#This is a sample file distributed with Galaxy that enables tools #to use a directory of Picard dict and associated files. You will need #to create these data files and then create a picard_index.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The picard_index.loc #file has this format (longer white space is the TAB character): # # # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # #hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: #hg18.fa #hg18.dict #hg18.fa.fai # #The dictionary file for each reference (ex. hg18.dict) must be #created via Picard (http://picard.sourceforge.net). Note that #the dict file does not have the .fa extension although the #path list in the loc file does include it. # hg19_rCRS_pUC18_phiX174 hg19_rCRS_pUC18_phiX174 Homo sapiens (hg19 with mtDNA replaced with rCRS, and containing pUC18 and phiX174) /cvmfs/data.galaxyproject.org/managed/picard_index/hg19_rCRS_pUC18_phiX174/hg19_rCRS_pUC18_phiX174.fa rn6 rn6 Rat Jul. 2014 (RGSC 6.0/rn6) (rn6) /cvmfs/data.galaxyproject.org/managed/picard_index/rn6/rn6.fa dm6 dm6 D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) (dm6) /cvmfs/data.galaxyproject.org/managed/picard_index/dm6/dm6.fa musFur1 musFur1 Ferret Apr. 2011 (MusPutFur1.0/musFur1) (musFur1) /cvmfs/data.galaxyproject.org/managed/picard_index/musFur1/musFur1.fa nomLeu3 nomLeu3 Gibbon Oct. 2012 (GGSC Nleu3.0/nomLeu3) (nomLeu3) /cvmfs/data.galaxyproject.org/managed/picard_index/nomLeu3/nomLeu3.fa cerSim1 cerSim1 White rhinoceros May 2012 (CerSimSim1.0/cerSim1) (cerSim1) /cvmfs/data.galaxyproject.org/managed/picard_index/cerSim1/cerSim1.fa danRer10 danRer10 Zebrafish Sep. 2014 (GRCz10/danRer10) (danRer10) /cvmfs/data.galaxyproject.org/managed/picard_index/danRer10/danRer10.fa papAnu2 papAnu2 Baboon Mar. 2012 (Baylor Panu_2.0/papAnu2) (papAnu2) /cvmfs/data.galaxyproject.org/managed/picard_index/papAnu2/papAnu2.fa bosTau8 bosTau8 Cow Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8) (bosTau8) /cvmfs/data.galaxyproject.org/managed/picard_index/bosTau8/bosTau8.fa vicPac1 vicPac1 Alpaca Jul. 2008 (Broad/vicPac1) (vicPac1) /cvmfs/data.galaxyproject.org/managed/picard_index/vicPac1/vicPac1.fa vicPac2 vicPac2 Alpaca Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2) (vicPac2) /cvmfs/data.galaxyproject.org/managed/picard_index/vicPac2/vicPac2.fa allMis1 allMis1 American alligator Aug. 2012 (allMis0.2/allMis1) (allMis1) /cvmfs/data.galaxyproject.org/managed/picard_index/allMis1/allMis1.fa dasNov3 dasNov3 Armadillo Dec. 2011 (Baylor/dasNov3) (dasNov3) /cvmfs/data.galaxyproject.org/managed/picard_index/dasNov3/dasNov3.fa felCat8 felCat8 Cat Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) (felCat8) /cvmfs/data.galaxyproject.org/managed/picard_index/felCat8/felCat8.fa gadMor1 gadMor1 Atlantic cod May 2010 (Genofisk GadMor_May2010/gadMor1) (gadMor1) /cvmfs/data.galaxyproject.org/managed/picard_index/gadMor1/gadMor1.fa panPan1 panPan1 Bonobo May. 2012 (Max-Planck/panPan1) (panPan1) /cvmfs/data.galaxyproject.org/managed/picard_index/panPan1/panPan1.fa aptMan1 aptMan1 Brown Kiwi Jun. 2015 (MPI-EVA AptMant0/aptMan1) (aptMan1) /cvmfs/data.galaxyproject.org/managed/picard_index/aptMan1/aptMan1.fa apiMel4 apiMel4 A. mellifera 04 Nov 2010 (Amel_4.5/apiMel4) (apiMel4) /cvmfs/data.galaxyproject.org/managed/picard_index/apiMel4/apiMel4.fa Amel_4.5 Amel_4.5 A. mellifera Nov. 2010 (GCF_000002195.4/Amel_4.5) (Amel_4.5) /cvmfs/data.galaxyproject.org/managed/picard_index/Amel_4.5/Amel_4.5.fa