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Merge branch 'release_16.07' into dev

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	doc/source/admin/conda_faq.rst
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Nicola Soranzo
2016-10-05 20:34:50 +01:00
parent 16c2227b93 f32b6446a7
commit a2ee8d10af
9 changed files with 72 additions and 59 deletions
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doc/source/admin/conda_faq.rst
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@@ -50,13 +50,17 @@ Below we answer some common questions (collected by Lance Parsons):
Galaxy's dependency job resolution is managed via
``dependency_resolvers_conf.xml`` configuration file. Most Galaxy administrators
have not set up a dependency resolvers configuration file, which means they are
using Galaxy's default ( ``dependency_resolvers_conf.xml.sample`` ). With
release 16.04, Galaxy has enabled Conda dependency resolution by default when
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 will look for job
``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.
@@ -101,7 +105,7 @@ See `galaxy.ini.sample`_ for the complete list.
2. How do Conda dependencies work? Where do things get installed?
*********************************************************************************
In contrast to the old dependency system, which was used exclusively by Galaxy,
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
@@ -170,19 +174,28 @@ systems newer than 2007.
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. Further, if
``conda_auto_install`` is enabled, Galaxy will install Trinity via Conda only
when a Trinity job is launched and Trinity is not yet installed.
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.
More improvements to the UI will be coming in future releases. To see if Galaxy
has created a Trinity environment for you have a look at folder under
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?
*********************************************************************************
@@ -198,7 +211,8 @@ The order in which resolvers are tried is listed in the
- Packages manually installed by administrators
- Conda packages
The first system that satisfies a requirement will be used.
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?
@@ -206,10 +220,7 @@ The first system that satisfies a requirement will be used.
The Galaxy log will show which dependency resolution system is used
to satisfy each tool dependency and you can specify priorities using the
``dependency_resolution_conf.xml`` file. If you put Conda on
top, Galaxy will first try to use Conda to resolve a tool dependency;
if this does not work, the following dependency resolver is used, as
listed. See `resolver docs`_ for detailed documentation. Starting from Galaxy
``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.