#This file lists the locations and dbkeys of all the fasta files #under the "genome" directory (a directory that contains a directory #for each build). The script extract_fasta.py will generate the file #all_fasta.loc. This file has the format (white space characters are #TAB characters): # # # #So, all_fasta.loc could look something like this: # #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa # #Your all_fasta.loc file should contain an entry for each individual #fasta file. So there will be multiple fasta files for each build, #such as with hg19 above. # taeGut2 taeGut2 Zebra finch Feb. 2013 (WashU taeGut324/taeGut2) /cvmfs/data.galaxyproject.org/managed/seq/taeGut2.fa rn6 rn6 Rat Jul. 2014 (RGSC 6.0/rn6) (rn6) /cvmfs/data.galaxyproject.org/managed/seq/rn6.fa dm6 dm6 D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) (dm6) /cvmfs/data.galaxyproject.org/managed/seq/dm6.fa musFur1 musFur1 Ferret Apr. 2011 (MusPutFur1.0/musFur1) (musFur1) /cvmfs/data.galaxyproject.org/managed/seq/musFur1.fa cerSim1 cerSim1 White rhinoceros May 2012 (CerSimSim1.0/cerSim1) (cerSim1) /cvmfs/data.galaxyproject.org/managed/seq/cerSim1.fa nomLeu3 nomLeu3 Gibbon Oct. 2012 (GGSC Nleu3.0/nomLeu3) (nomLeu3) /cvmfs/data.galaxyproject.org/managed/seq/nomLeu3.fa bosTau8 bosTau8 Cow Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8) (bosTau8) /cvmfs/data.galaxyproject.org/managed/seq/bosTau8.fa papAnu2 papAnu2 Baboon Mar. 2012 (Baylor Panu_2.0/papAnu2) (papAnu2) /cvmfs/data.galaxyproject.org/managed/seq/papAnu2.fa danRer10 danRer10 Zebrafish Sep. 2014 (GRCz10/danRer10) (danRer10) /cvmfs/data.galaxyproject.org/managed/seq/danRer10.fa vicPac1 vicPac1 Alpaca Jul. 2008 (Broad/vicPac1) (vicPac1) /cvmfs/data.galaxyproject.org/managed/seq/vicPac1.fa vicPac2 vicPac2 Alpaca Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2) (vicPac2) /cvmfs/data.galaxyproject.org/managed/seq/vicPac2.fa allMis1 allMis1 American alligator Aug. 2012 (allMis0.2/allMis1) (allMis1) /cvmfs/data.galaxyproject.org/managed/seq/allMis1.fa gadMor1 gadMor1 Atlantic cod May 2010 (Genofisk GadMor_May2010/gadMor1) (gadMor1) /cvmfs/data.galaxyproject.org/managed/seq/gadMor1.fa dasNov3 dasNov3 Armadillo Dec. 2011 (Baylor/dasNov3) (dasNov3) /cvmfs/data.galaxyproject.org/managed/seq/dasNov3.fa panPan1 panPan1 Bonobo May. 2012 (Max-Planck/panPan1) (panPan1) /cvmfs/data.galaxyproject.org/managed/seq/panPan1.fa felCat8 felCat8 Cat Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) (felCat8) /cvmfs/data.galaxyproject.org/managed/seq/felCat8.fa criGri1 criGri1 Chinese hamster Jul. 2013 (C_griseus_v1.0/criGri1) (criGri1) /cvmfs/data.galaxyproject.org/managed/seq/criGri1.fa latCha1 latCha1 Coelacanth Aug. 2011 (Broad/latCha1) (latCha1) /cvmfs/data.galaxyproject.org/managed/seq/latCha1.fa