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

tool-shed migration - dist version still shown in UI
by Shantanu Pavgi (Campus) 05 Sep '13

05 Sep '13

I have migrated few tools from dist to tool-shed and I am seeing two version select options in the UI. Both option contain same version number though. One of them is linking to dist path (underneath tools directory) and other one is using tool-shed path. The dist path isn't in place after the migration completed so if one selects that version option, then job fails. The tool-shed versioned path is working fine. The migrated tool xml file and integrated tool xml file both contain tool-shed related entries. Appreciate any help on how to fix this issue. Any pointers? -- Thanks, Shantanu [cid:2E575F19-219F-450F-BB27-6D7E63292D3E@bham.rr.com]

1 0

iRODS integration
by Zeeshan Ali Shah 05 Sep '13

05 Sep '13

Hi All, Is there any update on iRods integration in galaxy ? One major concern presented in deployment of Galaxy is that all of the researcher data is access by a user id (linux) running galaxy server. This is typical webserver problem. May be it is some how resolved by iRods or any other better Authn based FS. any suggestion ? -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah

2 4

Trackster: alignment is not showing up as 'squish'
by Joachim Jacob | VIB | 05 Sep '13

05 Sep '13

Hi all, I have a problem that the mappings of an experiment suddenly don't show up anymore in Trackster, only when I choose 'squish' as visualisation format. 'Coverage' and 'dense' provide the expected output. So 'squish' shows nothing. But 'Pack' shows only the names, without the bars. Note: 'squish' and 'pack' used to work. Currently I am on 2013_08_12. Other mappings (from other experiments) show up as expected. The 2 cases side by side in this screenshot (thanks to the scratchbook functionality!): https://dl.dropboxusercontent.com/u/18352887/Selection_151.png Thanks for any help, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

2 2

For constructing workflow of workflows
by patra 05 Sep '13

05 Sep '13

Hi, This is Deblina. I am working as a PhD student in Martin Luther University Wittenberg, Halle, Germany. For a project I want to use Galaxy. I need to construct a master workflow with sub-workflows connected to each other. Is it possible to construct "workflows of workflows" in galaxy? Best Regards, Deblina.

1 0

Mercurial updates not working
by Alistair Chilcott 05 Sep '13

05 Sep '13

Hello all, Mercurial has recently started throwing errors: galaxy@hitmsbhpc1:~/galaxy-dist> hg incoming abort: error: _ssl.c:517: error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol It has previously worked with issues has anyone seen this before? I don't think anything has changed that would have caused this problem but googling error has proved to be unhelpful so far. Regards, Alistair

2 1

Typo in Wiki Page - Purge History and Datasets
by Adam Brenner 04 Sep '13

04 Sep '13

http://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20… > There are 5 scripts included in the Galaxy distribution that > can be used to clean up unwanted histories, libraries and > datasets. There are located in the <<<nwwl(GALAXY_ROOT)>>>/scripts/cleanup_datasets > directory and are named: Should be changed to 6 scripts Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

2 1

about Galaxy
by Jennifer Jackson 04 Sep '13

04 Sep '13

Hello, To use Velvet, a local, cloud, or slipstream Galaxy is needed. Then the tool can be installed from the Tool Shed and used. The screencasts "Introduction to Galaxy ToolShed 1/2/3" walk through the general process when using CloudMan Galaxy: http://vimeo.com/user20484153 http://wiki.galaxyproject.org/Cloud http://wiki.galaxyproject.org/BigPicture/Choices If you need help with set up, or just have more questions about these options, the list is: "galaxy-dev(a)bx.psu.edu" http://wiki.galaxyproject.org/MailingLists Best, Jen Galaxy team On 9/4/13 5:31 AM, Jingjing Peng wrote: > Hi, > Nowadays I am using Galaxy to analyze my data. It is really very good. > But there is sth I cannot work it out by this program. My sequences > were sequenced by Illumina Miseq 2*250bp,paired end method. I want to > assembly this large transcriptom sequences. I didn't find velvet in > this website:https://main.g2.bx.psu.edu/ . > So how can I find it and make this work. I am sorry to trouble you. > Thanks a lot. > > Best wishes, > > Jingjing Peng > -- Jennifer Hillman-Jackson http://galaxyproject.org

1 0

Accessing parameter defined within conditional from option filter
by Peter Briggs 04 Sep '13

04 Sep '13

Hello Galaxy folks I'm building a tool to run the Trimmomatic program, and I've encountered an issue with filtering options from an external .loc file based on the value of a parameter which is defined within a conditional block. The parameter definition looks like this: ... <conditional name="paired_end"> <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" /> <when value="no"> ... Subsequently I try to access the value of "is_paired_end" within a filter tag (to select a subset of items from a .loc file), using "ref_attribute" (based on the assumption that I'm trying to access "paired_end.is_paired_end"): ... <options from_file="adapters.loc"> <filter type="param_value" column="1" ref="paired_end" ref_attribute="is_paired_end" /> ... However this doesn't work, in that no options are returned by the filter. A debug statement in the relevant code for the ParamValueFilter (in dynamic_options.py) tells me that there's no "is_paired_end" attribute. The only other tool I could find which uses "ref_attribute" is bfast_wrapper.xml, but this is accessing the "extension" attribute of a parameter not within a conditional (i.e. not the same as my example). Should it be possible to do what I'm trying? Or is there a different way to do it? Thanks for any help or suggestions, Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

1 0

Updating Galaxy Instance
by Richard Kuo 03 Sep '13

03 Sep '13

I can't seem to find any information on the Galaxy wiki website about the procedure for updating a local Galaxy instance to the newest release. Is there a tutorial for this somewhere? Thank you, Richard

3 3

Re: [galaxy-dev] [galaxy-user] Questions regarding Galaxy Tool XML File
by Jeremy Goecks 03 Sep '13

03 Sep '13

This question is best directed to the galaxy-dev mailing list because it concerns developing around Galaxy, so I've moved it there. > However, if I understand it right, the idea of the XML tool config is to provide a description of the galaxy graphical user interface rather then a general description of the actual tool's interface. No, the XML config describes a tool in abstract/essence: inputs, parameters, and outputs. Rendering of a tool can be done any number of ways. > - param tag: I havent really understood how you define a parameter to be mandatory or optional. I see when it is the child of the repeat element that there is (maybe) a minimum defined. But when this is not the case, how can I conclude that the parameter is optional vs. mandatory ? Parameters have an 'optional' attribute. See here for details on tool and parameter config in general: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax > - param tag's help attribute: can I assume any format, or is it simply the output of the tools help command ? Format is simply text. > - when do you update the tools and in turn the XML configs. (e.g. the gatk stuff is kind of outdated: 1.4 vs 2.6 ) The depends on a number of factors, including tool stability, dependencies, usage level, and ease of updating. The tool shed makes it easy to follow tool updates for a local instance: http://wiki.galaxyproject.org/Tool%20Shed You might be able to reuse some of that code in a stand-alone script. Good luck, J.

2 2