streptomyces/norodeodock repository overview

⁠norod.sh

⁠Pull the docker image

docker pull streptomyces/norodeodock

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 ${PWD}:/home/mnt streptomyces/norodeodock
docker run -it -v /home/tom/work:/home/mnt streptomyces/norodeodock

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

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.

⁠The Pfam-A database

This image does not include the Pfam-A database which is needed to run the analyses. Including it would make the image very big and it will be difficult to keep the database updated to the latest release.

Your directory which appears as /home/mnt/ on the container side should contain the Pfam database inside a directory named pfam.

From inside a running container you could make the database by stepping through the commands below. This needs to be done only once everytime the Pfam-A models are updated.

cd /home/mnt/
mkdir pfam # Only if it does not already exist.
cd pfam
wget \
'https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz'
gunzip Pfam-A.hmm.gz
hmmpress Pfam-A.hmm
cd /home/work/

The above should result in the following files in /home/mnt/pfam/.

Pfam-A.hmm
Pfam-A.hmm.h3f
Pfam-A.hmm.h3i
Pfam-A.hmm.h3m
Pfam-A.hmm.h3p

⁠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. There is also a microtest.txt which has just the top three lines of minitest.txt.

./norod.sh microtest.txt
./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 your 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 of 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. The output of egn_ni.pl is in the folder named pna.

⁠Build commands (For Govind only. Others please ignore.)

If you don't already have a buildx builder then make one.

docker buildx create --name strepbuilder
docker buildx use strepbuilder
docker buildx inspect --bootstrap
docker buildx ls

If you are not already logged into Docker hub then login.

docker login

Clone from Github and checkout the norodeodock branch.

git clone https://github.com/streptomyces/ripper.git
cd ripper
git checkout norodeodock

Finally step through the commands in builds.sh.