Managing Custom Tools

Contents

• Versioning Custom/Local Tools
  • By Git Releases
  • Local Toolshed
• Conda Envs for Private Git Repos

Versioning Custom/Local Tools

By Git Release

We expect the code base or tool to be tagged and released in order to appropriately organize the tool in galaxy.

1. Tag the code:

#Create a Tag
git tag -a v0.1.0 -m "my version 0.1.0"

#Tag a specific commit
git tag -a v0.1.0 9fceb02

#Push your tag
git push origin v0.1.0

2. Create a release that points to the tag just created.

3. Contact your friendly Galaxy admin and request to install your tool for the release just created. Wait, you are the admin? Oh, keep following along then.

4. Create a new directory under galaxy/tools named after the git repo.

cd galaxy/tools
mkdir my_galaxy_tool

5. Download the archived release.

cd my_galaxy_tool
wget https://github.com/organization/my_galaxy_tool/archive/v0.1.0.tar.gz
tar -zxvf v0.1.0.tar.gz

6. Add the tool to the galaxy/tool_conf.xml

<section id="best_tool" name="Best Tool Ever">
    <tool file="my_galaxy_tool/v0.1.0/tool.xml"/>
</section>

Local Toolshed

This section describes the process for preparing tools for a toolshed (usually local). This documentation does not thoroughly describe preparing tools for the public Galaxy Toolshed, but instead the "bare minimum" needed for our local toolshed.

Set up planemo config in ~/.planemo.yml:

shed_username: "creason"
sheds:
  galaxy2shed:
    key: "rAndOMaPIkEy123"
    url: "https://galaxy.ohsu.edu/toolshed/"

Create .shed.yml file:

owner: "creason"
remote_repository_url: "https://github.com/ohsu-comp-bio/compbio-galaxy-wrappers/tree/master/bam-matcher"
homepage_url: "https://bitbucket.org/sacgf/bam-matcher/wiki/Home"
categories:
  - "CompBio Galaxy Wrappers"
repositories:
  bam-matcher:
    description: "Compare two BAM files to see if they are from the same samples"
    include:
      - bam-matcher.conf
      - bam-matcher.xml
      - tool_data_table_conf.xml.sample
      - tool-data/all_fasta.loc.sample

Lint tool:

planemo shed_lint --tools

Create and Upload tool to shed:

planemo shed_create --shed_target galaxy2shed

More docs for .shed.yaml file.

Conda Envs for Private Git Repos

This section describes the process for creating a conda environment for galaxy when the source repository is private (and a conda package does not exist).

As the normal user, clone the git repository into the src directory on exacloud.

cd /home/exacloud/lustre1/galaxy/src
git clone https://github.com/ohsu-comp-bio/smmart_utils.git
sudo chown -R galaxyuser:galaxy smmart_utils

Switch to galaxyuser and create a python conda env. Be sure to follow the correct format for naming conda envs in galaxy __name_of_env@version.

sudo su - galaxyuser
/home/exacloud/lustre1/galaxy/galaxy/database/dependencies/_conda/bin/conda create -y --channel bioconda --channel conda-forge --channel defaults --name [email protected] python=3.5.5

Activate the env and install the local git repository using pip.

source /home/exacloud/lustre1/galaxy/galaxy/database/dependencies/_conda/bin/activate [email protected]
pip install git+file:///home/exacloud/lustre1/galaxy/src/smmart_utils

If you receive an Cannot uninstall 'certifi'. error during pip install, run with --ignore-installed flag.

pip install --ignore-installed git+file:///home/exacloud/lustre1/galaxy/src/smmart_utils