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add more literal includes

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Martin Cech
2016-08-23 17:41:07 -04:00
parent 453c98d8ad
commit aedfdffafe
1 changed files with 33 additions and 33 deletions
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doc/source/admin/conda_faq.rst
+33 -33
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@@ -51,7 +51,7 @@ installations ?
Most Galaxy administrators have not set up a dependency resolvers
configuration file ( ``dependency_resolvers_conf.xml`` ) which means they
are using Galaxy's default ( dependency\_resolvers\_conf.xml.sample ).
are using Galaxy's default ( ``dependency_resolvers_conf.xml.sample`` ).
Galaxy has enabled Conda dependency resolution by default since release
16.04 (if Conda was installed already), so many existing installations
can use Conda dependencies. Having Conda enabled in ``dependency_resolvers_conf.xml`` means that Galaxy will
@@ -64,38 +64,38 @@ Shed is available since the 16.07 version of Galaxy.
The most important configuration settings related to Conda are listed in Table 1.
+--------------------------+--------------------------+--------------------------+
| Setting | Default setting | Meaning |
+--------------------------+--------------------------+--------------------------+
| ``conda_prefix`` | <tool\_dependency\_dir>/ | the location |
| | \_conda | 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_install`` | False | Set to True to instruct |
| | | Galaxy to look for and |
| | | install Conda packages |
| | | for missing tool |
| | | dependencies before |
| | | running a job |
+--------------------------+--------------------------+--------------------------+
| ``conda_auto_init`` | False | Set to True to instruct |
| | | Galaxy to install Conda |
| | | automatically if it |
| | | cannot find a local copy |
+--------------------------+--------------------------+--------------------------+
+--------------------------+--------------------------+---------------------------+
| Setting | Default setting | Meaning |
+--------------------------+--------------------------+---------------------------+
| ``conda_prefix`` | <tool\_dependency\_dir>/ | the location |
| | \_conda | 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_install`` | False | Set to True to instruct |
| | | Galaxy to look for and |
| | | install Conda packages |
| | | for missing tool |
| | | dependencies before |
| | | running a job |
+--------------------------+--------------------------+---------------------------+
| ``conda_auto_init`` | False | Set to True to instruct |
| | | Galaxy to install Conda |
| | | automatically if it |
| | | cannot find a local copy |
+--------------------------+--------------------------+---------------------------+
*Table 1: Important configuration options for Conda in Galaxy*