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Galaxy Administrators Course

Tool Management Exercise

by @martenson, @mvdbeek

#usegalaxy #GAT2018 @galaxyproject

Task 1

Your users want to use bedtools on the instance you administer.

  • Find what Tool Shed repository has bedtools tools in it.

Hint: You can use search in https://toolshed.g2.bx.psu.edu/.

Task 2

  • Install iuc/bedtools from MTS in revision 10:c78cf6fe3018 (2016-10-03) into new section 'BEDtools' using TS dependencies.

Hints:

  • Note the revision, it is NOT the latest.
  • If you did not set tool_config_file and tool_dependency_dir in the production basics session, you'll need to do it now.

Task 3

New bedtools revision has been uploaded to the MTS.

  • Install iuc/bedtools from MTS in revision 16:e0cec48a4695 into section 'New BEDtools'.

Task 4

You want to show both versions of bedtools and allow users to switch versions on the tool form

  • Move bedtools revision 10:c78cf6fe3018 into 'New BEDtools' section and display it.

Hint: tools with the same ID and different version in the same section will 'collapse' into one and offer the switch button.

Task 5

Now there is only one section we might not want to call it 'New'.

  • Rename the 'New BEDtools' section to just 'BEDtools'.

Hints:

  • You can rename sections using configuration file(s).
  • When renaming you need to be consistent across the configs.

Task 6

The old bedtools version is no longer useful

  • Uninstall the revision 10:c78cf6fe3018 of bedtools.

Task 7

We want to use Conda package manager to satisfy tool dependencies

  • Verify Conda is installed

Hint: Conda will be installed automatically if you use run.sh. The default location is <tool_dependency_dir>/_conda.

Task 8

Check the version of Conda

Hint: conda --version will show the version

Task 9

Check which channels Conda is going to use

Hint: You can find this information in galaxy.ini

Task 10

Install latest seqtk and install only Conda dependencies for it

Hints:

  • By default Galaxy installs packages from both TS and Conda if available.
  • You can follow the installation process by looking at galaxy's log file(s).

Task 11

Find where the dependencies are present on the filesystem

Hint: The information is in the config.

Task 12

Uninstall the TS package and verify that the Conda package will be used

Hints:

  • To uninstall a package find the package in the Manage Tools section of the admin panel.
  • You can see which dependency will be used in the Manage dependencies section.

Task 13

We want to use ephemeris to automate tool installation

  • Let's install ephemeris

Hints:

  • If you don't have virtualenv installed you can install it with sudo apt-get install -y python-virtualenv
  • This can be done on your local machine or on the cloud vm.
  • If you don't have a python virtualenv, create and activate one now with virtualenv ~/.venv && source ~/.venv/bin/activate Hint: You can install ephemeris by running pip install ephemeris

Task 14

Create a list of tool to install

  • Ephemeris requires a yaml file with the following syntax:
tools:
  - name: <repository_name>
    owner: <repository_owner>
    tool_panel_section_label: <section label>
    tool_shed_url: <tool_shed_url>
    revisions:
      - <revision_1>
      - <revision_2>

Hints:

  • You can supply as many installable revisions as you would like, they will all be installed
  • If no revision is given the latest revision will be installed.

Task 15

Install fastqc using ephemeris into the section "FastQC"

  • The syntax for installing tools using a yaml file is:
shed-tools install -t <tool_list.yml> -a <api_key> -g <galaxy_url>

Task 16

Verify that fastqc is correctly installed

Hint: You can see the installation status in the admin panel

Task 17

Update all installed repositories of a galaxy instance

The command is:

shed-tools update -g <galaxy_url> -a <api_key>