#This is a sample file distributed with Galaxy that enables tools #to use a directory of Samtools indexed sequences data files. You will need #to create these data files and then create a fasta_indexes.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The fasta_indexes.loc #file has this format (white space characters are TAB characters): # # # #So, for example, if you had hg19 Canonical indexed stored in # # /depot/data2/galaxy/hg19/sam/, # #then the fasta_indexes.loc entry would look like this: # #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa # #and your /depot/data2/galaxy/hg19/sam/ directory #would contain hg19canon.fa and hg19canon.fa.fai files. # #Your fasta_indexes.loc file should include an entry per line for #each index set you have stored. The file in the path does actually #exist, but it should never be directly used. Instead, the name serves #as a prefix for the index file. For example: # #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa 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/sam_indexes/hg19_rCRS_pUC18_phiX174/hg19_rCRS_pUC18_phiX174.fa Araly1 Araly1 Arabidopsis lyrata: Araly1 /cvmfs/data.galaxyproject.org/managed/sam_indexes/Araly1/Araly1.fa rn6 rn6 Rat Jul. 2014 (RGSC 6.0/rn6) (rn6) /cvmfs/data.galaxyproject.org/managed/sam_indexes/rn6/rn6.fa dm6 dm6 D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) (dm6) /cvmfs/data.galaxyproject.org/managed/sam_indexes/dm6/dm6.fa musFur1 musFur1 Ferret Apr. 2011 (MusPutFur1.0/musFur1) (musFur1) /cvmfs/data.galaxyproject.org/managed/sam_indexes/musFur1/musFur1.fa cerSim1 cerSim1 White rhinoceros May 2012 (CerSimSim1.0/cerSim1) (cerSim1) /cvmfs/data.galaxyproject.org/managed/sam_indexes/cerSim1/cerSim1.fa nomLeu3 nomLeu3 Gibbon Oct. 2012 (GGSC Nleu3.0/nomLeu3) (nomLeu3) /cvmfs/data.galaxyproject.org/managed/sam_indexes/nomLeu3/nomLeu3.fa bosTau8 bosTau8 Cow Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8) (bosTau8) /cvmfs/data.galaxyproject.org/managed/sam_indexes/bosTau8/bosTau8.fa papAnu2 papAnu2 Baboon Mar. 2012 (Baylor Panu_2.0/papAnu2) (papAnu2) /cvmfs/data.galaxyproject.org/managed/sam_indexes/papAnu2/papAnu2.fa danRer10 danRer10 Zebrafish Sep. 2014 (GRCz10/danRer10) (danRer10) /cvmfs/data.galaxyproject.org/managed/sam_indexes/danRer10/danRer10.fa vicPac1 vicPac1 Alpaca Jul. 2008 (Broad/vicPac1) (vicPac1) /cvmfs/data.galaxyproject.org/managed/sam_indexes/vicPac1/vicPac1.fa vicPac2 vicPac2 Alpaca Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2) (vicPac2) /cvmfs/data.galaxyproject.org/managed/sam_indexes/vicPac2/vicPac2.fa allMis1 allMis1 American alligator Aug. 2012 (allMis0.2/allMis1) (allMis1) /cvmfs/data.galaxyproject.org/managed/sam_indexes/allMis1/allMis1.fa dasNov3 dasNov3 Armadillo Dec. 2011 (Baylor/dasNov3) (dasNov3) /cvmfs/data.galaxyproject.org/managed/sam_indexes/dasNov3/dasNov3.fa gadMor1 gadMor1 Atlantic cod May 2010 (Genofisk GadMor_May2010/gadMor1) (gadMor1) /cvmfs/data.galaxyproject.org/managed/sam_indexes/gadMor1/gadMor1.fa panPan1 panPan1 Bonobo May. 2012 (Max-Planck/panPan1) (panPan1) /cvmfs/data.galaxyproject.org/managed/sam_indexes/panPan1/panPan1.fa felCat8 felCat8 Cat Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) (felCat8) /cvmfs/data.galaxyproject.org/managed/sam_indexes/felCat8/felCat8.fa aptMan1 aptMan1 Brown Kiwi Jun. 2015 (MPI-EVA AptMant0/aptMan1) (aptMan1) /cvmfs/data.galaxyproject.org/managed/sam_indexes/aptMan1/aptMan1.fa apiMel4 apiMel4 A. mellifera 04 Nov 2010 (Amel_4.5/apiMel4) (apiMel4) /cvmfs/data.galaxyproject.org/managed/sam_indexes/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/sam_indexes/Amel_4.5/Amel_4.5.fa