The script needs clodius, which has a lot of requirements. So the best way to install is to create a conda environment and install the most important requirements using conda and then install this package into the conda environment via pip:
pip install git+https://github.com/gerlichlab/higlassupload
This will set up a command called higlassUp in your environment, which is the entry point for usage of this script.
Accounts for https://gerlich.higlass.vbc.ac.at/ can be created by our lab using the admin panel
https://gerlich.higlass.vbc.ac.at/admin/login/?next=/admin/.
At the moment, the script can handle bedfiles (.bed extension), bedpe files (.bedpe extension),mcooler files (.mcool) and biwig files (.bw). It will recognize how to dispatch clodius based on the extension and then upload the resulting file to a higlass server. The login credentials need to be available as environment variables, with your username being stored in HIGLASSUSER and your password being stored in HIGLASSPWD.
On linux this can be done by:
export HIGLASSUSER=username
export HIGLASSPWD=supersecretpassword
Note: The username and your password should not contain $ signs if you add it to your .bashrc file, since they will be interpreted by bash.
The upload command will then be the following:
higlassUp file
This will preprocess the file (if necessary) with clodius and upload to the default higlass instance using the filename as name. If you want to specify a different name:
higlassUp --name TEST file
If you want to specify a specific project onto which to upload the file you can do it as follows:
higlassUp --project PROJECT file
Moreover, you can specify the genome assembly to be used for the specific file. Currently, assembly hg19 and hg38 are available. The specification is done as follows:
higlassUp --assemblh hg19|hg38 file
This tool can be found ready to use in our main container on dockerhub.
To automate the upload process, the chromsizes for hg19 in this repo will be used for all aggregation scripts. Moreover, .bedpe files need to have a certain format:
| chrom1 | start1 | end1 | chrom2 | start2 | end2 |
|---|---|---|---|---|---|
| chr2 | 1 | 2 | chr2 | 1 | 2 |
For rectangle domains , the .bedpe file needs to specify the upper left corner of the rectangle by (start1, start2) and the lower left corner by (end1, end2). So for rectangle domains centered on the diagonal, start1 = start2 and end1 = end2.