- galaxy-user - lists.galaxyproject.org

does galaxy support the UCSC data points format?
by Mikhail Spivakov 01 Apr '09

01 Apr '09

Hi everyone, I'm wondering if galaxy understands the UCSC data points format (for example, the one produced by exporting phastcons17way scores. All I managed to do so far is import these data into galaxy, but I couldn't find any supported operations for this format. It would be very useful, for example, if galaxy could convert these data into genomic intervals using a user-defined threshold (eg, extract regions with phastcons scores > 0.5) - but maybe it can already do it and I just don't know how? Many thanks Mikhail -- Mikhail Spivakov, PhD Postdoctoral Fellow European Molecular Biology Laboratory Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD UK Tel +44 (0) 1223 49 26 60 Mob +44 (0) 7985 09 66 75 spivakov(a)ebi.ac.uk

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Is Galaxy LDAP-aware?
by Erick Antezana 01 Apr '09

01 Apr '09

Hi, is it possible to use LDAP authentication in the Galaxy framework? If not, any plans to consider it? thanks, Erick

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Conditional execution (workflow)
by Erick Antezana 01 Apr '09

01 Apr '09

Hello, is there a tool or an intelligent way to add an conditional execution of a step within a workflow? and as an extension of such tool/feature I would be interested in just executing for instance a particular brach of my workflow (depending on a condition from a previous step)... thanks, Erick

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New Galaxy Tools
by Assaf Gordon 31 Mar '09

31 Mar '09

Hello, I'd like to share some new tools for Galaxy, which you can install on your local Galaxy server: FASTX-Toolkit - tools for FASTA/FASTQ pre-processing: http://hannonlab.cshl.edu/fastx_toolkit/ Unix-Tools - wrappers for common unix command line programs: http://hannonlab.cshl.edu/galaxy_unix_tools/ Comments are welcomed, Gordon.

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change_format
by SHAUN WEBB 30 Mar '09

30 Mar '09

Hi, I am using the <change_format> tag to decide on the appropriate output file format based on user input. eg: <param name="format" type="select" label="Format" > ...... ...... <data format="txt" name="out" > <change_format> <when input="format" value="tabular" format="tabular" /> </change_format> This works fine except when the input parameter is nested in a <conditional> tag. <conditional name="fileType"> <param name="format" type="select" label="Format" > Usually I would reference this as fileType.format, $fileType.format, ${fileType.format}, but this doesn't seem to work in the input attribute of <when>. Can anyone help me out? Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Workflows: Naming files
by Alastair Kerr 27 Mar '09

27 Mar '09

Hi, is there a way (or is there a feature planned) that allows a users to name/label files in a workflow? The issue is that for larger workflows that generate many files, it can be a bit onerous to work out what each file is from the history. The ability to clearly label them as part of the workflow or indeed hide/delete intermediate files would be a huge advantage. thanks - Alastair -- Alastair Kerr, Ph.D., Bioinformatician, Wellcome Trust Centre for Cell Biology, 2.21, Michael Swann Building, Kings buildings, The University of Edinburgh, Edinburgh, EH9 3JR, UK Tel: 44-(0)131-650-7527 http://bifx1.bio.ed.ac.uk/ The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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running a workflow from command line
by Erick Antezana 24 Mar '09

24 Mar '09

Hi, is there a way to run a workflow that was built using the galaxy web interface from the command line? thanks, Erick

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zoom in/out in workflows
by Erick Antezana 23 Mar '09

23 Mar '09

Hi, We are dealing with workflows with about 40 steps and sometimes it is not easy to visualise them or simply work with them due to the complexity of links among the steps.....Is it possible to zoom in/out the workflows view? If not, would it be possible to consider such feature in future developments? thanks! Erick

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maf format - bx_python missing in local galaxy install?
by Rochak Neupane 19 Mar '09

19 Mar '09

Hello, When importing MAF file, local galaxy install loads the data but shows an error: No data: global name 'bx' is not defined When I tried to convert maf to fasta, I got the following error: Traceback (most recent call last): File "/home/rochak/galaxy_latest/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py", line 7, in import bx.align.maf File "/home/rochak/galaxy_latest/eggs/py2.5-linux-x86_64-ucs2/bx_python-0.5.0_dev_r459-py2.5-linux-x86_64.egg/bx/align/__init__.py", line 7, in File "/home/rochak/galaxy_latest/eggs/py2.5-linux-x86_64-ucs2/bx_python-0.5.0_dev_r459-py2.5-linux-x86_64.egg/bx/align/core.py", line 8, in File "/home/rochak/galaxy_latest/eggs/py2.5-linux-x86_64-ucs2/bx_python-0.5.0_dev_r459-py2.5-linux-x86_64.egg/bx/misc/__init__.py", line 5, in ImportError: No module named bz2 Does galaxy install bx_python in its initial setup? /home/rochak/galaxy_latest/eggs/py2.5-linux-x86_64-ucs2/bx_python-0.5.0_dev_r459-py2.5-linux-x86_64.egg is a file, not a directory. How should I proceed forward to fix this? Thanks, Rochak

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Re: [galaxy-user] [Gmod-help] GMOD and Galaxy
by Dave Clements, GMOD Help Desk 18 Mar '09

18 Mar '09

Hi Rashad, GBrowse is currently the only other GMOD component that Galaxy talks to. There has been discussion in the past about getting it work with Chado as well, but there hasn't yet been sufficient interest to justify that work. I'm forwarding this e-mail to the Galaxy-user list in case I'm wrong about that. Documentation on how to get Galaxy and GBrowse to talk with one another is at: http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Track_Sharing_Options There may be more doc at the Galaxy web site. Please let me know if this does not answer your questions. Regards, Dave C. GMOD Help Desk Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback On Tue, Mar 17, 2009 at 2:54 PM, Rashad Arafeh <arafeh(a)gmail.com> wrote: > hello, > > My name is Rashad Arafeh, I just recently graduated in Computer Science, and > have been encouraged to look into a career in Bioinformatics and > Computational BIology. > > I am volunteering to help a professor at the University of Texas - Arlington > set up his lab with some bioinformatics tools that he thinks are necessary, > and from there i will begin to solve some bioinformatics problems with him. > > Since we are both new to GMOD and its components, we are pretty much > learning as we go, but he has it clear in his mind that he wants "in-house" > functionality similar to that of the UCSC Genome Browser and Galaxy system. > > My questions are: > > -I noticed that Galaxy is listed as a GMOD component, and i want to downlaod > and install it and have it run locally, how do i get it to interact with > GBrowse and other components? > > -What set of components, if there are any, would give me functionality > similar to that of UCSC Genome Browser with Galaxy? > > Thank you, > Rashad Arafeh >

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