Issue with Liftover loc file on local galaxy

Question: Issue with Liftover loc file on local galaxy

2.1 years ago by

djevo1 • 60

djevo1 • 60 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
#...etc...
#
#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 COMMENT • link •

modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by djevo1 • 60

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 2.1 years ago by djevo1 • 60

Similar posts • Search »