Commit 1b0a340b authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

Fixed the links between pages

No more warnings when compiling the manual !
parent 6a171b3d
.. _script-beekeeper:
.. script_documentation:: beekeeper
.. _script-db_cmd:
.. script_documentation:: db_cmd
.. _script-generate_graph:
.. script_documentation:: generate_graph
.. _script-generate_timeline:
.. script_documentation:: generate_timeline
.. _script-hoover_pipeline:
.. script_documentation:: hoover_pipeline
.. _script-init_pipeline:
.. script_documentation:: init_pipeline
.. _script-load_resource_usage:
.. script_documentation:: load_resource_usage
.. _script-runWorker:
.. script_documentation:: runWorker
.. _script-seed_pipeline:
.. script_documentation:: seed_pipeline
.. _script-standaloneJob:
.. script_documentation:: standaloneJob
.. _script-tweak_pipeline:
.. script_documentation:: tweak_pipeline
.. _script-visualize_jobs:
.. script_documentation:: visualize_jobs
......@@ -17,7 +17,7 @@ Check that your system is set up to run eHive
Some pipelines may have other dependencies beyond eHive (e.g. the
Ensembl Core API, BioPerl, etc). Make sure you have installed them
and configured your environment (PATH and PERL5LIB).
:ref:`../appendix/scripts/init_pipeline` will
:ref:`script-init_pipeline` will
try to compile all the analysis modules, which ensures that most of
the dependencies are installed, but some others can only be found
at runtime.
......@@ -36,27 +36,27 @@ done or failed.
Running the pipeline involves the following steps:
#. Using the :ref:`../appendix/scripts/init_pipeline` script to create an
#. Using the :ref:`script-init_pipeline` script to create an
instance pipeline database from a "PipeConfig" file
#. (optionally) Using the :ref:`appendix/scripts/seed_pipeline` script to
#. (optionally) Using the :ref:`script-seed_pipeline` script to
add jobs to be run
#. Running the :ref:`appendix/scripts/beekeeper` script that will look
#. Running the :ref:`script-beekeeper` script that will look
after the pipeline and maintain a population of Worker processes on
the compute resource that will take and perform all the jobs of the
#. (optionally) Monitoring the state of the running pipeline:
- by using your local |guiHive| web interface
- by using your local guiHive web interface
- by periodically running the :ref:`appendix/scripts/generate_graph`
- by periodically running the :ref:`script-generate_graph`
script, which will produce a fresh snapshot of the pipeline
- by connecting to the database using the
:ref:`appendix/scripts/db_cmd` script and issuing SQL commands
:ref:`script-db_cmd` script and issuing SQL commands
Initialise and run a pipeline
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