStradamus

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Galaxy tools' priority level (nice)
by Peter Cock 22 Apr '11

22 Apr '11

Hi all, Our Galaxy is running on a shared server which will sometimes be running other computationally demanding jobs (outside of Galaxy). In some cases I'd like these to have priority, perhaps by having Galaxy run the tool child processes at a nice level of 10 (say). Is there any built in way to control the Unix priority level (e.g. nice or ionice) used to run tasks? I don't see anything on here, but perhaps I'm looking in the wrong place: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScali… Thanks, Peter

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Re: [galaxy-dev] Plotting tools - best output format? PDF, PNG, ... SVG!
by Peter Cock 21 Apr '11

21 Apr '11

On Thu, Apr 21, 2011 at 10:50 AM, Pieter Neerincx <pieter.neerincx(a)gmail.com> wrote: > Hi Peter, > > On Apr 20, 2011, at 5:47 PM, Peter Cock wrote: > >> On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx >> <pieter.neerincx(a)gmail.com> wrote: >>> Hi Peter, >>> >>> On Apr 20, 2011, at 11:07 AM, Peter Cock wrote: >>> >>>> Hi all, >>> >>> ...<cut>... >>> >>>> How about SVG? Don't most of the mainline browsers have >>>> reasonably good SVG support built in (possibly via a plugin)? >>> >>> Yep, SVG support is pretty good nowadays especially in FireFox >>> and Opera. Safari, IE and Chrome have only partial support, but >>> for simple charts without 3D filters it works fine. I've added SVG >>> as a datatype to my Galaxy and this works great. You won't need >>> a plugin; in fact the old Adobe SVG plugin is depreciated already >>> for a few years now and no longer compatible with recent browser >>> versions. >> >> I looked at SVG about a year ago, and was pretty impressed. >> I did run into some issues, particularly with links, and opted to >> use PNG files in the end. Since then we've finally dropped IE6, >> so hopefully SVG would be safe now. >> >> Are your changes to add SVG as a datatype to Galaxy public? >> I'd like to suggest that be merged to the trunk. > > I simply added this line to my datatypes_conf.xml: > > <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/> > > I didn't make a sniffer as I don't have a use case for users > uploading SVGs, so I didn't have to create a Python class and > SVG is just another instance of galaxy.datatypes.images:Image > from a plain vanilla Galaxy. That makes sense if the sniffer is only used on upload. > To make sure the client displays the SVG you may have to add > the SVG mimetype to your web server's config too. Where this > is defined may differ per linux distro. I use apache as a proxy > and had to add > > image/svg+xml svg svgz > > to /etc/mime.types. Thanks for the details - it looks simple enough to add here too. If/when any SVG producing tools are added to Galaxy or the Galaxy Tool Shed, then it would be nice to have this done in the main repository. >>> The nice benefit of SVG in addition to not needing a plugin is >>> that the image can scale with the surrounding text if you zoom >>> in your browser (without loosing resolution). >>> >>> The disadvantage is that although my users know what a PDF >>> file is and can process them for posters/manuscripts, most of >>> them never heard of SVG and get stuck when it doesn't import >>> into PowerPoint et al. :( >> >> Do they cope with PDF? > > Well, they know how to view and print one :). Importing them > directly into PowerPoint and Word is just as problematic though, > so that usually involves opening the PDF in a different program > and copy/paste or exporting to another format. Still a hassle, but > they manage... Getting a PDF into PowerPoint or Word is easy on a Mac ;) But yes, point taken - even though a PDF is easier to work with than an SVG (or a postscript file), it can still be a hassle. Peter

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Access control for galaxy
by Raghuraman Ramamurthy 21 Apr '11

21 Apr '11

Hello, I would first like to thank and appreciate the Galaxy team for their efforts. I want to clone galaxy and host it in my website. In doing so, I want to restrict the users who use galaxy on my website. So, is there any access control module which could be integrated with galaxy, to make it secure and grant access to only a set number of people. Thanks, Raghu

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Sample Tracking: How datasets are transferred from Sequencer to Galaxy
by Joe Cruz 20 Apr '11

20 Apr '11

Hello, I was hoping someone could explain the process of how a dataset is transfered from a configured Sequencer to a Galaxy library within sample tracking. Particularly how RabbitMQ, API keys, transfer_manager_port and enable_sequencer_communication (in universe_wsgi.ini file) work in this process. Your help is greatly appreciated! Thanks Joe A. Cruz

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