norod.sh

Pull the docker image

docker pull streptomyces/norodeo

Following installation, run the container using the following command, where your input accession list file is stored in /home/tom/work on Linux and MacOS systems or C:/Users/tom/work on a MS Windows system. (substitute your relevant directories in place of these):

Get a container

# Example usage on Linux
docker run -it -v /home/tom/work:/home/mnt streptomyces/norodeo

# Example usage on MS Windows.
docker run -it -v C:/Users/tom/work:/home/mnt streptomyces/norodeo

Do not change the /home/mnt part. This refers to a directory in the container and scripts in the container expect to find this directory. The host directory you mount on /home/mnt in the container is where the output directories and files are written to. You can place your input list in the mounted host directory on the host side and access it in /home/mnt/ on the container side. See the example Run on your own list below.

Carrying out an analysis in the running container

Following the docker run command above, to ensure that norod.sh is working correctly, you can run a small test analysis on the accessions that are included in a test file named minitest.txt. Use the following command:

./norod.sh minitest.txt

Run on your own list

Use the following command to analyse your own list, substituting in a relevant filename for te_accessions.txt:

./norod.sh /home/mnt/te_accessions.txt

Modification of analysis parameters

Some configuration is read from the file local.conf. If you have a NCBI API key then you should place it in this file. Please also put you email address in this file. It is sent to NCBI along with requests so they can analyse usage of their services.

Output files

The output consists genbank files in the folder orgnamegbk. There should be one genbank file for each protein accession for which a genbank file was successfully retrieved from Genbank.