diff --git a/README.md b/README.md index fd58fc6..21ee34e 100644 --- a/README.md +++ b/README.md @@ -54,14 +54,25 @@ If you don't have a sequence database follow the steps explained on HHblits [ext 2. Extract the files using command: `tar xzvf UniRef[date]_hhsuite.tar.gz` -### Build and run the Docker container -The container is based on the image [tensorflow/tensorflow:2.3.0](https://hub.docker.com/layers/tensorflow/tensorflow/2.3.0/images/sha256-7bc36fe0ca1a051a808122e87f5438614b371263515df4794abef9a78440af8b?context=explore) +### Download the docker image -```bash -# Build the container and name (tag) it conveniently: medusa +You can download the latest build of Medusa docker image (recommanded): + +``` +$ docker pull dsimb/medusa +``` + +or build it yourself from the git repository: + +``` $ docker build -t medusa . -# Run it. Change paths and names accordingly +``` + +### Run the Docker container + +```bash +# Change paths and names accordingly $ docker run -it --rm \ --user "$(id -u):$(id -g)" \ # Launch docker as user's id -v /path/to/database:/database:ro \ # Bind mount as read-only the database for HHblits @@ -69,10 +80,10 @@ $ docker run -it --rm \ medusa \ # The name of the container we launch -i data/sequence.fasta \ # Fasta file containing the target sequence -d uniclust30_2016_09 \ # Name of the database for HHblits (c.f --help for more details) - -o ./output_dir # Directory which will contain results + -o ./results # Directory which will contain results # One-liner, for convenience -$ docker run -it --user "$(id -u):$(id -g)" -v /path/to/database:/database:ro -v $(pwd):/project medusa -i data/sequence.fasta -d uniclust30_2016_09 -o output_dir +$ docker run -it --user "$(id -u):$(id -g)" -v /path/to/database:/database:ro -v $(pwd):/project medusa -i data/sequence.fasta -d uniclust30_2016_09 -o results ``` ### Help @@ -97,7 +108,7 @@ Usage: ### Example ```bash -$ docker run -it --user "$(id -u):$(id -g)" -v /home/cretin/uniclust:/database:ro -v $(pwd):/project medusa -i data/test.seq.fasta -d uniclust30_2016_09 -o ./outdir +$ docker run -it --user "$(id -u):$(id -g)" -v /home/cretin/uniclust:/database:ro -v $(pwd):/project medusa -i data/sequence.fasta -d uniclust30_2016_09 -o ./results -c 0 -m 0 Run HHblits ... done Run HHfilter ... done Reformat ... done @@ -107,8 +118,8 @@ Translate encodings into vectors ... done Merge vectors ... done Run predictions ... done -Results can be found in ./outdir/MEDUSA.jy5J-20201208215144 +Results can be found in ./results/MEDUSA.jy5J-20201208215144 -$ ls ./outdir/MEDUSA.jy5J-2020120 +$ ls ./results/MEDUSA.jy5J-2020120 logs medusa_job_results.tar.gz prediction ```