diff --git a/doc/source/admin/conda_faq.rst b/doc/source/admin/conda_faq.rst index 553f9078084..1c6e201908b 100644 --- a/doc/source/admin/conda_faq.rst +++ b/doc/source/admin/conda_faq.rst @@ -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`` | / | 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`` | / | 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*