biotechvana/gpro repository overview

⁠GPRO Server side

To run an instance of the GPRO server you can use the following command :

local_path="/path/to/local_home"
docker run -d -p 80:80 -p 20-22:20-22 -p 65500-65515:65500-65515 -v ${local_path}:/data biotechvana/gpro

This will run the container with default username and password as described in the configuration section below.

If you want to configure it with different username and password you can use the following commands :

local_path="/path/to/local_home"
GPRO_USER="myUserName"
GPRO_USER_PASS="myPass"
docker run -d -p 80:80 -p 20-22:20-22 -p 65500-65515:65500-65515 -v ${local_path}:/data biotechvana/gpro

⁠Configuration Options

• GPRO_USER : specify username that will be created within the application, default is g_user.
• GPRO_USER_PASS: specify user's password, default is g_user

⁠Notes :

• Current version only support one user usage, further updates will be available soon

For more details please refer to https://gpro.biotechvana.com/⁠

⁠Container management

⁠Notes

All third-party command line interface software are integrated in the server-side docker image excepting Varscan2. This is because the license for VarScan2 usage distinguishes between academic users and commercial users. Academic users can use VarScan2 without restrictions for academic purposes, while commercial users need to contact the VarScan2 authors to get the corresponding commercial license (for more details see https://github.com/dkoboldt/varscan/releases⁠ ). Taking this into consideration, the server-side image does not include VarScan2 and this tool must be integrated by the own user into the running container. The rest of CLI software dependencies used by “RNAseq” and “VariantSeq” are already installed in the docker image and have licenses of use allowing unrestricted use for every kind of author (if they are appropriately cited and accredited). To integrate VarScan2 in the docker please proceed as follows.

To manage the image you need to get image name first if you did not set it in the run command, you can get the image name by running docker ps

$ docker ps
################## Sample output
# CONTAINER ID   IMAGE          COMMAND        CREATED       STATUS       PORTS                                                                                                                                                     NAMES
# 5121b762b39f   d82c97fcc2c7   "/gpro_init"   2 hours ago   Up 2 hours   0.0.0.0:20-22->20-22/tcp, :::20-22->20-22/tcp, 0.0.0.0:80->80/tcp, :::80->80/tcp,  
# 0.0.0.0:65500-65515->65500-65515/tcp, :::65500-65515->65500-65515/tcp   hungry_boyd

Here the name is hungry_boyd

⁠Adding VarScan to the gpro server : run the following command

$ docker exec hungry_boyd gpro install varscan

Commercial users should proceed in the same way but must contact first the VarScan2 authors to get the license if they want to comply with the VarScan2 terms of use.