Sign inSign up

urgi/docker_vre_aio

By urgi

•Updated about 3 years ago

Virtual Research Environment (VRE) docker All In One with REPET package

Image
4

7.2K

urgi/docker_vre_aio repository overview

⁠How to use the image Docker

This docker image contains the REPET package⁠ with its dependencies and other tools such as Jalview, S-Mart, IGV, EMBOSS, BEDtools.

⁠How to install Docker

/!\ The docker image does not work with macs that have the new apple processors.

/!\ The docker image does not work with Debian.

  • For Windows :

/!\ The docker image does not work with Windows.

⁠How to install the docker image

  • Download the image :
docker pull urgi/docker_vre_aio:latest

The latest image now is REPET v.3.0.2

*If you want the image with REPET v3.0, run :

docker pull urgi/docker_vre_aio:v3.0

*If you want the image with REPET v2.5, run :

docker pull urgi/docker_vre_aio:v2.5

To find out if the image is downloaded, use the command :

docker image ls

> REPOSITORY        TAG     IMAGE ID      CREATED     SIZE
urgi/docker_vre_aio latest  f2e46f157981  1 days ago  16GB
  • Create a container from the image 
docker run -p 222:22 --name test -d urgi/docker_vre_aio

Here, we have forwarded the port 22 to 222. It will allow the ssh connection :

ssh -p 222 centos@localhost
> The authenticity of host \'[localhost]:222 ([127.0.0.1]:222)\' can\'t be established.
RSA key fingerprint is SHA256:0CBOfQGRiAo5+cH5C3EK8IlXgqDgYFveg+wWyceTTEk.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added \'[localhost]:222\' (RSA) to the list of known hosts.
centos@localhost\'s password:

By default, the password is "centos".

If you want to mount a directory in you docker, try this command :

docker run -p 222:22 --name test -v /home/XXX/workdir/:/home/centos/workdir -d urgi/docker_vre_aio
  • List running containers (to see if the container is created)
docker ps
>CONTAINER ID IMAGE               COMMAND       CREATED       STATUS        PORTS               NAMES
4ed103a8ae1c  urgi/docker_vre_aio "./start.sh"  8 seconds ago Up 4 seconds  0.0.0.0:222->22/tcp test

To list all the containers, use the command docker ps -a. A container can have different status : "created", "restarting", "running", "removing", "paused", "exited" and "dead".

If the status is "exited" or you have stopped your container, you can start it using the command docker start <container_name>

  • Execute an interactive bash shell on the container
docker exec -it test bash
  • To stop the container
docker stop test

⁠Example to test

⁠Tutorial of the new image v3.0.1 / v3.0.2

You can find the tutorial for the new image here :https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/tutorial-with-Docker-image-of-REPET⁠

Practical course: Transposable Elements identification with The REPET package⁠

If you want to learn more about REPET, please check our website : https://urgi.versailles.inrae.fr/Tools/REPET⁠.
You can also download the package REPET and have tutorials and courses.

⁠Test TEdenovo with an existed example in docker image (REPET v3.0)
  • Create a directory with config files
mkdir $HOME/DmelChr4_TEdenovo
cd DmelChr4_TEdenovo
ln -s $REPET_PATH/db/DmelChr4.fa .
cp $REPET_PATH/config/TEdenovo.cfg .
  • TEdenovo config file settings
[repet_env]
repet_version: 3.0
repet_host: localhost
repet_user: orepet
repet_pw: repet_pw
repet_db: repet
repet_port: 3306
repet_job_manager: slurm

[project]
project_name: DmelChr4
project_dir: /home/centos/DmelChr4_TEdenovo

...
  • Launch TEdenovo
#launch_TEdenovo.py -P <project_name> -C <TEdenovo_configuration_file> -v <level_verbosity> > <redirection_log> &
launch_TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -v 3 > launchTEdenovo.txt &
⁠Test TEannot (REPET v3.0)
  • Create a directory with config files and input files (the consensus file (DmelChr4_refTEs.fa) is the output from TEdenovo)
mkdir $HOME/DmelChr4_TEannot
cd DmelChr4_TEannot
ln -s $REPET_PATH/db/DmelChr4.fa .
ln -s /home/centos/DmelChr4_TEdenovo/DmelChr4_Blaster_GrpRecPil_Struct_Map_TEclassif_Filtered/DmelChr4_denovoLibTEs_filtered.fa DmelChr4_refTEs.fa
cp $REPET_PATH/config/TEannot.cfg TEannot.cfg
  • TEannot config file settings
[repet_env]
repet_version: 3.0
repet_host: localhost
repet_user: orepet
repet_pw: repet_pw
repet_db: repet
repet_port: 3306
repet_job_manager: slurm

[project]
project_name: DmelChr4
project_dir: /home/centos/DmelChr4_TEannot

...
  • Launch TEannot
#launch_TEannot.py -P <project_name> -C <TEannot_configuration_file> -v <level_verbosity> > <redirection_log> &
launch_TEannot.py -P DmelChr4 -C TEannot.cfg -v 3 > launchTEannot.txt &

If you have some issue with REPET, you can have a look to our FAQ⁠ or contact us at [email protected]⁠.

Tag summary

Content type

Image

Digest

sha256:8cbd3845e…

Size

6.3 GB

Last updated

about 3 years ago

docker pull urgi/docker_vre_aio