Mercurial > repos > glogobyte > armdb
changeset 5:5eaef131313c draft
Uploaded
| author | glogobyte |
|---|---|
| date | Wed, 13 Oct 2021 16:24:14 +0000 |
| parents | fbb1f770ab77 |
| children | 41f5a0616dbb |
| files | mirbase.loc.sample |
| diffstat | 1 files changed, 39 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mirbase.loc.sample Wed Oct 13 16:24:14 2021 +0000 @@ -0,0 +1,39 @@ +# 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: +# +# +hg38 Homo sapiens - GRCh38 hsa.gff3 Homo sapiens +mm10 Mus musculus - GRCm38 mmu.gff3 Mus musculus +BosTau5 Bos taurus - Btau_5.0.1 bta.gff3 Bos taurus +Arabidopsis_thaliana_TAIR10 Arabidopsis thaliana - TAIR10 ath.gff3 Arabidopsis thaliana +droSim1 Drosophila simulans - dsim_caf1 dsi.gff3 Drosophila simulans +# +# +# +#