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Merge pull request #2850 from martenson/docs_conda

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[16.07] conda docs - add TOC
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John Chilton
2016-08-24 13:37:39 -04:00
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parent df47bd2007 7326498335
commit 3248b679ac
1 changed files with 25 additions and 27 deletions
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doc/source/admin/conda_faq.rst
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@@ -46,8 +46,8 @@ to this decision:
Below we answer some common questions (collected by Lance Parsons):
1. How do I enable Conda dependency resolution for existing Galaxy
installations ?
1. How do I enable Conda dependency resolution for existing Galaxy installations?
*********************************************************************************
Most Galaxy administrators have not set up a dependency resolvers
configuration file ( ``dependency_resolvers_conf.xml`` ) which means they
@@ -100,8 +100,8 @@ The most important configuration settings related to Conda are listed in Table 1
*Table 1: Important configuration options for Conda in Galaxy*
2. How do Conda dependencies work?
Where do things get installed?
2. How do Conda dependencies work? Where do things get installed?
*********************************************************************************
In contrast to the old dependency system, which was used exclusively by
Galaxy, Conda is a pre-existing, independent project. With Conda it
@@ -153,8 +153,8 @@ be configured in the ``dependency_resolvers_conf.xml`` and the ``galaxy.ini`` fi
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.?
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
@@ -168,8 +168,8 @@ includes CentOS 6). So all packages will run on all \*nix operating
systems newer than 2007.
4. How do I know what system is being used
by a given tool?
4. How do I know what system is being used by a given tool?
*********************************************************************************
The Galaxy log will tell you which dependency resolution system is used
to satisfy each tool dependency and you can specify priorities using the
@@ -180,9 +180,8 @@ specified. See `resolver docs`_ for detailed documentation. Starting from galaxy
see which dependency will be used (“resolved”) in the admin panel.
5. 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.
5. 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.
@@ -198,9 +197,8 @@ We will gradually adjust the documentation about ``tool_dependencies.xml`` and
deprecate it everywhere.
6. During tool installation what if there is no Conda package available
for given requirement? What if the requirement is resolved in a
different software than the original wrapper author meant to use?
6. During tool installation what if there is no Conda package available for 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 successfully, and can be used if its dependencies are
@@ -212,8 +210,8 @@ is no equivalent of the “owner” concept used in Galaxy packages
installed from the Tool Shed.
7. 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?
7. 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 installed run:
@@ -226,8 +224,8 @@ Galaxy. If you find your package your are ready to go. If not please
`create a Conda package`_ and submit_ it to BioConda_ or get in `contact with the IUC`_.
8. How can I create a new Conda package for a
dependency?
8. 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
@@ -240,8 +238,8 @@ offers you, so called \`skeleton\` generators, generating recipes from
pypi, cran, cpan for you (mostly) automatically.
9. Is there a way to convert traditional Tool Shed package recipes that
are not yet in a Conda channel?
9. 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
@@ -253,9 +251,8 @@ 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.
10. What is the recommendation for existing installations? Will I
continue to maintain both systems or migrate to the new Conda system
eventually?
10. 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 to install old tools. This we promised to our
@@ -263,9 +260,8 @@ community to guarantee sustainability and reproducibility. New tools
from the IUC, may be Conda only.
11. 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 dependencies are installed?
11. 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 dependencies are installed?
*********************************************************************************
This depends on your ``galaxy.ini`` setting. Galaxy will install Conda for
you if you have enabled ``conda_auto_init``. If ``conda_auto_install`` is
@@ -282,6 +278,7 @@ has created a Trinity environment for you have a look at folder under
12. 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
@@ -298,6 +295,7 @@ The first system that satisfies a requirement will be used.
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,
@@ -310,7 +308,7 @@ characters long.
If this is your problem, you should see a warning similar to the
following in your galaxy log files:
.. code-block:: guess
.. code-block:: bash
ERROR: placeholder '/home/ray/r_3_3_1-x64-3.5/envs/_build_placehold_placehold_placehold_placehold_pl' too short