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view n_spiecies.loc.sample @ 10:f229307a77a7 draft
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| author | glogobyte |
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| date | Fri, 16 Oct 2020 19:05:49 +0000 |
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# bowtie2_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. # # <unique_build_id> <dbkey> <display_name> <file_base_path> # # 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: # Acacia auriculiformis Acacia auriculiformis Acacia auriculiformis Acacia mangium Acacia mangium Acacia mangium Acyrthosiphon pisum Acyrthosiphon pisum Acyrthosiphon pisum Aedes aegypti Aedes aegypti Aedes aegypti Aegilops tauschii Aegilops tauschii Aegilops tauschii Alligator mississippiensis Alligator mississippiensis Alligator mississippiensis Amborella trichopoda Amborella trichopoda Amborella trichopoda Amphimedon queenslandica Amphimedon queenslandica Amphimedon queenslandica Anas platyrhynchos Anas platyrhynchos Anas platyrhynchos Anolis carolinensis Anolis carolinensis Anolis carolinensis Anopheles gambiae Anopheles gambiae Anopheles gambiae Apis mellifera Apis mellifera Apis mellifera Aquilegia caerulea Aquilegia caerulea Aquilegia caerulea Arabidopsis lyrata Arabidopsis lyrata Arabidopsis lyrata Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana Arachis hypogaea Arachis hypogaea Arachis hypogaea Artibeus jamaicensis Artibeus jamaicensis Artibeus jamaicensis Ascaris suum Ascaris suum Ascaris suum Asparagus officinalis Asparagus officinalis Asparagus officinalis Astatotilapia burtoni Astatotilapia burtoni Astatotilapia burtoni Ateles geoffroyi Ateles geoffroyi Ateles geoffroyi Avicennia marina Avicennia marina Avicennia marina BK polyomavirus BK polyomavirus BK polyomavirus Bactrocera dorsalis Bactrocera dorsalis Bactrocera dorsalis Bandicoot papillomatosis Bandicoot papillomatosis Bandicoot papillomatosis Biston betularia Biston betularia Biston betularia Bombyx mori Bombyx mori Bombyx mori Bos taurus Bos taurus Bos taurus Bovine foamy Bovine foamy Bovine foamy Bovine herpesvirus Bovine herpesvirus Bovine herpesvirus Bovine leukemia Bovine leukemia Bovine leukemia Brachypodium distachyon Brachypodium distachyon Brachypodium distachyon Branchiostoma belcheri Branchiostoma belcheri Branchiostoma belcheri Branchiostoma floridae Branchiostoma floridae Branchiostoma floridae Brassica napus Brassica napus Brassica napus Brassica oleracea Brassica oleracea Brassica oleracea Brassica rapa Brassica rapa Brassica rapa Brugia malayi Brugia malayi Brugia malayi Bruguiera cylindrica Bruguiera cylindrica Bruguiera cylindrica Bruguiera gymnorhiza Bruguiera gymnorhiza Bruguiera gymnorhiza Caenorhabditis brenneri Caenorhabditis brenneri Caenorhabditis brenneri Caenorhabditis briggsae Caenorhabditis briggsae Caenorhabditis briggsae Caenorhabditis elegans Caenorhabditis elegans Caenorhabditis elegans Caenorhabditis remanei Caenorhabditis remanei Caenorhabditis remanei Callithrix jacchus Callithrix jacchus Callithrix jacchus Camelina sativa Camelina sativa Camelina sativa Canis familiaris Canis familiaris Canis familiaris Capitella teleta Capitella teleta Capitella teleta Capra hircus Capra hircus Capra hircus Carica papaya Carica papaya Carica papaya Cavia porcellus Cavia porcellus Cavia porcellus Cerebratulus lacteus Cerebratulus lacteus Cerebratulus lacteus Chlamydomonas reinhardtii Chlamydomonas reinhardtii Chlamydomonas reinhardtii Chrysemys picta Chrysemys picta Chrysemys picta Ciona intestinalis Ciona intestinalis Ciona intestinalis Ciona savignyi Ciona savignyi Ciona savignyi Citrus clementina Citrus clementina Citrus clementina Citrus reticulata Citrus reticulata Citrus reticulata Citrus sinensis Citrus sinensis Citrus sinensis Citrus trifoliata Citrus trifoliata Citrus trifoliata Columba livia Columba livia Columba livia Cricetulus griseus Cricetulus griseus Cricetulus griseus Cucumis melo Cucumis melo Cucumis melo Cucumis sativus Cucumis sativus Cucumis sativus Culex quinquefasciatus Culex quinquefasciatus Culex quinquefasciatus Cunninghamia lanceolata Cunninghamia lanceolata Cunninghamia lanceolata Cynara cardunculus Cynara cardunculus Cynara cardunculus Cyprinus carpio Cyprinus carpio Cyprinus carpio Danio rerio Danio rerio Danio rerio Daphnia pulex Daphnia pulex Daphnia pulex Dasypus novemcinctus Dasypus novemcinctus Dasypus novemcinctus Daubentonia madagascariensis Daubentonia madagascariensis Daubentonia madagascariensis Dictyostelium discoideum Dictyostelium discoideum Dictyostelium discoideum Digitalis purpurea Digitalis purpurea Digitalis purpurea Dinoponera quadriceps Dinoponera quadriceps Dinoponera quadriceps Drosophila ananassae Drosophila ananassae Drosophila ananassae Drosophila erecta Drosophila erecta Drosophila erecta Drosophila grimshawi Drosophila grimshawi Drosophila grimshawi Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster Drosophila mojavensis Drosophila mojavensis Drosophila mojavensis Drosophila persimilis Drosophila persimilis Drosophila persimilis Drosophila pseudoobscura Drosophila pseudoobscura Drosophila pseudoobscura Drosophila sechellia Drosophila sechellia Drosophila sechellia Drosophila simulans Drosophila simulans Drosophila simulans Drosophila virilis Drosophila virilis Drosophila virilis Drosophila willistoni Drosophila willistoni Drosophila willistoni Drosophila yakuba Drosophila yakuba Drosophila yakuba Duck enteritis Duck enteritis Duck enteritis Echinococcus granulosus Echinococcus granulosus Echinococcus granulosus Echinococcus multilocularis Echinococcus multilocularis Echinococcus multilocularis Ectocarpus siliculosus Ectocarpus siliculosus Ectocarpus siliculosus Elaeis guineensis Elaeis guineensis Elaeis guineensis Electrophorus electricus Electrophorus electricus Electrophorus electricus Epstein Barr Epstein Barr Epstein Barr Eptesicus fuscus Eptesicus fuscus Eptesicus fuscus Equus caballus Equus caballus Equus caballus Eugenia uniflora Eugenia uniflora Eugenia uniflora Fasciola hepatica Fasciola hepatica Fasciola hepatica Festuca arundinacea Festuca arundinacea Festuca arundinacea Fragaria vesca Fragaria vesca Fragaria vesca Fugu rubripes Fugu rubripes Fugu rubripes Gadus morhua Gadus morhua Gadus morhua Gallus gallus Gallus gallus Gallus gallus Glottidia pyramidata Glottidia pyramidata Glottidia pyramidata Glycine max Glycine max Glycine max Glycine soja Glycine soja Glycine soja Gorilla gorilla Gorilla gorilla Gorilla gorilla Gossypium arboreum Gossypium arboreum Gossypium arboreum Gossypium herbaceum Gossypium herbaceum Gossypium herbaceum Gossypium hirsutum Gossypium hirsutum Gossypium hirsutum Gossypium raimondii Gossypium raimondii Gossypium raimondii Gyrodactylus salaris Gyrodactylus salaris Gyrodactylus salaris Haemonchus contortus Haemonchus contortus Haemonchus contortus Haliotis rufescens Haliotis rufescens Haliotis rufescens Helianthus annuus Helianthus annuus Helianthus annuus Helianthus argophyllus Helianthus argophyllus Helianthus argophyllus Helianthus ciliaris Helianthus ciliaris Helianthus ciliaris Helianthus exilis Helianthus exilis Helianthus exilis Helianthus paradoxus Helianthus paradoxus Helianthus paradoxus Helianthus petiolaris Helianthus petiolaris Helianthus petiolaris Helianthus tuberosus Helianthus tuberosus Helianthus tuberosus Heliconius melpomene Heliconius melpomene Heliconius melpomene Heligmosomoides polygyrus Heligmosomoides polygyrus Heligmosomoides polygyrus Herpes B Herpes B Herpes B Herpes Simplex Herpes Simplex Herpes Simplex Herpesvirus of Herpesvirus of Herpesvirus of Herpesvirus saimiri Herpesvirus saimiri Herpesvirus saimiri Hevea brasiliensis Hevea brasiliensis Hevea brasiliensis Hippoglossus hippoglossus Hippoglossus hippoglossus Hippoglossus hippoglossus Homo sapiens Homo sapiens Homo sapiens Hordeum vulgare Hordeum vulgare Hordeum vulgare Human cytomegalovirus Human cytomegalovirus Human cytomegalovirus Human herpesvirus Human herpesvirus Human herpesvirus Human immunodeficiency Human immunodeficiency Human immunodeficiency Hydra magnipapillata Hydra magnipapillata Hydra magnipapillata Ictalurus punctatus Ictalurus punctatus Ictalurus punctatus Infectious laryngotracheitis Infectious laryngotracheitis Infectious laryngotracheitis Ixodes scapularis Ixodes scapularis Ixodes scapularis JC polyomavirus JC polyomavirus JC polyomavirus Kaposi sarcoma-associated Kaposi sarcoma-associated Kaposi sarcoma-associated Lagothrix lagotricha Lagothrix lagotricha Lagothrix lagotricha Lemur catta Lemur catta Lemur catta Leucosolenia complicata Leucosolenia complicata Leucosolenia complicata Linum usitatissimum Linum usitatissimum Linum usitatissimum Locusta migratoria Locusta migratoria Locusta migratoria Lottia gigantea Lottia gigantea Lottia gigantea Lotus japonicus Lotus japonicus Lotus japonicus Lytechinus variegatus Lytechinus variegatus Lytechinus variegatus Macaca mulatta Macaca mulatta Macaca mulatta Macaca nemestrina Macaca nemestrina Macaca nemestrina Macropus eugenii Macropus eugenii Macropus eugenii Malus domestica Malus domestica Malus domestica Manduca sexta Manduca sexta Manduca sexta Manihot esculenta Manihot esculenta Manihot esculenta Mareks disease Mareks disease Mareks disease Marsupenaeus japonicus Marsupenaeus japonicus Marsupenaeus japonicus Medicago truncatula Medicago truncatula Medicago truncatula Melibe leonina Melibe leonina Melibe leonina Merkel cell Merkel cell Merkel cell Mesocestoides corti Mesocestoides corti Mesocestoides corti Metriaclima zebra Metriaclima zebra Metriaclima zebra Microcebus murinus Microcebus murinus Microcebus murinus Monodelphis domestica Monodelphis domestica Monodelphis domestica Mouse cytomegalovirus Mouse cytomegalovirus Mouse cytomegalovirus Mouse gammaherpesvirus Mouse gammaherpesvirus Mouse gammaherpesvirus Mus musculus Mus musculus Mus musculus Nasonia giraulti Nasonia giraulti Nasonia giraulti Nasonia longicornis Nasonia longicornis Nasonia longicornis Nasonia vitripennis Nasonia vitripennis Nasonia vitripennis Nematostella vectensis Nematostella vectensis Nematostella vectensis Neolamprologus brichardi Neolamprologus brichardi Neolamprologus brichardi Nicotiana tabacum Nicotiana tabacum Nicotiana tabacum Nomascus leucogenys Nomascus leucogenys Nomascus leucogenys Oikopleura dioica Oikopleura dioica Oikopleura dioica Ophiophagus hannah Ophiophagus hannah Ophiophagus hannah Oreochromis niloticus Oreochromis niloticus Oreochromis niloticus Ornithorhynchus anatinus Ornithorhynchus anatinus Ornithorhynchus anatinus Oryctolagus cuniculus Oryctolagus cuniculus Oryctolagus cuniculus Oryza sativa Oryza sativa Oryza sativa Oryzias latipes Oryzias latipes Oryzias latipes Otolemur garnettii Otolemur garnettii Otolemur garnettii Ovis aries Ovis aries Ovis aries Paeonia lactiflora Paeonia lactiflora Paeonia lactiflora Pan paniscus Pan paniscus Pan paniscus Pan troglodytes Pan troglodytes Pan troglodytes Panagrellus redivivus Panagrellus redivivus Panagrellus redivivus Panax ginseng Panax ginseng Panax ginseng Papio hamadryas Papio hamadryas Papio hamadryas Paralichthys olivaceus Paralichthys olivaceus Paralichthys olivaceus Parasteatoda tepidariorum Parasteatoda tepidariorum Parasteatoda tepidariorum Patiria miniata Patiria miniata Patiria miniata Petromyzon marinus Petromyzon marinus Petromyzon marinus Phaeodactylum tricornutum Phaeodactylum tricornutum Phaeodactylum tricornutum Phaseolus vulgaris Phaseolus vulgaris Phaseolus vulgaris Physcomitrella patens Physcomitrella patens Physcomitrella patens Phytophthora infestans Phytophthora infestans Phytophthora infestans Phytophthora ramorum Phytophthora ramorum Phytophthora ramorum Phytophthora sojae Phytophthora sojae Phytophthora sojae Picea abies Picea abies Picea abies Pinus densata Pinus densata Pinus densata Pinus taeda Pinus taeda Pinus taeda Plutella xylostella Plutella xylostella Plutella xylostella Polistes canadensis Polistes canadensis Polistes canadensis Pongo pygmaeus Pongo pygmaeus Pongo pygmaeus Populus euphratica Populus euphratica Populus euphratica Populus trichocarpa Populus trichocarpa Populus trichocarpa Pristionchus pacificus Pristionchus pacificus Pristionchus pacificus Prunus persica Prunus persica Prunus persica Pseudorabies virus Pseudorabies virus Pseudorabies virus Pteropus alecto Pteropus alecto Pteropus alecto Pundamilia nyererei Pundamilia nyererei Pundamilia nyererei Pygathrix bieti Pygathrix bieti Pygathrix bieti Python bivittatus Python bivittatus Python bivittatus Raccoon polyomavirus Raccoon polyomavirus Raccoon polyomavirus Rattus norvegicus Rattus norvegicus Rattus norvegicus Rehmannia glutinosa Rehmannia glutinosa Rehmannia glutinosa Rhesus lymphocryptovirus Rhesus lymphocryptovirus Rhesus lymphocryptovirus Rhesus monkey Rhesus monkey Rhesus monkey Rhipicephalus microplus Rhipicephalus microplus Rhipicephalus microplus Ricinus communis Ricinus communis Ricinus communis Saccharum officinarum Saccharum officinarum Saccharum officinarum Saccharum sp. Saccharum sp. Saccharum sp. Saccoglossus kowalevskii Saccoglossus kowalevskii Saccoglossus kowalevskii Saguinus labiatus Saguinus labiatus Saguinus labiatus Saimiri boliviensis Saimiri boliviensis Saimiri boliviensis Salicornia europaea Salicornia europaea Salicornia europaea Salmo salar Salmo salar Salmo salar Salvia miltiorrhiza Salvia miltiorrhiza Salvia miltiorrhiza Salvia sclarea Salvia sclarea Salvia sclarea Sarcophilus harrisii Sarcophilus harrisii Sarcophilus harrisii Schistosoma japonicum Schistosoma japonicum Schistosoma japonicum Schistosoma mansoni Schistosoma mansoni Schistosoma mansoni Schmidtea mediterranea Schmidtea mediterranea Schmidtea mediterranea Selaginella moellendorffii Selaginella moellendorffii Selaginella moellendorffii Simian foamy Simian foamy Simian foamy Simian virus Simian virus Simian virus Solanum lycopersicum Solanum lycopersicum Solanum lycopersicum Solanum tuberosum Solanum tuberosum Solanum tuberosum Sorghum bicolor Sorghum bicolor Sorghum bicolor Spodoptera frugiperda Spodoptera frugiperda Spodoptera frugiperda Strigamia maritima Strigamia maritima Strigamia maritima Strongylocentrotus purpuratus Strongylocentrotus purpuratus Strongylocentrotus purpuratus Strongyloides ratti Strongyloides ratti Strongyloides ratti Sus scrofa Sus scrofa Sus scrofa Sycon ciliatum Sycon ciliatum Sycon ciliatum Symbiodinium microadriaticum Symbiodinium microadriaticum Symbiodinium microadriaticum Symphalangus syndactylus Symphalangus syndactylus Symphalangus syndactylus Taeniopygia guttata Taeniopygia guttata Taeniopygia guttata Terebratulina retusa Terebratulina retusa Terebratulina retusa Tetranychus urticae Tetranychus urticae Tetranychus urticae Tetraodon nigroviridis Tetraodon nigroviridis Tetraodon nigroviridis Theobroma cacao Theobroma cacao Theobroma cacao Torque teno Torque teno Torque teno Tribolium castaneum Tribolium castaneum Tribolium castaneum Triops cancriformis Triops cancriformis Triops cancriformis Triticum aestivum Triticum aestivum Triticum aestivum Triticum turgidum Triticum turgidum Triticum turgidum Tupaia chinensis Tupaia chinensis Tupaia chinensis Vigna unguiculata Vigna unguiculata Vigna unguiculata Vitis vinifera Vitis vinifera Vitis vinifera Vriesea carinata Vriesea carinata Vriesea carinata Xenopus laevis Xenopus laevis Xenopus laevis Xenopus tropicalis Xenopus tropicalis Xenopus tropicalis Xenoturbella bocki Xenoturbella bocki Xenoturbella bocki Zea mays Zea mays Zea mays # #More examples: # #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 #