- galaxy-dev - lists.galaxyproject.org

Locally cached alignments
by David Hoover 08 Nov '10

08 Nov '10

We have a local copy of MAF files for hg18, and I modified the ~/tool-data/maf_index.loc file to list the full paths to the .maf files. After restarting Galaxy, the MAF Source and Type are listed in the MAF Coverage Stats tool, as expected. However, after trying to run with an interval file, it gives an error "The MAF source specified (17_WAY_MULTIZ_hg18) appears to be invalid". Is there somewhere else I need to edit to get to the locally cached MAF files? David Hoover Helix Systems Staff http://helix.nih.gov

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Integrating tools with variable inputs
by Branden Timm 04 Nov '10

04 Nov '10

Hi All, Is there any documentation on how to integrate tools that take a variable number of input files? We'd like to integrate a tool with the following command line syntax: tool-name <n input files> <n column names> output1 output2 Thanks! -- Branden Timm System Administrator Great Lakes Bioenergy Research Center btimm(a)glbrc.wisc.edu

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Galaxy using PBSPro
by David Hoover 04 Nov '10

04 Nov '10

Has anyone had success with Galaxy using PBSPro? Do you use pbs_python or DRMAA? Does pbs_python work with more recent versions of PBSPro (>=10)? David Hoover Helix Systems Staff http://helix.nih.gov

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Output redirect
by Zhe Chen 03 Nov '10

03 Nov '10

Hi, For general galaxy output, I need to define sth like <outputs> <data format="input" name="out_file1" metadata_source="input"/> </outputs> and put $out_file1 as a parameter in the command tag. To my understanding, Galaxy will save the $out_file1 into a file and retrieve and display it on the result panel. I have a *.pl file which takes inputs and generate a file (result.txt) in my local server and return a file path. Can I redirect the galaxy output to this file? Currently, I am reading the file using the file path and push the content in the file into $out_file1. For large files, it is a waste of computing time and resource (since Galaxy will generate another file). Is there a solution for this? Thanks

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how to set PATH variable
by David Hoover 03 Nov '10

03 Nov '10

I'm trying to enable the EMBOSS tools, and Galaxy is complaining it can't find the executables. Our local installation of EMBOSS is in a non-standard location (/usr/local/emboss/bin). I tried setting the $PATH variable in ~/.bashrc_profile and ~/.profile, but this had no effect. Where can I add the path to the EMBOSS tools so that Galaxy can find them? David Hoover Helix Systems Staff http://helix.nih.gov

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Number of elements from a REPEAT block
by Branden Timm 03 Nov '10

03 Nov '10

Hi, I'd like to be able to ascertain the length of an array of input files captured by the REPEAT tag. For example: <repeat name="infiles"> <param name="infile" type="data" format"txt" /> </repeat> How can I get the length of $infiles to pass in my command line? Something like $infiles.length ? -- Branden Timm btimm(a)glbrc.wisc.edu

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using local Genome Browser mirror
by David Hoover 03 Nov '10

03 Nov '10

Is there any way of having Galaxy use a local mirror of the UCSC Genome Browser instead of the main site? Is there a central config file somewhere that I can just change genome.ucsc.edu to something else? David Hoover Helix Systems Staff http://helix.nih.gov

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MySQL timeout problem
by David Hoover 03 Nov '10

03 Nov '10

I am using MySQL as the backend database. If I leave a Galaxy browser session sitting for more than 30 minutes, the MySQL connection goes to sleep. Then, when I try some action, there is an error displayed on the browser window and in the logfile. It looks something like this: Error - sqlalchemy.exc.OperationalError: (OperationalError) (2013, 'Lost connection to MySQL server during query') u'SELECT galaxy_session.id AS galaxy_session_id, galaxy_session.create_time AS galaxy_session_create_time, galaxy_session.update_time AS galaxy_session_update_time, galaxy_session.user_id AS galaxy_session_user_id, galaxy_session.remote_host AS galaxy_session_remote_host, galaxy_session.remote_addr AS galaxy_session_remote_addr, galaxy_session.referer AS galaxy_session_referer, galaxy_session.current_history_id AS galaxy_session_current_history_id, galaxy_session.session_key AS galaxy_session_session_key, galaxy_session.is_valid AS galaxy_session_is_valid, galaxy_session.prev_session_id AS galaxy_session_prev_session_id \nFROM galaxy_session \nWHERE galaxy_session.session_key = %s AND galaxy_session.is_valid = %s \n LIMIT 0, 1' ['911e5446281a234467a4812eab1cad30', 1] I have seen this sleeping problem for other applications that use MySQL. There are couple of ways to fix this. The simplest is to capture the MySQL error and retry the operation if the error is 'Lost connection'. Another is to continuously 'ping' the MySQL server periodically with very short requests. Does anyone have a fix for this problem, or am I the first to notice this? David Hoover Helix Systems Staff http://helix.nih.gov

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Correction to docstring for Tool.build_param_dict
by Peter 03 Nov '10

03 Nov '10

Hi all, Here is a small fix to the docstring for Tool.build_param_dict. Peter diff -r 53d1fa98fa05 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Oct 21 16:10:26 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Fri Oct 22 13:32:31 2010 +0100 @@ -1333,7 +1333,7 @@ line. Each value is wrapped in a `InputValueWrapper`, which allows all the attributes of the value to be used in the template, *but* when the __str__ method is called it actually calls the - `to_param_dict_value` method of the associated input. + `to_param_dict_string` method of the associated input. """ param_dict = dict() # All parameters go into the param_dict

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Re: [galaxy-dev] [galaxy-user] installation problem
by Nate Coraor 03 Nov '10

03 Nov '10

Wei,Xintao wrote: > Dear Sir., > > We are going to install Galaxy local server on our Windows PC. Are there any requirements for the hardware, for example the size of CUP or other things, in order to run Galaxy smoothly? Hi Xintao, I've moved this over to the galaxy-dev list since it is better suited for local installation discussion. There aren't any hardware requirements beyond a system that is not terribly outdated, and that has the CPU/memory/disk capacity to run the tools which you plan to run. Galaxy itself is not very resource intensive except when doing certain tasks like setting the metadata on datasets. Resources used for that specific task will depend on the data format and size. Galaxy is not officially supported under Windows, nor have we known of anyone running it under Windows recently. That said, there should not be any code in Galaxy which would not work under Windows. Cygwin is a requirement, however, since Galaxy needs a POSIX-like environment in which to run. Unless you have a specific need to use Windows, you may want to look in to using some sort of virtualization technology (VirtualBox, for example) under which you can run Linux. Running Galaxy under Linux would be simpler and would allow us to provide better support for any problems you may encounter. --nate > > Thank you! > > Xintao > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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