1. Genomics Virtual Lab
  2. Untitled project
  3. loc_files

Overview

HTTPS SSH
Getting and preparing indexes from Galaxy Main
1. rsync galaxy main's indexes
   http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

2. Use create_2bit_to_fa.py 
   to create fa files


Using Galaxy Main's .loc files
1. Edit replace.sh (rsync command is in script)
   a) (optional) "files" line needs to point to (rsync'ed) galaxy main's loc files
   b) "index_dir" needs to point to your local indexes
   c) "outf" needs an appropriate output folder



Special cases
-------------
More info:
find ./galaxy_main/location | xargs grep -v "/afs/bx.psu.edu/depot/data/genome/" | grep -v "#" | less

gd.rand.loc (and other gd.*.loc files)
    - /galaxy/data/

regions.loc
    - files not in datacache.g2.bx.psu.edu/indexes/

tmap_index.loc
    - OK?

encode_datasets.loc
    - files not in datacache.g2.bx.psu.edu/indexes/
    - Autogenerated?

faseq.loc
    - genome fa files for each chr (eg chr1.fa, chr2.fa) is in not in datacache.g2.bx.psu.edu/indexes/

binned_scores.loc

gorGor3
    - seemed to be wrong throughout