Conda for Tool Dependencies

Galaxy tools (also called wrappers) traditionally use Tool Shed package recipes to install their dependencies. At the tool’s installation time the recipe is downloaded and executed in order to provide the underlying software executables. Introduction of these Galaxy-specific recipes was a necessary step at the time, however nowadays there are other more mature and stable options to install software in a similar manner. The Galaxy community has taken steps to improve the tool dependency system in order to enable new features and expand its reach. This document aims to describe these and answer the FAQ.

Galaxy has adopted a new standard for tool dependencies: Conda packages!

Not only do Conda packages make tool dependencies more reliable and stable, they are also easier to test and faster to develop than the traditional Tool Shed package recipes.

Conda is a package manager like apt-get, yum, pip, brew or guix. We don’t want to argue about the relative merits of various package managers here, in fact Galaxy supports multiple package managers and we welcome community contributions (such as implementing a Guix package manager or enhancing the existing brew support to bring it on par with Conda).

As a community, we have decided that Conda is the one that best fulfills community’s needs. The following are some of the crucial Conda features that led to this decision:

  • Installation of packages does not require root privileges (installation at any location the Galaxy user has write access to)
  • Multiple versions of software can be installed on the system
  • HPC-ready
  • Faster and more robust package installations through pre-compiled packages (no build environment complications)
  • Independent of programming language (R, Perl, Python, Julia, Java, pre-compiled binaries, and more)
  • Easy to write recipes (1 YAML description file + 1 Bash install script)
  • An active, large and growing community (with more and more software authors managing their own recipes)
  • Extensive documentation: Conda documentation and Conda quick-start

Below we answer some common questions (collected by Lance Parsons):

1. How do I enable Conda dependency resolution for Galaxy jobs?

Galaxy’s dependency job resolution is managed via dependency_resolvers_conf.xml configuration file. Most Galaxy administrators should be using Galaxy’s default dependency resolvers configuration file ( dependency_resolvers_conf.xml.sample ). With release 16.04, Galaxy has enabled Conda dependency resolution by default when Conda was already installed on the system. Having Conda enabled in dependency_resolvers_conf.xml means that Galaxy can look for job dependencies using the Conda system when it attempts to run tools.

Note that the order of resolvers in the file matters and the <tool_shed_packages /> entry should remain first. This means that tools that have specified Tool Shed packages as their dependencies will work without a change.

The most common configuration settings related to Conda are listed in Table 1. See galaxy.ini.sample for the complete list.

Setting Default setting Meaning
conda_prefix <tool_dependency_dir>/ _conda

the location on the filesystem where Conda packages and environments are installed

IMPORTANT : Due to a current limitation in Conda, the total length of the

conda_prefix and the job_working_directory path should be less than 50 characters!

conda_auto_init False Set to True to instruct Galaxy to install Conda (the package manager) automatically if it cannot find a local copy already on the system.
conda_auto_install False Set to True to instruct Galaxy to look for and install Conda packages for missing tool dependencies before running a job.

Table 1: Commonly used configuration options for Conda in Galaxy.

2. How do Conda dependencies work? Where do things get installed?

In contrast to the TS dependency system, which was used exclusively by Galaxy, Conda is a pre-existing, independent project. With Conda, it is possible for an admin to install and manage packages without touching Galaxy at all. Galaxy can handle these dependencies for you, but admins are not required to use Galaxy for dependency management.

There are a few new config options in the galaxy.ini file (see Table 1 or galaxy.ini.sample for more information), but by default Galaxy will install Conda (the package manager) and the required packages in the <tool_dependency_dir>/_conda/ directory. In this directory, Galaxy will create an envs folder with all of the environments managed by Galaxy. Each environment contains a lib, bin, share, and include subdirectory, depending on the tool, and is sufficient to get a Galaxy tool up and running. Galaxy simply sources this folder via Conda and makes everything available before the tool is executed on your system.

To summarize, there are four ways to manage Conda dependencies for use with Galaxy. For all of these options, Conda dependency management must be configured in the dependency_resolvers_conf.xml and the galaxy.ini file.

  1. Manual Install - Conda dependencies may be installed by administrators from the command line. Conda (and thus the Conda environments) should be installed in the location specified by the conda_prefix path (defined in galaxy.ini and by default <tool_dependency_dir>/_conda/ directory). Galaxy will search these environments for required packages when tools are run. Conda environment names have to follow a specific naming pattern. As an example, to install samtools in version 0.1.19, the administrator can run the command:

    $ conda create --name __samtools@0.1.19 samtools==0.1.19 --channel bioconda
    

    Tools that require samtools version 0.1.19 will then be able to find and use the installed Conda package.

  2. Galaxy Admin Interface (>= 16.07) - Galaxy will install Conda tool dependencies when tools are installed from the Tool Shed if the option “When available, install externally managed dependencies (e.g. Conda)? Beta” is checked. Admins may also view and manage Conda dependencies via the Admin interface.

  3. Automatically at tool run time - When a tool is run and a dependency is not found, Galaxy will attempt to install the dependency using Conda if conda_auto_install is activated in the configuration.

  4. Via the API (>= 16.07) - The Galaxy community maintains an ansible role that uses BioBlend and the Galaxy API to install tools.

3. What is required to make use of this? Any specific packages, Galaxy revision, OS version, etc.?

The minimum required version of Galaxy to use Conda is 16.01, however version 16.07 or greater is recommended. The 16.07 release of Galaxy has a graphical user interface to manage packages, but this is not required to have Conda dependencies managed and used by Galaxy.

Conda packages should work on all compatible operating systems with glibc version 2.5 or newer (this includes Centos 5). We will most likely switch soon to glibc version 2.12 as a minimum requirement (this includes CentOS 6). So all packages will run on all *nix operating systems newer than 2007.

4. If I have Conda enabled, what do I need to do to install tools using it? For example, how can I install the latest Trinity? And how will I know the dependencies are installed?

This depends on your galaxy.ini setting. Starting with release 16.07, Galaxy can automatically install the Conda package manager for you if you have enabled conda_auto_init. Galaxy can then install Trinity along with its dependencies using one of the methods listed in question 2 above. In particular, if conda_auto_install is True and Trinity is not installed yet, Galaxy will try to install it via Conda when a Trinity job is launched.

With release 16.07 you can see which dependencies are being used in the “Manage installed tools” section of the Admin panel and you can select whether or not to install Conda packages or Tool Shed package recipes when you install new tools there, even if conda_auto_install is disabled.

During a tool installation, the Galaxy admin has control over which systems will be used to install the tool requirements. The default settings will trigger installation of both TS and Conda packages (if Conda is present), thus depending on the dependency resolvers configuration with regards to what will actually be used during the tool execution.

To check if Galaxy has created a Trinity environment, have a look at folders under <tool_dependency_dir>/_conda/envs/``(or ``<conda_prefix>/envs if you have changed conda_prefix in your galaxy.ini file).

We recommend to use Conda on a tool-per-tool basis, by unchecking the checkbox for TS dependencies during the tool installation, and for tools where there are no available TS dependencies.

5. Can I mix traditional Galaxy packages and Conda packages?

Yes, the way this works is that Galaxy goes through the list of requirements for a tool, and then determines for each requirement if it can be satisfied by any of the active resolver systems.

The order in which resolvers are tried is listed in the dependency_resolvers_conf.xml file. The default order is

  • Tool Shed packages
  • Packages manually installed by administrators
  • Conda packages

The first system that satisfies a requirement will be used. See resolver docs for detailed documentation.

6. How do I know what system is being used by a given tool?

The Galaxy log will show which dependency resolution system is used to satisfy each tool dependency and you can specify priorities using the dependency_resolvers_conf.xml file (see question 5 above). Starting from Galaxy release 16.07, you can see which dependency will be used (“resolved”) in the Admin panel.

7. How do I go about specifying Conda dependencies for a tool? All the docs still seem to recommend (or exclusively discuss) the tool_dependencies.xml method.

The simple answer is: you don’t need to do much to make Conda work for a tool.

The <requirement> tag in the tool XML file is enough. The name and the version should correspond to a Conda package in the default, r, bioconda or iuc Conda channel (you can extend this list if you like in your galaxy.ini ). If this is the case you are ready to go. Read more about Conda channels and browse their packages on https://anaconda.org/ url followed by the channel name (e.g. https://anaconda.org/bioconda ).

We will gradually adjust the documentation about tool_dependencies.xml and deprecate it everywhere.

8. During tool installation what if there is no Conda package available for a given requirement? What if the requirement is resolved in a different software than the original wrapper author meant to use?

If there is no Conda package available during tool installation the tool will install automatically, and can be used if its dependencies are satisfied by another dependency system such as Tool Shed package recipes, Docker containers or modules.

If there is a package of correct name and version it will be used. There is no equivalent of the “owner” concept used in Galaxy packages installed from the Tool Shed.

9. Where can I find a list of existing Conda packages that I can point to, so I don’t have to reinvent the wheel for common dependencies?

With Conda package manager installed on your system, run:

$ conda search <package_name> -c bioconda -c iuc

This will search in all channels that are activated by default in Galaxy. If you find your package, you are ready to go. If not please create a Conda package and submit it to BioConda or get in contact with the IUC.

10. How can I create a new Conda package for a dependency?

Adding a package to the BioConda or IUC Conda channels will make it available for Galaxy tools to use as a dependency. To learn how, get in touch with the awesome BioConda community. They have great documentation and assist with all development. You will also see a few of us at this project to get you started :)

Don’t be scared! Conda recipes are really simple to write. Conda also offers so called `skeleton` generators that generate recipes from pypi, cran, or cpan for you (mostly) automatically.

11. Is there a way to convert traditional Tool Shed package recipes that are not yet in a Conda channel?

First, you do not need to do anything to your wrapper as long as the package name in the requirement tag matches the name of correct Conda package. (You may want to mention in the README or a comment the Conda channel that contains the package).

If you want to migrate some recipes from XML to Conda, IUC is happy to give you a hand. We are trying to get all new versions under Conda and leave the old versions as they are – simply because of time.

12. What is the recommendation for existing installations? Will I continue to maintain both systems or migrate to the new Conda system eventually?

Old tools will use the traditional installation system; this system will stay and will be supported for installing old tools to guarantee sustainability and reproducibility. New tools from the IUC, may be Conda only.

13. What can I do if Conda doesn’t work for me?

There is currently a limitation in the way Conda packages are being built. This limitation will be addressed shortly by the Conda community, however this requires all packages to be rebuilt.

To work around this limitation, please make sure that the total length of the conda_prefix and job_working_directory path is less than 50 characters long.

If this is your problem, you should see a warning similar to the following in your galaxy log files:

ERROR: placeholder '/home/ray/r_3_3_1-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_pl' too short

In rare cases Conda may not have been properly installed by Galaxy. A symptom for this is if there is no activate script in <conda_prefix>/bin folder. In that case you can delete the conda_prefix folder and restart Galaxy, which will again attempt to install Conda.

If this does not solve your problem or you have any trouble following the instructions, please ask on the Galaxy mailing list or the Galaxy IRC channel.