changeset 10:f229307a77a7 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/n_spiecies.loc.sample	Fri Oct 16 19:05:49 2020 +0000
@@ -0,0 +1,300 @@
+# 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
+#