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1 # bowtie2_indices.loc.sample
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2 # This is a *.loc.sample file distributed with Galaxy that enables tools
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3 # to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
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4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
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5 # First create these data files and save them in your own data directory structure.
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6 # Then, create a bowtie_indices.loc file to use those indexes with tools.
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7 # Copy this file, save it with the same name (minus the .sample),
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8 # follow the format examples, and store the result in this directory.
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9 # The file should include an one line entry for each index set.
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10 # The path points to the "basename" for the set, not a specific file.
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11 # It has four text columns seperated by TABS.
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12 #
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13 # <unique_build_id> <dbkey> <display_name> <file_base_path>
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14 #
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15 # So, for example, if you had hg18 indexes stored in:
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16 #
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17 # /depot/data2/galaxy/hg19/bowtie2/
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18 #
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19 # containing hg19 genome and hg19.*.bt2 files, such as:
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20 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
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21 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
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22 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
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23 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
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24 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
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25 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
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26 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
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27 #
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28 # then the bowtie2_indices.loc entry could look like this:
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29 #
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30 #
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31 Hsa Human (Homo sapiens) - hg38
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32 Mml Rhesus monkey (Macaca mulatta) - rheMac8
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33 Mmu House mouse (Mus musculus) - mm10
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34 Rno Norway rat (Rattus norvegicus) - rn6
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35 Cpo Guinea pig (Cavia porcellus) - cavPor3
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36 Ocu Rabbit (Oryctolagus cuniculus) - oryCun2
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37 Cfa Dog (Canis familiaris) - canFam3
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38 Bta Cow (Bos taurus) - bosTau8
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39 Dno Nine-banded armadillo (Dasypus novemcinctus) - dasNov3
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40 Ete Lesser hedgehog tenrec (Echinops telfairi) - echTel2
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41 Sha Tasmanian devil (Sarcophilus harrisii) - DEVIL7_traces
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42 Mdo Gray short-tailed opossum (Monodelphis domestica) - monDom5
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43 Oan Platypus (Ornithorhynchus anatinus) - mOrnAna1.p.v1_plustraces
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44 Gga Chicken (Gallus gallus) - galGal5
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45 Cli Rock pigeon (Columba livia) - colLiv2
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46 Tgu Zebra finch (Taeniopygia guttata) - taeGut3.2.4
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47 Ami American alligator (Alligator mississippiensis) - allMis1
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48 Cpi Western painted turtle (Chrysemys picta bellii) - chrPic1
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49 Aca Green anole lizard (Anolis carolinensis) - anoCar2
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50 Xtr Tropical clawed frog (Xenopus tropicalis) - xenTro7
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51 Dre Zebrafish (Danio rerio) - danRer11
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52 Sto Cloudy Catshark (Scyliorhinus torazame) - miRNA_loci_genome
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53 Cin Sea Squirt (Ciona intestinalis) - ci3
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54 Bfl Florida lancelet (Branchiostoma floridae) - BFL_v2.0
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55 Sko Saccoglossus (Saccoglossus kowalevskii) - Skow_1.1
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56 Pfl Ptychodera (Ptychodera flava) - Pfl
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57 Spu Purple sea urchin (Strongylocentrotus purpuratus) - Spur_3.1
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58 Pmi Bat starfish (Patiria miniata) - Pmin1
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59 Dme Fruit fly (Drosophila melanogaster) - dm6
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60 Dan Fruit fly (Drosophila ananassae) - Dana_caf1
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61 Dmo Fruit fly (Drosophila mojavensis) - Dmoj_caf1
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62 Aae Yellow fever mosquito (Aedes aegypti) - Aaeg_L3
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63 Hme Longwing butterfly (Heliconius melpomene) - Hmel_1
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64 Tca Red flour beetle (Tribolium castaneum) - Tcas5.2
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65 Bge Cockroach (Blattella germanica) - Bger_2.0
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66 Dpu Common water flea (Daphnia pulex) - Daphnia_pulex.V1.0
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67 Isc Deer tick (Ixodes scapularis) - IscaWI
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68 Cel Roundworm (Caenorhabditis elegans) - ce11
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69 Cbr Roundworm (Caenorhabditis briggsae) - CB4
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70 Asu Large roundworm (Ascaris suum) - ASU_PRJNA80881_plustraces
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71 Cte Polychaete worm (Capitella teleta) - Capitella_teleta_v1.0
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72 Efe Common brandling worm (Eisenia fetida) - Efe_combined
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73 Lgi Owl limpet (Lottia gigantea) - Lotgi1
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74 Cgi Pacific oyster (Crassostrea gigas) - CGI_GCA_000297895.1
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75 Lan Lingula (Lingula anatina) - LinAna_1.0
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76 #
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77 #
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78 #
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79 #
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80 #
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