- galaxy-user - lists.galaxyproject.org

Questions regarding Galaxy Tool XML File
by Marian Thieme 16 Aug '13

16 Aug '13

Hi, I am working on a project to automate workflow generation and its execution and I found the XML tool config schema kind of interesting, in order to properly specify a tool interface. 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. So I started to write an XSLT to transform the galaxy tool config to another xml, which I believe, better fits my needs. In order to achieve this, I have a few questions: - 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 ? - param tag's help attribute: can I assume any format, or is it simply the output of the tools help command ? - 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 (e.g. the gatk stuff is kind of outdated: 1.4 vs 2.6 ) Thanks, Marian

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Name workflow output dynamically on input name
by Daniel Gorelik 14 Aug '13

14 Aug '13

Hello, I have been just getting the hang of workflows and finding them very useful. I have one question, though. Is there any way to name an output of a workflow dynamically based on the input? Thank you, Daniel Gorelik dgorelik(a)bu.edu

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Re: [galaxy-user] Egg build failed for numpy 1.6.0
by Fabrice BESNARD 14 Aug '13

14 Aug '13

Hi, I am preferentially using the main server. But recently I have also tried to build a local Galaxy server. I also have a mac (Mac Pro OSx 10.6.8). Since I am not a specialist at all, I asked some kind of "expert" people from my institute. They told me that installing Galaxy on Mac can really be nightmare because there are some conflicts in the versions of python... This could explain the problem you are encountering with the egg dependencies. So they advised me to install an Ubuntu (12.04) operating system in a virtual machine using Virtual box. This is supposed to be much easier to install Galaxy and indeed, the installation of my local galaxy server ran fast and well. However, I don't know whether the tip is good or not, because I am now facing big problems with the virtual machine: the Ubuntu virtual machine is very unstable and often crashes while running big datas on Galaxy... The problem does not come from Galaxy, but from either Ubuntu guest system, the virtual machine or the communication with the mac host system and I haven't found out how to fix it yet. But since your version of Mac is different, you can try this solution, it might work better in your configuration. Hope that helps, Fabrice But at the moment, I have lots of problem with the > Hi, > I am trying to install a local version of galaxy on my mac book (x86_64, OSx 10.8.4). I seem to be having a lot of trouble with fetching and installing specific egg dependencies. Initially pysam was giving me trouble, but once I ran scramble.py -e pysam, the problem was fixed. Now I have trouble with the numpy egg dependency. Does anyone have any idea > why a egg would fail to build. I am assuming it is because I have a more recent numpy version (1.7.1) installed already. What should I do, short of > uninstalling the newer version of numpy ? > Any help on the matter would be greatly appreciated. > Thank you. > L > -- > =================================== >>Dr. Lahcen Campbell < >>Contact: lahcencampbell(a)gmail.com < >>http://bioinf.may.ie/index.html < > =================================== > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > http://lists.bx.psu.edu/listinfo/galaxy-dev > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > http://lists.bx.psu.edu/ > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard(a)biologie.ens.fr Tel: +33-1-44-32-39-44

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ftp access on https://test.g2.bx.psu.edu/
by Amit Pande 14 Aug '13

14 Aug '13

Hi, Kindly allow the ftp access to work ....I want to upload big files....not working... regards, Amit.

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adding reference genome
by Vijay Kumar 14 Aug '13

14 Aug '13

Dear sir, please add reference genome of Zebra finch genome in Bowtie2 and Tophat2 option in galaxy. thank u

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Join the HOMER Galaxy wrapper development!
by Bjoern Gruening 13 Aug '13

13 Aug '13

Hi Galaxy Tool developers! I have started to integrate the HOMER suite into Galaxy. My initial attempt can be found here: https://github.com/bgruening/galaxytools/tree/master/homer Currently, we make use of: - Tool Shed definitions of all required 3rd Party Software - datatype definitions - loc files to define different HOMER datasets - macros - compostite datatypes (html output) I think that project can be a good start to learn Galaxy Tool development with all its simple and enhanced features. Also HOMER is a complex suite and you can add small and really big features if you like. If you are interested but did not have any experience in Tool development, do not hesitate to ask. I will try to help and explain as much as I can. For the beginning I included only 3 tools, and only one of them with a bunch of parameters. So there are many things to do ... If anyone is interested in leaning Galaxy Tool development and want to contribute. Fell free to join and contact me. Cheers, Bjoern P.S. I do not mind to merge my changes to the already existing repository from Kevin, but I was not able to contact him. http://toolshed.g2.bx.psu.edu/view/kevyin/homer

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Galaxy Distribution Aug 12, 2013
by Jennifer Jackson 13 Aug '13

13 Aug '13

*Galaxy Distribution **Aug 12, 2013* / / /////http://bit.ly/galaxy20130812/ *Highlights:* * Upgrades to *Data Manager* including improved installation actions * *Visualization* Framework tunings, plus updates to *Phyloviz*, *Scatterplot*, and *Trackster *** * *Workflows* include new reproducibility controls and editing features * Multiple *Tool Shed* enhancements, features, and tunings * Plus additional updates to the *UI*, *Admin* and *Core*, and *API*, an important *Security Fix* reminder, and *Bug Fixes* http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist http://galaxy-dist.readthedocs.org new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg update release_2013.08.12 /Thanks for using Galaxy,/ The Galaxy Team -- Jennifer Hillman-Jackson http://galaxyproject.org

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how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini
by tin h 13 Aug '13

13 Aug '13

Hello galaxy gurus, I am trying to configure a local galaxy server to submit to SGE using DRMAA, it works, but I would like to specify the equivalent of "-v TMPDIR=/scratch" for qsub. I tried updating universe_wsgi.ini with something like: default_cluster_job_runner = drmaa://-q default.q -V -v TMPDIR=/scratch/ but that doesn't work because "/" is a delimiter, and I have not been able to find way to escape it. Is there any tricks for this? Much thanks in advance for your help in this matter. -Tin

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fastq file generated by SAMTOOLS can't be recognized
by Mark Edward Fabreag 09 Aug '13

09 Aug '13

Good day. I'm trying to use Galaxy's FASTQ to FASTA converter. However, the fastq file I generated using SAMTOOLS, can't be recognized. Hope you could help me with this problem. Thank you..

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Grooming on Galaxy
by Scott Tighe 08 Aug '13

08 Aug '13

Dear Galaxy Recently grooming has taken a few days. Is this typical? Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core University of Vermont Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2557 On 8/7/2013 3:37 AM, Fabrice BESNARD wrote: > Hi, > > Using SnpEff in the Galaxy main server, I need the Caenorhabditis briggsae > genome as a reference, which is not an option in the genome list given by > the tool as implemented in Galaxy right now. > > In the doc of SnpEff, it is said that this database is available > (c_briggsae_WS230, down-load link here : > http://sourceforge.net/projects/snpeff/files/databases/v3_3/) > However, the version of SnpEff in Galaxy is 1.0. It is said in the SnpEff > docs that the database version should match the SnpEff version > (http://snpeff.sourceforge.net/download.html) I found that the first > release of a C. briggsae database dates back to the version 2.1 of SnpEff > (See here: http://sourceforge.net/projects/snpeff/files/databases/v2_1/) > > Would it be to possible to up-date the list of databases of SnpEff in the > main server, to include the C. briggsae WS230? > If versions are not compatible, would it be possible to update SnpEff to a > more recent version? > > If this is not possible right now (I must confess I don't know how much > work this upddate would require), I guess the best and quickest > alternative option would be to install a SnpEff locally. Do you think it's > worth trying this, knowing that I don't feel very comfortable with > informatics (In other words, is the installation easy) ? > > many thanks in advance for your comments and advices, >

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