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Retropath2.0 docker

Docker implementation of the KNIME retropath2.0 workflow. Takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The docker mounts a local folder and expects the following files: rules.csv, sinl.csv and source.csv.

How to run using Galaxy

WARNING: The galaxy tool .xml must be in the same folder as the script it calls

WARNING: need to add docker to sudo

sudo groupadd docker
sudo gpasswd -a $USER docker
sudo service docker restart

We will cover calling RetroPath2.0 using Galaxy where the docker is installed locally and when the docker is remotely located using the Pulsar package. In both cases one needs to build the docker using the following command:

docker build -t ibisba/retropath2 .

It is recommended that one tests the docker using the following commands. First enter the docker in bash using:

docker run -it ibisba/retropath2 /bin/bash

Once inside the docker in bash, use the following command to call a KNIME job using the example files provided:

pyKnime.py -source "/home/src/tutorial_data/carotene/source.csv" -sink "/home/src/tutorial_data/carotene/sink.csv" -rules "/home/src/tutorial_data/carotene/rules.csv" -dmin 0 -dmax 1000 -maxSteps 5 -outDir "/home/src/data" -results "NEWresults.csv" -sourceinsink "NEWsource-in-sink.csv" -scopeJSON "NEWscope.json" -scopeCSV "NEWscope.csv"

The pyKnime.py script will write the output files in the "outDir" as well as locally as named using the NEW keyword. This is required to make the docker compatible with the manner by which Galaxy requires the data to be returned to it.

Local docker

If one has the docker and the Galaxy services on the same machine, then the following Galaxy configurations are required to make them run.

Add the tool to Galaxy's tool_conf.xml

Create a new section in the Galaxy tool_cong.xml

<section id="retro" name="Retro Nodes">
  <tool file="/local/path/retroPath_galaxy.xml" />
</section>
Modify the job_conf.xml
<?xml version="1.0"?>
<job_conf>
  <plugins>
    <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
  </plugins>
  <destinations default="docker_local">
    <destination id="local" runner="local" />
    <destination id="docker_local" runner="local">
      <param id="docker_enabled">true</param>
      <param id="docker_sudo">false</param>
      <param id="docker_auto_rm">true</param>
      <param id="docker_set_user">root</param>
    </destination>
  </destinations>
</job_conf>

It is important to run the docker as root user since we will be calling a script that writes files to a temporary folder inside the docker before sending bask to Galaxy

Pulsar docker call

To run the tool on a remote server and call it using any Galaxy instance, we need to install and configure Pulsar and the docker of the tool

Add the tool your LOCAL Galaxy's tool_conf.xml
<section id="retro" name="Retro Nodes">
  <tool file="/local/path/retroPath_galaxy.xml" />
</section>
Make sure that this is on top of the retroPath_galaxy.xml
<requirements>
  <container type="docker">ibisba/retropath2:latest</container>
</requirements>
Modify the LOCAL job_conf.xml
<?xml version="1.0"?>
<job_conf>
  <plugins>
    <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
    <plugin id="pulsar" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner" />
  </plugins>
  <destinations default="docker_local">
    <destination id="local" runner="local" />
    <destination id="docker_local" runner="local">
      <param id="docker_enabled">true</param>
      <param id="docker_sudo">false</param>
      <param id="docker_auto_rm">true</param>
      <param id="docker_set_user">root</param>
    </destination>
    <destination id="remote_cluster" runner="pulsar">
      <param id="url">http://pulsar_server_ip_address:8913</param>
      <param id="docker_enabled">true</param>
      <param id="docker_sudo">false</param>
      <param id="docker_auto_rm">true</param>
      <param id="docker_set_user">root</param>
    </destination>
  </destinations>
  <tools>
    <tool id="retropath2" destination="remote_cluster" />
  </tools>
</job_conf>

How to cite RetroPath2.0?

Please cite:

Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: https://doi.org/10.1016/j.ymben.2017.12.002