alsmith151 / tracknado

Command line utility to generate UCSC hubs from a set of files (e.g. bigWig, bigBed etc)

TrackNado

Simple command line tool to quickly generate a UCSC hub from a set of files.

Installation

pip install tracknado

Usage

See the help for more details on the options that can be provided.

tracknado --help

Example

Minimal example with no track details

tracknado \
create \ 
--hub-name HUB_NAME_HERE \
--hub-email EMAIL_ADDRESS \
--genome-name hg38 \
-o /datashare/asmith/ \
-i bigwigs/deeptools/*.bigWig peaks/lanceotron/*.bigBed

Example with track details

tracknado \
create \
--hub-name HUB_NAME_HERE \
--hub-email EMAIL_ADDRESS \
--genome-name hg38 \
-o /datashare/asmith/ \
-d PATH_TO_TRACK_DETAILS_FILE \

Example with a custom genome

tracknado \
create \
--hub-name HUB_NAME_HERE \
--hub-email EMAIL_ADDRESS \
--genome-name CUSTOM_GENOME_NAME \
--genome-organism CUSTOM_GENOME_ORGANISM \
--genome-two-bit-path PATH_TO_TWO_BIT_FILE \
-i bigwigs/deeptools/*.bigWig peaks/lanceotron/*.bigBed
-o /datashare/asmith/ \

Merging hubs

It is possible to merge the outputs from tracknado create into a single hub by using the merge command. This requires that hubs have been created with the --save-hub-design flag. This will create a file called hub_design.pkl in the output directory. This file contains all the information required to recreate the hub. This does require that the hubs are for the same genome.

First create a couple of example hubs as above:

tracknado \
create \
--hub-name HUB_NAME_HERE \
--hub-email EMAIL_ADDRESS \
--genome-name hg38 \
-o /datashare/asmith/path1 \
-i bigwigs/deeptools/*.bigWig peaks/lanceotron/*.bigBed \
--save-hub-design

tracknado \
create \
--hub-name HUB_NAME_HERE \
--hub-email EMAIL_ADDRESS \
--genome-name hg38 \
-o /datashare/asmith/path2 \
-i bigwigs/deeptools/*.bigWig peaks/lanceotron/*.bigBed \
--save-hub-design

Then merge them:

tracknado \
merge \
--hub-name HUB_NAME_HERE \
--hub-email EMAIL_ADDRESS \
--genome-name hg38 \
-o /datashare/asmith/merged \
-i /datashare/asmith/path1/hub_design.pkl /datashare/asmith/path2/hub_design.pkl

This will create a new hub in /datashare/asmith/merged that contains all the tracks from the two input hubs. You can also supply all of the standard arguments to the merge command to change the hub name, email, genome etc.

tracknado's Issues

GTF track type not supported

• Need to convert to supported format

--convert option not being used when flag is set