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5
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1 #This is a sample file distributed with Galaxy that enables tools
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2 #to use a directory of Bowtie indexed sequences data files. You will
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3 #need to create these data files and then create a bowtie_indices.loc
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4 #file similar to this one (store it in this directory) that points to
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5 #the directories in which those files are stored. The bowtie_indices.loc
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6 #file has this format (longer white space characters are TAB characters):
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7 #
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8 #<unique_build_id> <dbkey> <display_name> <file_base_path>
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9 #
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10 #So, for example, if you had hg18 indexed stored in
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11 #/depot/data2/galaxy/bowtie/hg18/,
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12 #then the bowtie_indices.loc entry would look like this:
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13 #
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14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
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15 #
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16 #and your /depot/data2/galaxy/bowtie/hg18/ directory
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17 #would contain hg18.*.ebwt files:
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18 #
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
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22 #...etc...
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23 #
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24 #Your bowtie_indices.loc file should include an entry per line for each
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25 #index set you have stored. The "file" in the path does not actually
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26 #exist, but it is the prefix for the actual index files. For example:
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27 #
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28 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
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29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
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30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
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31 #...etc...
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32 #
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33
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34 #Banques temporaires mises en place au debut de l installation de Galaxy
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35 #AthalianaAllChr AthalianaAllChr AthalianaAllChr /bank/bowtiedb/AthalianaAllChr
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36 #Drosophila_melanogaster_AllChr Drosophila_melanogaster_AllChr Drosophila melanogaster All Chr /bank/bowtiedb/Drosophila_melanogaster_AllChr
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37 #Homo_sapiens_AllChr Homo_sapiens_AllChr Homo_sapiens_AllChr /bank/bowtiedb/Homo_sapiens_AllChr
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38 #yeast.nt yeast.nt yeast nt /bank/bowtiedb/yeast.nt
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39
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40 #Banques definitives transmises par l administrateur system sur /bank/bowtiedb
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41 STAR-Arabidopsis_thaliana STAR-Arabidopsis_thaliana STAR-Arabidopsis_thaliana /bank/STARdb/STAR-Arabidopsis_thaliana
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42 STAR-ensembl_gallus_gallus_genome_masked STAR-ensembl_gallus_gallus_genome_masked STAR-ensembl_gallus_gallus_genome_masked /bank/STARdb/STAR-ensembl_gallus_gallus_genome_soft_masked
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43 STAR-Gorilla_gorilla STAR-Gorilla_gorilla STAR-Gorilla_gorilla /bank/STARdb/STAR-Gorilla_gorilla
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44 STAR-hg38 hg38 STAR-ensembl_homo_sapiens_genome (GRCh38/hg38) /galaxydata/galaxy_bank/homo_sapiens/hg38/ensembl-89
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45 STAR-Homo_sapiens_AllChr STAR-Homo_sapiens_AllChr STAR-Homo_sapiens_AllChr /bank/STARdb/STAR-Homo_sapiens_AllChr
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46 STAR-ensembl_bos_taurus_genome STAR-ensembl_bos_taurus_genome STAR-ensembl_bos_taurus_genome /bank/STARdb/STAR-ensembl_bos_taurus_genome
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47 STAR-ensembl_homo_sapiens_genome_masked STAR-ensembl_homo_sapiens_genome_masked STAR-ensembl_homo_sapiens_genome_masked /bank/STARdb/STAR-ensembl_homo_sapiens_genome_soft_masked
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48 STAR-Macaca_mulatta STAR-Macaca_mulatta STAR-Macaca_mulatta /bank/STARdb/STAR-Macaca_mulatta
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49 STAR-ensembl_bos_taurus_genome_masked STAR-ensembl_bos_taurus_genome_masked STAR-ensembl_bos_taurus_genome_masked /bank/STARdb/STAR-ensembl_bos_taurus_genome_soft_masked
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50 STAR-ensembl_rattus_norvegicus_genome STAR-ensembl_rattus_norvegicus_genome STAR-ensembl_rattus_norvegicus_genome /bank/STARdb/STAR-ensembl_rattus_norvegicus_genome
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51 STAR-Nomascus_leucogenys STAR-Nomascus_leucogenys STAR-Nomascus_leucogenys /bank/STARdb/STAR-Nomascus_leucogenys
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52 STAR-ensembl_equus_caballus_genome STAR-ensembl_equus_caballus_genome STAR-ensembl_equus_caballus_genome /bank/STARdb/STAR-ensembl_equus_caballus_genome
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53 STAR-ensembl_rattus_norvegicus_genome_masked STAR-ensembl_rattus_norvegicus_genome_masked STAR-ensembl_rattus_norvegicus_genome_masked /bank/STARdb/STAR-ensembl_rattus_norvegicus_genome_soft_masked
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54 STAR-Pan_troglodytes STAR-Pan_troglodytes STAR-Pan_troglodytes /bank/STARdb/STAR-Pan_troglodytes
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55 STAR-ensembl_equus_caballus_genome_masked STAR-ensembl_equus_caballus_genome_masked STAR-ensembl_equus_caballus_genome_masked /bank/STARdb/STAR-ensembl_equus_caballus_genome_soft_masked
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56 # STAR-ensembl_sus_scrofa_genome susScr4 ensembl sus_scrofa genome /bank/STARdb/STAR-ensembl_sus_scrofa_genome
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57 # STAR-ensembl_sus_scrofa_genome_masked STAR-ensembl_sus_scrofa_genome_masked STAR-ensembl_sus_scrofa_genome_masked /bank/STARdb/STAR-ensembl_sus_scrofa_genome_soft_masked
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58 #
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59 STAR-ensembl_sus_scrofa_V10.2 susScr3 Ensembl sus_scrofa genome V10.2 /galaxydata/galaxy_bank/sus_scrofa/Sscrofa10.2/ensembl-89/STAR-ensembl_sus_scrofa_genome
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60 STAR-ensembl_sus_scrofa_V11.1 susScr11 Ensembl sus_scrofa genome V11.1 /galaxydata/galaxy_bank/sus_scrofa/Sscrofa11.1/ensembl-90/STAR-ensembl_sus_scrofa_genome
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61 #
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62 STAR-Papio_anubis STAR-Papio_anubis STAR-Papio_anubis /bank/STARdb/STAR-Papio_anubis
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63 STAR-ensembl_gallus_gallus_genome STAR-ensembl_gallus_gallus_genome STAR-ensembl_gallus_gallus_genome /bank/STARdb/STAR-ensembl_gallus_gallus_genome
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64 STAR-Pongo_abelii STAR-Pongo_abelii STAR-Pongo_abelii /bank/STARdb/STAR-Pongo_abelii
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65 STAR-ensembl_danio_rerio_genome STAR-ensembl_danio_rerio_genome STAR-ensembl_danio_rerio_genome /bank/STARdb/STAR-ensembl_danio_rerio_genome
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66 STAR-ensembl_danio_rerio_genome_masked STAR-ensembl_danio_rerio_genome_masked STAR-ensembl_danio_rerio_genome_masked /bank/STARdb/STAR-ensembl_danio_rerio_genome_soft_masked
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67 STAR-ensembl_oreochromis_niloticus_genome STAR-ensembl_oreochromis_niloticus_genome STAR-ensembl_oreochromis_niloticus_genome /bank/STARdb/STAR-ensembl_oreochromis_niloticus_genome
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68 STAR-ensembl_oreochromis_niloticus_genome_nonchomosomal STAR-ensembl_oreochromis_niloticus_genome_nonchomosomal STAR-ensembl_oreochromis_niloticus_genome_nonchomosomal /bank/STARdb/STAR-ensembl_oreochromis_niloticus_genome_non_chromosomal
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69 STAR_oryCun2_ucsc STAR_oryCun2_ucsc STAR oryCun2 ucsc /bank/STARdb/STAR-oryCun2_ucsc
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70 STAR-Capra_hircus STAR-Capra_hircus STAR-Capra_hircus /bank/STARdb/STAR-Capra_hircus
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71 STAR-ensembl_ovis_aries_genome STAR-ensembl_ovis_aries_genome STAR-ensembl_ovis_aries_genome /bank/STARdb/STAR-ensembl_ovis_aries_genome
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72 STAR-Mycoplasma_agalactiae_PG2_uid61619 STAR-Mycoplasma_agalactiae_PG2_uid61619 STAR-Mycoplasma_agalactiae_PG2_uid61619 /bank/STARdb/STAR-Mycoplasma_agalactiae_PG2_uid61619_test
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73 Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 /bank/STARdb/STAR-Mycoplasma_agalactiae_uid46679_test
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74 Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 /bank/STARdb/STAR-Mycoplasma_bovis_HB0801_uid168665_test
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75 Mycoplasma_bovis_Hubei_1_uid68691 Mycoplasma_bovis_Hubei_1_uid68691 Mycoplasma_bovis_Hubei_1_uid68691 /bank/STARdb/STAR-Mycoplasma_bovis_Hubei_1_uid68691_test
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76 Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 /bank/STARdb/STAR-Mycoplasma_bovis_PG45_uid60859_test
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77 Mycoplasma_capricolum_ATCC_27343_uid58525 Mycoplasma_capricolum_ATCC_27343_uid58525 Mycoplasma_capricolum_ATCC_27343_uid58525 /bank/STARdb/STAR-Mycoplasma_capricolum_ATCC_27343_uid58525_test
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78 Mycoplasma_hominis_ATCC_23114_uid41875 Mycoplasma_hominis_ATCC_23114_uid41875 Mycoplasma_hominis_ATCC_23114_uid41875 /bank/STARdb/STAR-Mycoplasma_hominis_ATCC_23114_uid41875_test
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79 Mycoplasma_mycoides_capri_LC_95010_uid66189 Mycoplasma_mycoides_capri_LC_95010_uid66189 Mycoplasma_mycoides_capri_LC_95010_uid66189 /bank/STARdb/STAR-Mycoplasma_mycoides_capri_LC_95010_uid66189_test
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80 Mycoplasma_mycoides_SC_Gladysdale_uid197153 Mycoplasma_mycoides_SC_Gladysdale_uid197153 Mycoplasma_mycoides_SC_Gladysdale_uid197153 /bank/STARdb/STAR-Mycoplasma_mycoides_SC_Gladysdale_uid197153_test
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81 Mycoplasma_mycoides_SC_PG1_uid58031 Mycoplasma_mycoides_SC_PG1_uid58031 Mycoplasma_mycoides_SC_PG1_uid58031 /bank/STARdb/STAR-Mycoplasma_mycoides_SC_PG1_uid58031_test
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82 Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 /bank/STARdb/STAR-Mycoplasma_pneumoniae_309_uid85495_test
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83 Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 /bank/STARdb/STAR-Mycoplasma_pneumoniae_FH_uid162027_test
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84 Mycoplasma_pneumoniae_M129_B7_uid185759 Mycoplasma_pneumoniae_M129_B7_uid185759 Mycoplasma_pneumoniae_M129_B7_uid185759 /bank/STARdb/STAR-Mycoplasma_pneumoniae_M129_B7_uid185759_test
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85 Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 /bank/STARdb/STAR-Mycoplasma_pneumoniae_M129_uid57709_test
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86 Mycoplasma_agalactiae_GCF_000089865 Mycoplasma_agalactiae_GCF_000089865 Mycoplasma_agalactiae_GCF_000089865 /bank/STARdb/STAR-Mycoplasma_agalactiae_GCF_000089865
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87 Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865 Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865 Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865 /bank/ncbi/genomes/Assembly_Bacteria/Assembly_Bacteria_2014-06-24/STAR/STAR-Mycoplasma_agalactiae_GCF_000089865
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88 STAR-ensembl_canis_familiaris_genome_soft_masked STAR-ensembl_canis_familiaris_genome_soft_masked STAR-ensembl_canis_familiaris_genome_soft_masked /bank/STARdb/STAR-ensembl_canis_familiaris_genome_soft_masked
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89 STAR-ensembl_canis_familiaris_genome STAR-ensembl_canis_familiaris_genome STAR-ensembl_canis_familiaris_genome /bank/STARdb/STAR-ensembl_canis_familiaris_genome
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90 STAR-ensembl_mus_musculus_primary_genome STAR-ensembl_mus_musculus_primary_genome STAR-ensembl_mus_musculus_primary_genome /bank/STARdb/STAR-ensembl_mus_musculus_primary_genome
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91 STAR-Ovis_aries_2015-12-19_NCBI STAR-Ovis_aries_2015-12-19_NCBI STAR-Ovis_aries_2015-12-19_NCBI /bank/ncbi/genomes/Ovis_aries/current/STAR/STAR-Ovis_aries
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92 #Note that for backwards compatibility with workflows, the unique ID of
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93 #an entry must be the path that was in the original loc file, because that
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94 #is the value stored in the workflow for that parameter. That is why the
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95 #hg19 entry above looks odd. New genomes can be better-looking.
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96 #
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