Hello Xianjun,

Xianjun Dong wrote:

hi,

We have a bunch of questions about using the local Galaxy:)

1. how to delete un-related species
For example, after uploading local file, the users are asked to tell the species it's related. There are bunch of species in the dropdown list, which is complete and nice. But for the group, we don;t need so much. So, it'll take time to find the spcies we want. Can I delete the species unrelated? where can I find the file?

The genome builds are contained in the file ~/tool-data/shared/ucsc/builds.txt

The file is read by the following code in ~/lib/galaxy/util/__init__.py:

dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) ) #this list is used in edit attributes and the upload tool

2. Trying to solve the above question, I went into the galaxy/tools/data_source/upload.xml, it says
...
<action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
...

instead of "<command interpreter="perl">toolExample.pl $input > $output</command>", as the example in the screencast shown. So, what's the difference? where can I get educated for the full set of grammar like this?

Hmm, the screen cast may be out of sync with the latest version of the Galaxy code, although either grammar should still work. The latest code is using the UploadToolAction class in the ~/lib/galaxy/tools/upload/upload.py code file and it is recommended over the grammar in the screen cast. The tools included in the Galaxy distribution are written in such a way that they can be executed from the command line and generally have the form:

<command interpreter="<python, perl, c or some other>"><tool executable code file - eg, joinWrapper.py> <list of inputs, possibly including command line options> <list of outputs></command>

the upload tool is a "special case" tool.

3. fix the URL bug for showing data in UCSC/test
We installed the local Galaxy at http://shire.bccs.uib.no/galaxy/, but for the "display at UCSC" link at each dataset, it's (for example)
http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr1:4402497-4402544&hgt.customText=http://shire.bccs.uib.no/display_as?id=241&display_app=ucsc
This will lead an error, saying "http://shire.bccs.uib.no/display_as?id=241&display_app=ucsc: 404 Not Found "

Obviously, it missed ../galaxy/ after the main domain. How/Where can I fix it?

Where Galaxy is installed is what we consider the "root_dir", and it is set at server start up in the Configuration class in the ~/lib/galaxy/config.py code file - the code line is:

self.root = kwargs.get( 'root_dir', '.' )

Since your root_dir setting is incorrect, it is probable that you have configured your apache server to run Galaxy at a location which is not the web server root. If this is the case, see our wiki at http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy - particularly the section "Apache configuration with Galaxy not at the web server root".

3. column number bug in join
When joining two queries, the default dataset is the latest(or the last-created) dataset, and the column for choosing is also the column for that dataset. BUT, if the user change the dataset, the column number does not change accordingly. I guess this bug is not only occurring in this category.

I'm not quite clear on this one. can you provide a snippet of data for both datasets you are attempting to join?

4. Command question for BLAT/blast/liftover/ENCODE etc. customized dataset
It seems that the default installation does not support the above function, maybe because there is no required data in the path. I noticed that the .loc files in galaxy/tool-data/ are commented for the file path. For example, for tool-data/blastdb.loc
#nt     /depot/data2/galaxy/blastdb/nt/nt.chunk
#wgs    /depot/data2/galaxy/blastdb/wgs/wgs.chunk
#test   /depot/data2/galaxy/blastdb/test/test.fa

My question is: can I download the data from your /depot/data2/galaxy/? which will make it looks same as the main galaxy ;)
If not, I may have another question: to integrate my own data on galaxy, just as ENCODE did, what's the steps? Could you describe in a simple way?

5. Error while doing plotting:
An error occurred running this job: Traceback (most recent call last): File "/export/biggles/opt/www/galaxy/tools/plotting/histogram.py", line 5, in ? from rpy import * ImportError: No module named rpy, report this error

There are several "3rd party" packages that Galaxy tools depend upon. See the http://g2.trac.bx.psu.edu/wiki/ToolDependencies wiki for a complete list. This wiki will point you to where you can download the required packages.

6. A by-side question: Is it possible to embed R script into Galaxy? which is a widely-used language for statistics and graphical display.

R is used in several tools included in the Galaxy distribution. For an example of how you can wrap it, see ~/tools/plotting/xy_plot.xml, which uses the r_wrapper.sh script. We do not have plans to embed rpy in the Galaxy distribution as it is very large and not maintained by the Galaxy development team.

Greg Von Kuster
Galaxy Development Team

Thanks

Xianjun


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