vera/masurca repository overview

⁠masurca

Dockerfile for the masurca assembler

⁠usage

first navigate to the folder with your data. all input data must be contained within this directory (but may be in a subdirectory within this directory).

masurca requires a sample configuration file. to copy the example configuration in the current directory, enter:

docker run --rm -v $(pwd):/data -it vera/masurca example

edit the configuration file, prefixing /data/ to the relative path of the files (relative to the current directory). For example, if a pacbio fasta file subreads.fa is in a directory called pacbio within the current directory, the path set in the configuration file should be /data/pacbio/subreads.fa. After the example configuration file sr_config_example.txt is edited, you can create and run assembly script by entering:

docker run --name assemblytest1 -v $(pwd):/data -it vera/masurca assemble 

If the configuration file has a different name (e.g., config.txt), you may define the CONFIG environmental variable with the file name as follows:

docker run -e CONFIG=config.txt --name assemblytest1 -v $(pwd):/data -it vera/masurca assemble 

You may follow the progress of the run by using the name of the container you specified:

docker logs -f assemblytest1