Question: Issue with Liftover loc file on local galaxy
gravatar for djevo1
2.1 years ago by
djevo160 wrote:

I installed crossmap to a local galaxy from the toolshed and added chain files to the associated .loc. However, None of the chain files I add appear within the tool so I an unable to use it. Below is the loc file.

#This is a sample file distributed with Galaxy that is used by the
#liftOver tools.  The liftOver.loc file has this format (white space 
#characters are TAB characters):
#<FromSpecies>  <ToSpecies> <PathToChainFile>
#So, for example, if you had the chain file to convert from anoCar1 to galGal3
#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
#then the liftOver.loc entry would look like this:
#anoCar1    galGal3     /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
#and your /depot/data2/galaxy/anoCar1/liftOver directory would 
#contain all of your "chain" files (e.g.):
#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
#Your liftOver.loc file should include an entry per line for each build you can
#convert.  For example:
#anoCar1    galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
#anoCar1    gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
#anoCar1    hg18    /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
hg19toGRCH37    UCSC2ENS    /home/eclark28/galaxy_production/galaxy/tool-data/genome/liftover/hg19ToGRCh37.over.chain
GRCH37tohg19    ENS2UCSC    /home/eclark28/galaxy_production/galaxy/tool-data/genome/liftover/GRCh37ToHg19.over.chain
indexes data galaxy local liftover • 775 views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by djevo160
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The entries in these bold fields must match an installed reference genome's "dbkey" identifier (exactly):

hg19toGRCH37 UCSC2ENS /home/eclark28/galaxy_production/galaxy/tool-data/genome/liftover/hg19ToGRCh37.over.chain

GRCH37tohg19 ENS2UCSC /home/eclark28/galaxy_production/galaxy/tool-data/genome/liftover/GRCh37ToHg19.over.chain

For example, the above would be:

hg19 GRCh37 /home/eclark28/galaxy_production/galaxy/tool-data/genome/liftover/hg19ToGRCh37.over.chain

GRCh37 hg19 /home/eclark28/galaxy_production/galaxy/tool-data/genome/liftover/GRCh37ToHg19.over.chain

Plus both hg19 and GRCh37 would be active on your local using a Data Manager. At a minimum, the fasta needs to be installed and have a dbkey assigned if it does not already exist. Then Samtools and Picard indexes. Other indexes are optional and depend on the target tools.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k

Thank you, that made them appear in liftover, but not in crossmap.

ADD REPLYlink written 2.1 years ago by djevo160
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