March 2009 - galaxy-user - lists.galaxyproject.org

An idea for sharing tools
by James Casbon 10 Jun '09

10 Jun '09

Hi Everyone, I have an "I want a pony" idea that I would like to kick onto the mailing list: It would be great if there was a way for sharing tool definitions between users. At the moment, the main repo is maintained by the galaxy team, and that is fine and makes sense. However, I'm sure there is a lot of duplicated work between the users when adding other tools in. For example, there was a conversation the other day about adding in awk. Someone had already done this, so the best idea would be if I could pull in that definition and enable it with minimum effort. I have already added tools (exonerate, restriction mapper, etc, etc) that may be of use to other people. Not sure the best way to go about this, but if my understanding of mercurial is right, we can simply offer another repo for people to pull changes from. If this is of interest to you, please can you reply? If we get enough interest and preferably some support of the core team, I could set up a free repo at, e.g., bitbucket and add users to it. Or perhaps there is a better way (eg patches submitted to trac)? Another question is what kind of tools would the core team accept for inclusion in the main dist? Cheers, James

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Exception when using remote_user.
by MORITA Hideyuki 10 Jun '09

10 Jun '09

Hi, The following error will occur under certain condition when using remote_user. AttributeError: 'NoneType' object has no attribute 'user' This error is thrown when: 1. using remote_user 2. browser has a valid session (cookie) 3. after logged in with an email address other than previously used This is caused by None value in prev_galaxy_session variable at L.231 in lib/galaxy/web/framework/__init__.py. I understand that galaxy_session instead of prev_galaxy_session should be referenced here. I created a patch to fix this problem by replacing prev_galaxy_session with galaxy_session. =================================================================================== diff -r a4214de3752e lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue Feb 03 18:34:27 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Mon Feb 16 13:31:02 2009 +0900 @@ -228,7 +228,7 @@ class UniverseWebTransaction( base.Defau invalidate_existing_session = True user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", - remote_user_email, prev_galaxy_session.user.email ) + remote_user_email, galaxy_session.user.email ) else: # No session exists, get/create user for new session user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) =================================================================================== Thanks. MORITA Hideyuki

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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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Data files
by Alastair Kerr 16 Mar '09

16 Mar '09

Hi, first a quick word of thanks to the galaxy devs: this is a great system thanks, we are using it to roll-out our own in-house tools/scripts. We are now in the about to gather the UCSC data files so that the rest of the tools (liftover, Fetch sequences/alignments etc) work. I am wondering whether there is an easy way of gathering this data? e.g. are there any wget /rsync scripts available or does each data source need to be added manually. 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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