# tophat2_indices.loc.sample # This is a *.loc.sample file distributed with Galaxy that enables tools # to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup # First create these data files and save them in your own data directory structure. # Then, create a bowtie_indices.loc file to use those indexes with tools. # Copy this file, save it with the same name (minus the .sample), # follow the format examples, and store the result in this directory. # The file should include an one line entry for each index set. # The path points to the "basename" for the set, not a specific file. # It has four text columns seperated by TABS. # # # # So, for example, if you had hg18 indexes stored in: # # /depot/data2/galaxy/hg19/bowtie2/ # # containing hg19 genome and hg19.*.bt2 files, such as: # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 # # then the bowtie2_indices.loc entry could look like this: # #hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon # #More examples: # #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 # # sacCer3 sacCer3 Yeast (Saccharomyces cerevisiae): sacCer3 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/sacCer3/sacCer3 sacCer2 sacCer2 Yeast (Saccharomyces cerevisiae): sacCer2 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/sacCer2/sacCer2 Schizosaccharomyces_pombe_1.1 Schizosaccharomyces_pombe_1.1 Fission Yeast (Schizosaccharomyces pombe): Schizosaccharomyces_pombe_1.1 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/Schizosaccharomyces_pombe_1.1/Schizosaccharomyces_pombe_1.1 galgal4 galGal4 Chicken (Nov 2011, Gallus gallus) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/galgal4/galgal4 loxAfr1 loxAfr1 Elephant (Loxodonta africana africana): loxAfr1 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/loxAfr1/loxAfr1 loxAfr3 loxAfr3 Elephant (Loxodonta africana africana): loxAfr3 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/loxAfr3/loxAfr3 oryza_sativa_japonica_nipponbare_IRGSP4.0 oryza_sativa_japonica_nipponbare_IRGSP4.0 Rice (Oryza sativa L. ssp. japonica var. Nipponbare): IRGSP4.0 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/oryza_sativa_japonica_nipponbare_IRGSP4.0/oryza_sativa_japonica_nipponbare_IRGSP4.0 rn6 rn6 Rat Jul. 2014 (RGSC 6.0/rn6) (rn6) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/rn6/rn6 dm6 dm6 D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) (dm6) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/dm6/dm6 musFur1 musFur1 Ferret Apr. 2011 (MusPutFur1.0/musFur1) (musFur1) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/musFur1/musFur1 cerSim1 cerSim1 White rhinoceros May 2012 (CerSimSim1.0/cerSim1) (cerSim1) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/cerSim1/cerSim1 nomLeu3 nomLeu3 Gibbon Oct. 2012 (GGSC Nleu3.0/nomLeu3) (nomLeu3) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/nomLeu3/nomLeu3 danRer10 danRer10 Zebrafish Sep. 2014 (GRCz10/danRer10) (danRer10) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/danRer10/danRer10 papAnu2 papAnu2 Baboon Mar. 2012 (Baylor Panu_2.0/papAnu2) (papAnu2) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/papAnu2/papAnu2 bosTau8 bosTau8 Cow Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8) (bosTau8) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/bosTau8/bosTau8 melGal1 melGal1 Turkey (Meleagris gallopavo): melGal1 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/melGal1/melGal1 equCab1 equCab1 Horse (Equus caballus): equCab1 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/equCab1/equCab1 rheMac2 rheMac2 Rhesus Macaque (Macaca mulatta): rheMac2 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/rheMac2/rheMac2 galGal4 galGal4 Chicken (Gallus gallus): galGal4 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/galGal4/galGal4 equCab2 equCab2 Horse (Equus caballus): equCab2 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/equCab2/equCab2 rheMac3 rheMac3 Rhesus Macaque (Macaca mulatta): rheMac3 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/rheMac3/rheMac3 eschColi_K12 eschColi_K12 Escherichia coli (str. K-12 substr. MG1655): eschColi_K12 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/eschColi_K12/eschColi_K12 melUnd1 melUnd1 Budgerigar (Melopsittacus undulatus): melUnd1 /cvmfs/data.galaxyproject.org/managed/bowtie2_index/melUnd1/melUnd1 vicPac1 vicPac1 Alpaca Jul. 2008 (Broad/vicPac1) (vicPac1) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/vicPac1/vicPac1 vicPac2 vicPac2 Alpaca Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2) (vicPac2) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/vicPac2/vicPac2 allMis1 allMis1 American alligator Aug. 2012 (allMis0.2/allMis1) (allMis1) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/allMis1/allMis1 gadMor1 gadMor1 Atlantic cod May 2010 (Genofisk GadMor_May2010/gadMor1) (gadMor1) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/gadMor1/gadMor1 dasNov3 dasNov3 Armadillo Dec. 2011 (Baylor/dasNov3) (dasNov3) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/dasNov3/dasNov3 panPan1 panPan1 Bonobo May. 2012 (Max-Planck/panPan1) (panPan1) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/panPan1/panPan1 felCat8 felCat8 Cat Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) (felCat8) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/felCat8/felCat8 aptMan1 aptMan1 Brown Kiwi Jun. 2015 (MPI-EVA AptMant0/aptMan1) (aptMan1) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/aptMan1/aptMan1 galGal3canon galGal3 Chicken (Gallus gallus): galGal3 Canonical /cvmfs/data.galaxyproject.org/managed/bowtie2_index/galGal3canon/galGal3canon galGal3full galGal3 Chicken (Gallus gallus): galGal3 Full /cvmfs/data.galaxyproject.org/managed/bowtie2_index/galGal3full/galGal3full apiMel4 apiMel4 A. mellifera 04 Nov 2010 (Amel_4.5/apiMel4) (apiMel4) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/apiMel4/apiMel4 Amel_4.5 Amel_4.5 A. mellifera Nov. 2010 (GCF_000002195.4/Amel_4.5) (Amel_4.5) /cvmfs/data.galaxyproject.org/managed/bowtie2_index/Amel_4.5/Amel_4.5