Hi, Additionally, the wiki page https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup gives a detailed explanation of how to create these files. Let us know if you have any further questions. Regards, Kelly On Oct 28, 2010, at 4:41 AM, Peter wrote:

On Wed, Oct 27, 2010 at 10:41 PM, Zhe Chen <zhe@lanl.gov> wrote:

...

Hi,

I got some errors with my local Galaxy.

IOError: [Errno 2] No such file or directory: '/usr/local/galaxy-python/galaxy_dist/tool-data/lastz_seqs.loc'

IOError: [Errno 2] No such file or directory: '/usr/local/galaxy-python/galaxy_dist/tool-data/lastz_seqs.loc'

IOError: [Errno 2] No such file or directory: '/usr/local/galaxy-python/galaxy_dist/tool-data/perm_color_index.loc'

Looks like I am missing some files. Where I can download them?

Thanks

Hi

These are local configuration files which you must edit according to your system setup. For each *.loc file there should be an example called *.loc.sample with some help text.

Peter

P.S. I have a patch to make the log less messy with these errors: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/ 003382.html _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

Hi Victor,

No we are working on writing a wrapper to start cassava from Galaxy, presumably from the information given to a data library. Does anybody have any ideas as to how to proceed on this?

We were thinking on creating a file with the run name and other details and then put this file into a data library. Then making this file as part of Galaxys history. Then the cassava wrapper will read the information from this file and populate an user interface which as much data from the run as possible. Then run cassava from galaxy.

What do you think?

This is doable in Galaxy. You may want to look at the 'Extract features from GFF file' tool under 'Filter and Sort' tools menu. Make sure that the dataset is reaady (green) before running the tool.

The idea is to:

1-Create a sequencing request via the tracking sample part. 2- Make a link between the run folder to a data library somehow. 3- Use the information from the run as a history so it will be the input of the cassava wrapper. 4- Start cassava via the wrapper tool.

Also, is there a way to have folder within a Data Library which points to an existing directory in the same galaxy server. So, when cassava is done, we can point to this folder to get the results?

Since your filesystem is mounted on the same server as Galaxy, you should be able to create a folder in your data library and use 'Upload a directory of files' option in the datasets upload page to add the datasets generated from the sequencer to your data library. For this the 'library_import_dir' config variable in the Galaxy config file (universe_wsgi.ini) should point to the directory containing the datasets. You can find more information at http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles . Alternatively, you also use the data transfer feature in sample tracking. This way you can connect resulting datasets to individual samples. The UI for sample tracking is being streamlined. More information on how to setup data transfer is available here: http://main.g2.bx.psu.edu/u/rkchak/p/sts-setup-data-transfer . Let me know if you have more questions. Thanks for using Galaxy rc