# 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:
#
#
Hsa	Human (Homo sapiens) - hg38
Mml	Rhesus monkey (Macaca mulatta) - rheMac8
Mmu	House mouse (Mus musculus) - mm10
Rno	Norway rat (Rattus norvegicus) - rn6
Cpo	Guinea pig (Cavia porcellus) - cavPor3
Ocu	Rabbit (Oryctolagus cuniculus) - oryCun2
Cfa	Dog (Canis familiaris) - canFam3
Bta	Cow (Bos taurus) - bosTau8
Dno	Nine-banded armadillo (Dasypus novemcinctus) - dasNov3
Ete	Lesser hedgehog tenrec (Echinops telfairi) - echTel2
Sha	Tasmanian devil (Sarcophilus harrisii) - DEVIL7_traces
Mdo	Gray short-tailed opossum (Monodelphis domestica) - monDom5
Oan	Platypus (Ornithorhynchus anatinus) - mOrnAna1.p.v1_plustraces
Gga	Chicken (Gallus gallus) - galGal5
Cli	Rock pigeon (Columba livia) - colLiv2
Tgu	Zebra finch (Taeniopygia guttata) - taeGut3.2.4
Ami	American alligator (Alligator mississippiensis) - allMis1
Cpi	Western painted turtle (Chrysemys picta bellii) - chrPic1
Aca	Green anole lizard (Anolis carolinensis) - anoCar2
Xtr	Tropical clawed frog (Xenopus tropicalis) - xenTro7
Dre	Zebrafish (Danio rerio) - danRer11
Sto	Cloudy Catshark (Scyliorhinus torazame) - miRNA_loci_genome
Cin	Sea Squirt (Ciona intestinalis) - ci3
Bfl	Florida lancelet (Branchiostoma floridae) - BFL_v2.0
Sko	Saccoglossus (Saccoglossus kowalevskii) - Skow_1.1
Pfl	Ptychodera (Ptychodera flava) - Pfl
Spu	Purple sea urchin (Strongylocentrotus purpuratus) - Spur_3.1
Pmi	Bat starfish (Patiria miniata) - Pmin1
Dme	Fruit fly (Drosophila melanogaster) - dm6
Dan	Fruit fly (Drosophila ananassae) - Dana_caf1
Dmo	Fruit fly (Drosophila mojavensis) - Dmoj_caf1
Aae	Yellow fever mosquito (Aedes aegypti) - Aaeg_L3
Hme	Longwing butterfly (Heliconius melpomene) - Hmel_1
Tca	Red flour beetle (Tribolium castaneum) - Tcas5.2
Bge	Cockroach (Blattella germanica) - Bger_2.0
Dpu	Common water flea (Daphnia pulex) - Daphnia_pulex.V1.0
Isc	Deer tick (Ixodes scapularis) - IscaWI
Cel	Roundworm (Caenorhabditis elegans) - ce11
Cbr	Roundworm (Caenorhabditis briggsae) - CB4
Asu	Large roundworm (Ascaris suum) - ASU_PRJNA80881_plustraces
Cte	Polychaete worm (Capitella teleta) - Capitella_teleta_v1.0
Efe	Common brandling worm (Eisenia fetida) - Efe_combined
Lgi	Owl limpet (Lottia gigantea) - Lotgi1
Cgi	Pacific oyster (Crassostrea gigas) - CGI_GCA_000297895.1
Lan	Lingula (Lingula anatina) - LinAna_1.0
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