BCBIO at sharc

bcbio-nextgen, https://github.com/chapmanb/bcbio-nextgen, is installed on sharc.

It is installed in /usr/local/community/bcbio-nextgen/.

Note that you cannot access this directory from the sharc login node. You must open a session on a worker node first, for example, by running qrshx.

There will be several versions.

The current version is at /usr/local/community/bcbio-nextgen/2017-08.

You can run it by naming it directly:

/usr/local/community/bcbio-nextgen/2017-08/tool/bin/bcbio_nextgen.py

or by adding /usr/local/community/bcbio-nextgen/2017-08/tool/bin to your PATH, and then running bcbio_nextgen.py.

I've not written a module yet, but when it is written you will be able to use the module system to add it to your PATH as well:

module add blah blah blah

A very brief intro

More comprehensive documentation is available at http://bcbio-nextgen.readthedocs.io/en/latest/contents/testing.html

To run the pipeline you need:

• fastq files (your bulk RNA data or whatever);
• A CSV file that names your sample files;
• a YAML template.

bcbio_nextgen.py is then used to convert the template and sample names into a full configuration file. For example

bcbio_nextgen.py -w template rnaseq-seqc.yaml input/seqc.csv input

Then you can run the analysis:

bcbio_nextgen.py ../config/seqc.yaml

Test materials

The test-rnaseq subdirectory of /usr/local/community/bcbio-nextgen/2017-08 contains the complete results of running the RNAseq test example from bcbio's documentation,.

System configuration

Installation configuration file is at /usr/local/community/bcbio-nextgen/2017-08/data/config/install-params.yaml.

Global Configuration file bcbio_system.yaml is at /usr/local/community/bcbio-nextgen/2017-08/data/galaxy/bcbio_system.yaml

Genomes: installed genomes are in the genomes directory. To see a list:

(cd /usr/local/community/bcbio-nextgen/2017-08/data/genomes; ls -d */*)

As of 2018-02 this is:

Drerio_Zebrafish/GRCz10
Hsapiens/GRCh37
Hsapiens/hg38
Mmusculus/mm10
Mmusculus/mm9

Running bcbio_setup_genome.py (no arguments) also produces a similar list.

Other genomes can be installed, run bcbio_nextgen.py upgrade -h to see the list of possible genomes.

Aligners:

Further bcbio documentation is at http://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html

Recommend script to invoke is:

Tests:

Install scripts: