streptomyces/riprep_ma repository overview

⁠MEME searches on the output of RiPPER

⁠Pull the docker image

docker pull streptomyces/riprep_ma

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/riprep_ma

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

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

⁠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.

⁠MEME searches

MEME searches on the files written by norod.sh in /home/mnt/orgnamegbk/.

First we make a list of the genbank files in /home/mnt/orgnamegbk/

 perl make_gbk_list.pl -outfile gbk.list -indir /home/mnt/orgnamegbk
 head -n 6 gbk.list

Then variables and a function to run the searches in parallel.

njobs=4; # Change this to the number or processors in your machine.
gbklist=gbk.list
errfn=/home/mnt/err
ofn=/home/mnt/riprep.out

para-riprep () {
for pf in $(seq 1 $njobs); do
 echo perl riprep.pl -job ${pf} -jobs $njobs \
 -errfile $errfn -outfile $ofn -gbklist $gbklist
done
}
para-riprep

Finally, run in parallel. The output and error files are opened for appending so it is important to delete them before starting. If you have old files you need to keep then rename them.

rm  $ofn $errfn
para-riprep | parallel --jobs $njobs

⁠Building

docker buildx build --no-cache --platform linux/amd64,linux/arm64 \
-f  riprep.dockerfile -t streptomyces/riprep_ma:latest --push .

docker buildx build --platform linux/amd64,linux/arm64 \
-f  riprep.dockerfile -t streptomyces/riprep_ma:latest --push .

cd; cd dockertest/riprep_ma
docker run -it -v ${PWD}:/home/mnt streptomyces/riprep_ma