Docker compose how to

Docker How To

IMP is provided as a docker container with all dependencies shipped inside. You 'only' need to install docker and you are ready to use IMP.

For more information about docker and how to install and use it, please refers to the Official documentation.

Run IMP latest container

• Run latest version of IMP. For the first run, it will download all dependencies. It can take some time.

docker run imp:latest
... downloading data ...
Error: Snakefile "Snakefile" not present.

Run IMP on your data

• The complete command is

docker run \
-v $DATA_DIR:/data \
-v $OUTPUT_DIR:/output \
-e MG="/data/$MGR1 /data/$MGR2" \
-e MT="/data/$MTR1 /data/$MTR2" \
imp:latest

• docker run: Run a docker container

• -v $DATA_DIR:/data : Where $DATA_DIR is the directory under your data is located. (All paths must be absolute*)

You need to provide the container your data. By default, IMP expect that you have metagenomic and metatransciptiomic data and will look into the container /data directory. You do it with the -v (for volume) flag.

• -v OUTPUT_DIR:/output: Where $OUTPUT_DIR is the directory where output data will be located.

As the $DATA_DIR, you need to mount an output directory to hold all result files from IMP.

• -e MG="/data/$MGR1 /data/$MGR2": Where $MGR1 and $MGR2 are the metagenomic paired-end reads.

• -e MT="/data/$MTR1 /data/$MTR2": Where $MTR1 and $MTR2 are the metatransciptiomic paired-end reads.

• imp:latest: The name of the container to use (:)

You may use sudo.

Example

$ pwd
/Users/imp/data
$ ls
MG.R1.fq MG.R2.fq MT.R1.fq MT.R2.fq
$ ls /Users/imp/build

$ docker run \
-v /Users/imp/data:/data \
-v /Users/imp/build:/output \
-e MG="/data/MG.R1.fq /data/MG.R2.fq" \
-e MT="/data/MT.R1.fq MG=/data/MT.R2.fq" \
imp:latest
$ ls /Users/imp/build
IMP.html
Preprocessing
Assembly
Mapping
Analysis
...

Use a configuration file.

Many parameters can be overridden in IMP via a config file. You may provide using it with the -e flag and using the CONFIGFILE environment variable.

docker run \
-e CONFIGFILE="path/to/config/file.json"
 ... other parameters ...

Build new container image

cd <IMP_DIR>/docker
docker build -t <name> .

Name can be abything you want. Then you can

docker run <name>

Use development version of IMP

You need to erase imp source code in the container and mount the latest version of the source code.

$ cd $DIR
$ git clone https://git-r3lab.uni.lu/shaman.narayanasamy/IMP.git
$ cd IMP
$ git checkout dev
$ docker run \
-v $DIR/IMP:/home/imp/integrated-metaomic-pipeline \
 ... other parameters ...

Any change to the source code will be applied immediatly inside the container.

Log in inside the container

If you want to enter the container and use IMP from there, you'll have to erase the docker entrypoint:

docker run \
--entrypoint /bin/bash -it \
 ... other parameters here ...