#This is a sample file distributed with Galaxy that enables tools #to use a directory of 2bit genome files for use with Lastz. You will #need to supply these files and then create a lastz_seqs.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The lastz_seqs.loc #file has this format (white space characters are TAB characters): # # # #So, for example, if your lastz_seqs.loc began like this: # #hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit #hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit #mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit # #then your /depot/data2/galaxy/twobit/ directory #would need to contain the following 2bit files: # #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit # #Your lastz_seqs.loc file should include an entry per line for #each file you have stored that you want to be available. Note that #your files should all have the extension '2bit'. # #Note that for backwards compatibility with workflows, the unique ID of #an entry must be the path that was in the original loc file, because that #is the value stored in the workflow for that parameter. # hg19_rCRS_pUC18_phiX174 Homo sapiens (hg19 with mtDNA replaced with rCRS, and containing pUC18 and phiX174) /cvmfs/data.galaxyproject.org/managed/seq/hg19_rCRS_pUC18_phiX174.2bit rn6 Rat Jul. 2014 (RGSC 6.0/rn6) (rn6) /cvmfs/data.galaxyproject.org/managed/seq/rn6.2bit dm6 D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) (dm6) /cvmfs/data.galaxyproject.org/managed/seq/dm6.2bit musFur1 Ferret Apr. 2011 (MusPutFur1.0/musFur1) (musFur1) /cvmfs/data.galaxyproject.org/managed/seq/musFur1.2bit nomLeu3 Gibbon Oct. 2012 (GGSC Nleu3.0/nomLeu3) (nomLeu3) /cvmfs/data.galaxyproject.org/managed/seq/nomLeu3.2bit cerSim1 White rhinoceros May 2012 (CerSimSim1.0/cerSim1) (cerSim1) /cvmfs/data.galaxyproject.org/managed/seq/cerSim1.2bit danRer10 Zebrafish Sep. 2014 (GRCz10/danRer10) (danRer10) /cvmfs/data.galaxyproject.org/managed/seq/danRer10.2bit papAnu2 Baboon Mar. 2012 (Baylor Panu_2.0/papAnu2) (papAnu2) /cvmfs/data.galaxyproject.org/managed/seq/papAnu2.2bit bosTau8 Cow Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8) (bosTau8) /cvmfs/data.galaxyproject.org/managed/seq/bosTau8.2bit melUnd1 Budgerigar (Melopsittacus undulatus): melUnd1 /cvmfs/data.galaxyproject.org/managed/seq/melUnd1.2bit allMis1 American alligator Aug. 2012 (allMis0.2/allMis1) (allMis1) /cvmfs/data.galaxyproject.org/managed/seq/allMis1.2bit vicPac1 Alpaca Jul. 2008 (Broad/vicPac1) (vicPac1) /cvmfs/data.galaxyproject.org/managed/seq/vicPac1.2bit vicPac2 Alpaca Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2) (vicPac2) /cvmfs/data.galaxyproject.org/managed/seq/vicPac2.2bit gadMor1 Atlantic cod May 2010 (Genofisk GadMor_May2010/gadMor1) (gadMor1) /cvmfs/data.galaxyproject.org/managed/seq/gadMor1.2bit dasNov3 Armadillo Dec. 2011 (Baylor/dasNov3) (dasNov3) /cvmfs/data.galaxyproject.org/managed/seq/dasNov3.2bit panPan1 Bonobo May. 2012 (Max-Planck/panPan1) (panPan1) /cvmfs/data.galaxyproject.org/managed/seq/panPan1.2bit felCat8 Cat Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) (felCat8) /cvmfs/data.galaxyproject.org/managed/seq/felCat8.2bit aptMan1 Brown Kiwi Jun. 2015 (MPI-EVA AptMant0/aptMan1) (aptMan1) /cvmfs/data.galaxyproject.org/managed/seq/aptMan1.2bit bosTau7 Cow (Bos taurus): bosTau7 /cvmfs/data.galaxyproject.org/managed/seq/bosTau7.2bit apiMel4 A. mellifera 04 Nov 2010 (Amel_4.5/apiMel4) (apiMel4) /cvmfs/data.galaxyproject.org/managed/seq/apiMel4.2bit Amel_4.5 A. mellifera Nov. 2010 (GCF_000002195.4/Amel_4.5) (Amel_4.5) /cvmfs/data.galaxyproject.org/managed/seq/Amel_4.5.2bit