Mercurial > repos > sarahinraauzeville > star
comparison STAR_indexes.loc.sample @ 6:b7ed4ee33fb6 draft default tip
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| author | sarahinraauzeville |
|---|---|
| date | Mon, 09 Dec 2019 10:55:33 -0500 |
| parents | c4fc8ff6e280 |
| children |
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| 5:c4fc8ff6e280 | 6:b7ed4ee33fb6 |
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| 1 #This is a sample file distributed with Galaxy that enables tools | |
| 2 #to use a directory of Bowtie indexed sequences data files. You will | |
| 3 #need to create these data files and then create a bowtie_indices.loc | |
| 4 #file similar to this one (store it in this directory) that points to | |
| 5 #the directories in which those files are stored. The bowtie_indices.loc | |
| 6 #file has this format (longer white space characters are TAB characters): | |
| 7 # | |
| 8 #<unique_build_id> <dbkey> <display_name> <file_base_path> | |
| 9 # | |
| 10 #So, for example, if you had hg18 indexed stored in | |
| 11 #/depot/data2/galaxy/bowtie/hg18/, | |
| 12 #then the bowtie_indices.loc entry would look like this: | |
| 13 # | |
| 14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 | |
| 15 # | |
| 16 #and your /depot/data2/galaxy/bowtie/hg18/ directory | |
| 17 #would contain hg18.*.ebwt files: | |
| 18 # | |
| 19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt | |
| 20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt | |
| 21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt | |
| 22 #...etc... | |
| 23 # | |
| 24 #Your bowtie_indices.loc file should include an entry per line for each | |
| 25 #index set you have stored. The "file" in the path does not actually | |
| 26 #exist, but it is the prefix for the actual index files. For example: | |
| 27 # | |
| 28 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon | |
| 29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full | |
| 30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 | |
| 31 #...etc... | |
| 32 # | |
| 33 | |
| 34 #Banques temporaires mises en place au debut de l installation de Galaxy | |
| 35 #AthalianaAllChr AthalianaAllChr AthalianaAllChr /bank/bowtiedb/AthalianaAllChr | |
| 36 #Drosophila_melanogaster_AllChr Drosophila_melanogaster_AllChr Drosophila melanogaster All Chr /bank/bowtiedb/Drosophila_melanogaster_AllChr | |
| 37 #Homo_sapiens_AllChr Homo_sapiens_AllChr Homo_sapiens_AllChr /bank/bowtiedb/Homo_sapiens_AllChr | |
| 38 #yeast.nt yeast.nt yeast nt /bank/bowtiedb/yeast.nt | |
| 39 | |
| 40 #Banques definitives transmises par l administrateur system sur /bank/bowtiedb | |
| 41 STAR-Arabidopsis_thaliana STAR-Arabidopsis_thaliana STAR-Arabidopsis_thaliana /bank/STARdb/STAR-Arabidopsis_thaliana | |
| 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 | |
| 43 STAR-Gorilla_gorilla STAR-Gorilla_gorilla STAR-Gorilla_gorilla /bank/STARdb/STAR-Gorilla_gorilla | |
| 44 STAR-hg38 hg38 STAR-ensembl_homo_sapiens_genome (GRCh38/hg38) /galaxydata/galaxy_bank/homo_sapiens/hg38/ensembl-89 | |
| 45 STAR-Homo_sapiens_AllChr STAR-Homo_sapiens_AllChr STAR-Homo_sapiens_AllChr /bank/STARdb/STAR-Homo_sapiens_AllChr | |
| 46 STAR-ensembl_bos_taurus_genome STAR-ensembl_bos_taurus_genome STAR-ensembl_bos_taurus_genome /bank/STARdb/STAR-ensembl_bos_taurus_genome | |
| 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 | |
| 48 STAR-Macaca_mulatta STAR-Macaca_mulatta STAR-Macaca_mulatta /bank/STARdb/STAR-Macaca_mulatta | |
| 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 | |
| 50 STAR-ensembl_rattus_norvegicus_genome STAR-ensembl_rattus_norvegicus_genome STAR-ensembl_rattus_norvegicus_genome /bank/STARdb/STAR-ensembl_rattus_norvegicus_genome | |
| 51 STAR-Nomascus_leucogenys STAR-Nomascus_leucogenys STAR-Nomascus_leucogenys /bank/STARdb/STAR-Nomascus_leucogenys | |
| 52 STAR-ensembl_equus_caballus_genome STAR-ensembl_equus_caballus_genome STAR-ensembl_equus_caballus_genome /bank/STARdb/STAR-ensembl_equus_caballus_genome | |
| 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 | |
| 54 STAR-Pan_troglodytes STAR-Pan_troglodytes STAR-Pan_troglodytes /bank/STARdb/STAR-Pan_troglodytes | |
| 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 | |
| 56 # STAR-ensembl_sus_scrofa_genome susScr4 ensembl sus_scrofa genome /bank/STARdb/STAR-ensembl_sus_scrofa_genome | |
| 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 | |
| 58 # | |
| 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 | |
| 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 | |
| 61 # | |
| 62 STAR-Papio_anubis STAR-Papio_anubis STAR-Papio_anubis /bank/STARdb/STAR-Papio_anubis | |
| 63 STAR-ensembl_gallus_gallus_genome STAR-ensembl_gallus_gallus_genome STAR-ensembl_gallus_gallus_genome /bank/STARdb/STAR-ensembl_gallus_gallus_genome | |
| 64 STAR-Pongo_abelii STAR-Pongo_abelii STAR-Pongo_abelii /bank/STARdb/STAR-Pongo_abelii | |
| 65 STAR-ensembl_danio_rerio_genome STAR-ensembl_danio_rerio_genome STAR-ensembl_danio_rerio_genome /bank/STARdb/STAR-ensembl_danio_rerio_genome | |
| 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 | |
| 67 STAR-ensembl_oreochromis_niloticus_genome STAR-ensembl_oreochromis_niloticus_genome STAR-ensembl_oreochromis_niloticus_genome /bank/STARdb/STAR-ensembl_oreochromis_niloticus_genome | |
| 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 | |
| 69 STAR_oryCun2_ucsc STAR_oryCun2_ucsc STAR oryCun2 ucsc /bank/STARdb/STAR-oryCun2_ucsc | |
| 70 STAR-Capra_hircus STAR-Capra_hircus STAR-Capra_hircus /bank/STARdb/STAR-Capra_hircus | |
| 71 STAR-ensembl_ovis_aries_genome STAR-ensembl_ovis_aries_genome STAR-ensembl_ovis_aries_genome /bank/STARdb/STAR-ensembl_ovis_aries_genome | |
| 72 STAR-Mycoplasma_agalactiae_PG2_uid61619 STAR-Mycoplasma_agalactiae_PG2_uid61619 STAR-Mycoplasma_agalactiae_PG2_uid61619 /bank/STARdb/STAR-Mycoplasma_agalactiae_PG2_uid61619_test | |
| 73 Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 /bank/STARdb/STAR-Mycoplasma_agalactiae_uid46679_test | |
| 74 Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 /bank/STARdb/STAR-Mycoplasma_bovis_HB0801_uid168665_test | |
| 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 | |
| 76 Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 /bank/STARdb/STAR-Mycoplasma_bovis_PG45_uid60859_test | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 82 Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 /bank/STARdb/STAR-Mycoplasma_pneumoniae_309_uid85495_test | |
| 83 Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 /bank/STARdb/STAR-Mycoplasma_pneumoniae_FH_uid162027_test | |
| 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 | |
| 85 Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 /bank/STARdb/STAR-Mycoplasma_pneumoniae_M129_uid57709_test | |
| 86 Mycoplasma_agalactiae_GCF_000089865 Mycoplasma_agalactiae_GCF_000089865 Mycoplasma_agalactiae_GCF_000089865 /bank/STARdb/STAR-Mycoplasma_agalactiae_GCF_000089865 | |
| 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 | |
| 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 | |
| 89 STAR-ensembl_canis_familiaris_genome STAR-ensembl_canis_familiaris_genome STAR-ensembl_canis_familiaris_genome /bank/STARdb/STAR-ensembl_canis_familiaris_genome | |
| 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 | |
| 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 | |
| 92 #Note that for backwards compatibility with workflows, the unique ID of | |
| 93 #an entry must be the path that was in the original loc file, because that | |
| 94 #is the value stored in the workflow for that parameter. That is why the | |
| 95 #hg19 entry above looks odd. New genomes can be better-looking. | |
| 96 # |