System dependencies for CWL workshop

[hubentu]

Hi,
Our workshop requires some system dependencies to work, including cwltool, docker (with user permission) and hisat2. Could you please to confirm these software to be installed in the AMI server? Thank you!
@markozecevic @dcassol

[seandavi]

Could you do me a favor and drop here how to install each on an ubuntu server? It saves a little homework.

[hubentu]

Sure, here are the installation notes. Thanks!

1. cwltool

$sudo apt install cwltool
$cwltool --version
/usr/bin/cwltool 1.0.20180302231433

2. hisat2

$sudo apt install hisat2
$hisat2 --version
/usr/bin/hisat2-align-s version 2.1.0
64-bit
Built on Debian unstable
Mon Sep  4 12:49:40 UTC 2017
Compiler: gcc version 7.2.0 (Ubuntu 7.2.0-12ubuntu1) 
Options: -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

3. docker

## install
$curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
$sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
   $(lsb_release -cs) \
   stable"
$sudo apt install docker-ce

## user permission
$sudo groupadd docker
$sudo usermod -aG docker $USER
## Log out and log back or reboot

## test
$docker run hello-world
Unable to find image 'hello-world:latest' locally
latest: Pulling from library/hello-world
1b930d010525: Pull complete 
Digest: sha256:41a65640635299bab090f783209c1e3a3f11934cf7756b09cb2f1e02147c6ed8
Status: Downloaded newer image for hello-world:latest
...

[seandavi]

@hubentu, how badly do you need the docker piece? I am asking because I am working to dockerize the workshop materials to make them more portable and reproducible. Docker-in-docker is not easy to set up, so if there is another approach that can avoid docker for your session, it might simplify things. This isn't a done-deal, but I thought I would ask.

And thanks for the details above!

[hubentu]

Hi @seandavi , @markozecevic will give an example to build a docker image for R script. I have an example to build and run a portable CWL pipeline, which will require dockerized tools and pull these tools automatically for a test run. I am not sure whether it will work within a container. I could help to test if you need. Thanks!