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?

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?

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?

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.

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

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.

Thanks

Xianjun