# HG changeset patch # User glogobyte # Date 1634142239 0 # Node ID fbb1f770ab77419150fab920f5cdcb293df3c160 # Parent 19628086a9bc63793d9cf17721ad91c59b9fe698 Uploaded diff -r 19628086a9bc -r fbb1f770ab77 mirgene.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mirgene.loc.sample Wed Oct 13 16:23:59 2021 +0000 @@ -0,0 +1,80 @@ +# 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. +# +# +# +# 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 +# +# +# +# +#