by @martenson, @mvdbeek
#usegalaxy #GAT2018 @galaxyproject
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/.
- Install
iuc/bedtools
from MTS in revision10: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
andtool_dependency_dir
in the production basics session, you'll need to do it now.
New bedtools revision has been uploaded to the MTS.
- Install
iuc/bedtools
from MTS in revision16:e0cec48a4695
into section 'New BEDtools'.
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.
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.
The old bedtools version is no longer useful
- Uninstall the revision
10:c78cf6fe3018
of bedtools.
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.
Check the version of Conda
Hint: conda --version
will show the version
Check which channels Conda is going to use
Hint: You can find this information in galaxy.ini
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).
Find where the dependencies are present on the filesystem
Hint: The information is in the config.
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.
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 runningpip install ephemeris
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>
- Create the tool list for devteam/fastqc versions 0.68 and 0.69
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.
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>
Verify that fastqc is correctly installed
Hint: You can see the installation status in the admin panel
Update all installed repositories of a galaxy instance
The command is:
shed-tools update -g <galaxy_url> -a <api_key>