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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 /path/to/bank/bowtiedb/AthalianaAllChr
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36 #Drosophila_melanogaster_AllChr Drosophila_melanogaster_AllChr Drosophila melanogaster All Chr /path/to/bank/bowtiedb/Drosophila_melanogaster_AllChr
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37 #Homo_sapiens_AllChr Homo_sapiens_AllChr Homo_sapiens_AllChr /path/to/bank/bowtiedb/Homo_sapiens_AllChr
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38 #yeast.nt yeast.nt yeast nt /path/to/bank/bowtiedb/yeast.nt
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39
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40 #Banques definitives transmises par l administrateur system sur /path/to/bank/bowtiedb
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41 Arabidopsis_thaliana Arabidopsis_thaliana Arabidopsis thaliana /path/to/bank/bowtie2db/Arabidopsis_thaliana
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42 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
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43 Capra_hircus Capra_hircus Capra_hircus /path/to/bank/bowtie2db/Capra_hircus
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44 Danio_rerio_Zv9_62_chr_22 Danio_rerio_Zv9_62_chr_22 Danio rerio Zv9 62 chr 22 /path/to/bank/bowtie2db/Danio_rerio.Zv9.62
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45 Drosophila_melanogaster_AllChr Drosophila_melanogaster_AllChr Drosophila melanogaster AllChr /path/to/bank/bowtie2db/Drosophila_melanogaster_AllChr
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46 ensembl_bos_taurus_genome ensembl_bos_taurus_genome ensembl bos taurus genome /path/to/bank/bowtie2db/ensembl_bos_taurus_genome
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47 ensembl_danio_rerio_genome ensembl_danio_rerio_genome ensembl danio rerio genome /path/to/bank/bowtie2db/ensembl_danio_rerio_genome
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48 ensembl_equus_caballus_genome ensembl_equus_caballus_genome ensembl equus caballus genome /path/to/bank/bowtie2db/ensembl_equus_caballus_genome
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49 ensembl_gallus_gallus_genome ensembl_gallus_gallus_genome ensembl gallus gallus genome /path/to/bank/bowtie2db/ensembl_gallus_gallus_genome
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50 ensembl_homo_sapiens_genome ensembl_homo_sapiens_genome ensembl homo sapiens genome /path/to/bank/bowtie2db/ensembl_homo_sapiens_genome
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51 ensembl_mus_musculus_genome ensembl_mus_musculus_genome ensembl mus musculus genome /path/to/bank/bowtie2db/ensembl_mus_musculus_genome
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52 ensembl_oreochromis_niloticus_genome ensembl_oreochromis_niloticus_genome ensembl oreochromis niloticus genome /path/to/bank/bowtie2db/ensembl_oreochromis_niloticus_genome
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53 ensembl_ovis_aries_genome ensembl_ovis_aries_genome ensembl ovis aries genome v3 /path/to/bank/bowtie2db/ensembl_ovis_aries_genome
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54 ensembl_rattus_norvegicus_genome ensembl_rattus_norvegicus_genome ensembl rattus norvegicus genome /path/to/bank/bowtie2db/ensembl_rattus_norvegicus_genome
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55 ensembl_sus_scrofa_genome susScr3 ensembl sus scrofa genome /path/to/bank/bowtie2db/ensembl_sus_scrofa_genome
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56 ensembl_gadus_morhua_genome ensembl_gadus_morhua_genome ensembl gadus morhua gadMor1 (Jan 2010) /path/to/bank/bowtie2db/ensembl_gadus_morhua_genome
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57 ensembl_oryzias_latipes_genome ensembl_oryzias_latipes_genome ensembl oryzias latipes HdrR Oct 2005 /path/to/bank/bowtie2db/ensembl_oryzias_latipes_genome
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58 Mycoplasma_agalactiae_GCF_000089865 Mycoplasma_agalactiae_GCF_000089865 Mycoplasma_agalactiae_GCF_000089865 /path/to/bank/ncbi/genomes/Assembly_Bacteria/Assembly_Bacteria_2014-06-24/bowtie2/Mycoplasma_agalactiae_GCF_000089865
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59 Mycoplasma_agalactiae_PG2_uid61619 Mycoplasma_agalactiae_PG2_uid61619 Mycoplasma_agalactiae_PG2_uid61619 /path/to/bank/bowtie2db/Mycoplasma_agalactiae_PG2_uid61619_test
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60 Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 /path/to/bank/bowtie2db/Mycoplasma_agalactiae_uid46679_test
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61 Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 /path/to/bank/bowtie2db/Mycoplasma_bovis_HB0801_uid168665_test
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62 Mycoplasma_bovis_Hubei_1_uid68691 Mycoplasma_bovis_Hubei_1_uid68691 Mycoplasma_bovis_Hubei_1_uid68691 /path/to/bank/bowtie2db/Mycoplasma_bovis_Hubei_1_uid68691_test
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63 Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 /path/to/bank/bowtie2db/Mycoplasma_bovis_PG45_uid60859_test
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64 Mycoplasma_capricolum_ATCC_27343_uid58525 Mycoplasma_capricolum_ATCC_27343_uid58525 Mycoplasma_capricolum_ATCC_27343_uid58525 /path/to/bank/bowtie2db/Mycoplasma_capricolum_ATCC_27343_uid58525_test
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65 Mycoplasma_hominis_ATCC_23114_uid41875 Mycoplasma_hominis_ATCC_23114_uid41875 Mycoplasma_hominis_ATCC_23114_uid41875 /path/to/bank/bowtie2db/Mycoplasma_hominis_ATCC_23114_uid41875_test
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66 Mycoplasma_mycoides_capri_LC_95010_uid66189 Mycoplasma_mycoides_capri_LC_95010_uid66189 Mycoplasma_mycoides_capri_LC_95010_uid66189 /path/to/bank/bowtie2db/Mycoplasma_mycoides_capri_LC_95010_uid66189_test
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67 Mycoplasma_mycoides_SC_Gladysdale_uid197153 Mycoplasma_mycoides_SC_Gladysdale_uid197153 Mycoplasma_mycoides_SC_Gladysdale_uid197153 /path/to/bank/bowtie2db/Mycoplasma_mycoides_SC_Gladysdale_uid197153_test
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68 Mycoplasma_mycoides_SC_PG1_uid58031 Mycoplasma_mycoides_SC_PG1_uid58031 Mycoplasma_mycoides_SC_PG1_uid58031 /path/to/bank/bowtie2db/Mycoplasma_mycoides_SC_PG1_uid58031_test
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69 Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_309_uid85495_test
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70 Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_FH_uid162027_test
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71 Mycoplasma_pneumoniae_M129_B7_uid185759 Mycoplasma_pneumoniae_M129_B7_uid185759 Mycoplasma_pneumoniae_M129_B7_uid185759 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_M129_B7_uid185759_test
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72 Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_M129_uid57709_test
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73 oryCun2_ucsc oryCun2_ucsc oryCun2 ucsc /path/to/bank/bowtie2db/oryCun2_ucsc
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74 #Note that for backwards compatibility with workflows, the unique ID of
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75 #an entry must be the path that was in the original loc file, because that
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76 #is the value stored in the workflow for that parameter. That is why the
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77 #hg19 entry above looks odd. New genomes can be better-looking.
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78 #
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