- galaxy-dev - lists.galaxyproject.org

help
by romain desprat 26 Jul '12

26 Jul '12

I am trying to work on 23 giga text file. My laptop being not powerful enough I have split it in 10 files and made some modification on them. Now I have made (linux and window) a double boot on my laptop and install galaxy ( on the linux partition). Unfortunately, galaxy doesn t have enough memory to work with this file. My question is : is it because I did not allocate enough memory to galaxy/linux partition when I did the double boot ( 5 giga f I recall right ) or is it because galaxy over 2 giga anyway will not be able to handle the situation. Thanks any advices are welcome, Romain romain.desprat(a)einstein.yu.edu

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Help to run a C program
by Rodrigo Faccioli 26 Jul '12

26 Jul '12

Hi, I'm newbie in Galaxy. In fact, this is my first post. I'd like to create a web-interface to run a C program. It is necessary a config file which is used as input to this program. Therefore, the values of parameters are informed by user through this web-interface. Its output is some files. I searched in Galaxy wiki some examples or tutorials. However, I didn't find anything that helped me. I'm confused in what I can do. Could you help me showing where I can find specific materials? Best regards, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structural Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-8739 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 Personal Blogg - http://rodrigofaccioli.blogspot.com/

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HMMER wrappers
by Peter Cock 26 Jul '12

26 Jul '12

Hello all, Has anyone done a wrapper for HMMER2 or HMMER3? http://hmmer.janelia.org/software I can't find anything in the Tool Shed http://toolshed.g2.bx.psu.edu/ so we are likely to look into doing this ourselves - starting with hmmerscan. Thanks, Peter

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having a directory and all contents retained as the 'output'
by Brian Haas 26 Jul '12

26 Jul '12

Greetings, I have a process that is going to generate dozens of output files, each of which I want to retain as a data repository that will be leveraged by other downstream tools. I could just point the downstream tool at the directory, and it'll know what to look for, rather than to have to list each output file as a separate parameter. Is it possible to do this in Galaxy? And is there a best practice (or example) for it? thanks! -b -- -- Brian J. Haas Manager, Genome Annotation and Analysis, Research and Development The Broad Institute http://broad.mit.edu/~bhaas

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Galaxy-distribution (Nouvelle version)
by CHEBBI Mohamed Amine 26 Jul '12

26 Jul '12

Bonsoir, Une nouvelle version de Galaxy vient de sortir. D’après le Monsieur du maling list de Galaxy, les bugs de crash liés à l'utilisation du visualiseur Trackster devraient être résolus. Pourriez vous me dire vos recommandations à ce propos. Merci Amine

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Browser refresh and autoscaling
by Wolosh, Glenn 26 Jul '12

26 Jul '12

If I turn on autoscale via the cloud console page, autoscale shows turned off on page refresh. This occurs with both safari and firefox on a Mac. I have not tried other OS/Browser combinations. Where on the server is the autoscale configuration? I would like to see whether or not the console page is lying to me. Thanks. Glenn (Gedaliah) Wolosh Scientific Programmer IST/High Performance and Research Computing University of Medicine & Dentistry of New Jersey (UMDNJ) 185 South Orange Avenue, MSB, Room C-631 University Heights, Newark, NJ 07101 Phone: 973.972.9835 Fax: 973.972.7412 woloshgm(a)umdnj.edu<mailto:woloshgm@umdnj.edu>

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galaxy database has two tables missing
by Derrick Lin 26 Jul '12

26 Jul '12

Hi guys, Recently we have discovered there is a bug in the database dump utility. And we had used the same utility to migrate the galaxy mysql database once. That resulted the on the current galaxy database, two tables are missing: genome_index_tool_data tool_dependency I am wondering if there is a safe way to repair the database so that these two tables get added back? Regards, Derrick

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Non-Library input for workflows
by Sascha Kastens 26 Jul '12

26 Jul '12

Hi all, I wrote a script which executes a workflow via the API. I was wondering whether it is possible to use non-library input for the workflow. At the moment the script submits each data into a library and then uses this data as input: for step_id, ds_in in workflow[?inputs?].iteritems(): wf_data[?ds_map?][step_id] = {?src?:?ld?, ?id?:ds[?id?]} What I am seeking for is something like this: wf_data[?ds_map?][step_id] = {?src?:?local?, ?path?:?path/to/file?} Cheers, Sascha Kastens Project Manager GATC Biotech AG Jakob-Stadler-Platz 7 D-78467 Konstanz Phone: +49 (0) 7531-81604110 Fax: +49 (0) 7531-816081 Email: s.kastens(a)gatc-biotech.com http://www.gatc-biotech.com http://www.twitter.com/gatcbiotech http://www.facebook.com/gatcbiotech http://www.xing.com/companies/gatcbiotechag GATC Biotech AG Chairman Supervisory Board: Fritz Pohl Board of Directors: Peter Pohl, Thomas Pohl, Dr. Marcus Benz UID: DE 142 315 733 | Registration: Konstanz, HRB 1757 | Registered Office: Konstanz The information contained in this email is intended solely for the addressee. Access to this email by anyone else unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately. The content of this email is not legally binding unless confirmed by letter.

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Question about SNP calling
by shamsher jagat 25 Jul '12

25 Jul '12

Is there a work flow/ tutorial how to call SNP and get significant SNP followed by their annotation. Thanks

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configuring job runner for toolshed tools
by David Hoover 25 Jul '12

25 Jul '12

Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost? David Hoover Helix Systems Staff

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