Galaxy Wrappers

This repository contains wrappers for Galaxy for the following applications:

• SPAN - a tool for analyzing and comparing ChIP-Seq data

It doesn't contain source code of the applications.

Local Galaxy installation

• Install Galaxy. Checkout latest release: git clone -b release_18.05 https://github.com/galaxyproject/galaxy.git
• Galaxy relies on Conda in dependencies management, sometimes conda packages can conflict with locally installed packages, e.g. installed by pip, conda or homebrew on MacOS. The workaround is to removed them. Workaround is to disable/uninstall them while developing with Galaxy.
• Launch bash run.sh and ensure Galaxy is serving at http://127.0.0.1:8080
• Configure admin user to be able to install 3rd party tools from ToolShed. Create config by copying config/galaxy.yml.sample to config/galaxy.yml and change #admin_users: null record.
• Install span from the official Galaxy ToolShed. To verify installation went smoothly and dependencies are installed you should get 2 files available:

ls <GALAXY_FOLDER>/database/dependencies/package_span_jar/<VERSION>/jetbrains/span/<HASH>
env.sh              span-<VERSION>.jar

Local applications development

• Copy span folder to your local Galaxy installation under tools folder. For development purposes you can create symbolic link instead of copying, Galaxy recognizes all the filesystem changes and reloads tools on the fly.
• Add the following line to config/tool_conf.xml.sample

    <section id="jetbrains" name="JetBrains Research tools">
        <tool file="span/span.xml" />
    </section>

• Restart Galaxy, SPAN should be registered as a new tool. Check within tools search window. If everything goes successfully you should see the following output:

galaxy.tools.toolbox.base DEBUG 2018-10-30 16:31:45,941 [p:8990,w:0,m:0] [MainThread] Loading section: JetBrains Research tools

Example of files produced by SPAN.

Development

Galaxy updates tools definitions on-the-fly, the only limitation is that dependencies ARE NOT PROCESSED for locally installed tools. In span case we should configure $SPAN_JAR environmental variable to point to span java archive file to overcome this limitation.

See for details: https://biostar.usegalaxy.org/p/10433/

Publish to tool shed

• Login to ToolShed
• Create repository at Toolshed via Available Actions | Create new repository
• Update tool files
• Invoke Repository Actions | Reset all repository metadata
• Voila, tool shed version is synchronized with mercurial repo
• Now you will be able to install SPAN from official tool shed

There are 2 options to update repository files:

• Upload files from UI action Upload files to repository

  1. Create .tar.gz archive with command tar -czvf span.tar.gz * within span folder.
  2. Upload it

• Clone mercurial repository locally

  1. Clone repository locally. Visit https://www.mercurial-scm.org/wiki/CACertificates in case of error: abort: error: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:726)
  2. Copy application folder to dedicated mercurial repository
  3. Commit and push to mercurial

Error reporting

Report any errors or comments regarding SPAN in the public issue tracker.

Resources

• JetBrains Research BioLabs homepage
• Develop Galaxy apps
• Add Galaxy tool tutorial
• Biostar Galaxy