Hi All,

We have a galaxy local install. Thanks to Carlos's suggestion, I was able to 
get the reference genome index to show up in the interface. Now, I am trying to 
get the data into the galaxy system. I have followed the instructions in the 
link below to create data libraries.


I have modified the following sections in the universe_wsgi.ini file:

# Add an option to the library upload form which allows administrators to

# upload a directory of files.

library_import_dir = /media/FreeAgent GoFlex Drive_/HDD1/Project

# Add an option to the admin library upload tool allowing admins to paste
# filesystem paths to files and directories in a box, and these paths will be
# added to a library.  Set to True to enable.  Please note the security
# implication that this will give Galaxy Admins access to anything your Galaxy
# user has access to.
allow_library_path_paste = True

I created a data library and using the "Add dataset" function, I pasted the 
path of my data directory in the galaxy UI and selected the "link to files 
without copying into galaxy" option. This picked up all the files that were 
present in the directory and except for a couple of files, the job seems to 
have completed successfully. Now I am not sure how to actually analyze this 
data. I performed the "Import to current history" operation on two paired end 
fastq files I want to analyze. These show up in the history with the 
appropriate size. But when I choose the "Map with BWA for Illumina" option, the 
two fastq files do not show up in the FASTQ file drop down.

These files do show up in the list of files for running fastqc

I have also restarted the server after importing the data in the history, but 
the problem persists.

Any input on how to go about analyzing the data in the local galaxy instance 
once it has been brought into the galaxy frame work is highly appreciated.

Thanks for the help.



Aarti Desai, Ph.D | Domain Specialist - Life Sciences
aarti_de...@persistent.co.in<mailto:aarti_de...@persistent.co.in> | Cell: 
+91-9673009492 | Tel: + 91-20-67036348
Persistent Systems Ltd. | Partners in Innovation | 

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