changeset 4:fbb1f770ab77 draft

Uploaded

--- /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.
+#
+# <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
+#
+#
+#
+#
+#