Commit 52059658 authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

Ran linkcheck

parent f501a11e
......@@ -17,9 +17,9 @@ institute <http://mediawiki.internal.sanger.ac.uk/index.php/How_to_run_MPI_jobs_
You can find real examples in the
`ensembl-compara <https://github.com/Ensembl/ensembl-compara>`__
repository. It ships Runnables used for phylogenetic trees inference:
`RAxML <https://github.com/Ensembl/ensembl-compara/blob/release/77/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/RAxML.pm>`__
`RAxML <https://github.com/Ensembl/ensembl-compara/blob/HEAD/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/RAxML.pm>`__
and
`ExaML <https://github.com/Ensembl/ensembl-compara/blob/feature/update_pipeline/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/ExaML.pm>`__.
`ExaML <https://github.com/Ensembl/ensembl-compara/blob/HEAD/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/ExaML.pm>`__.
They look very light-weight (only command-line definitions) because most
of the logic is in the base class (*GenericRunnable*), but nevertheless
show the command lines used and the parametrization of multi-core and
......@@ -152,7 +152,7 @@ define the correct resource class and comand lines in Hive.
- ``same[model]`` is needed to ensure that the selected compute nodes
all have the same hardware. You may also need something like
``select[avx]`` to select the nodes that have the `AVX instruction
set <http://en.wikipedia.org/wiki/Advanced_Vector_Extensions>`__
set <https://en.wikipedia.org/wiki/Advanced_Vector_Extensions>`__
- ``span[ptile=4]``, this option specifies the granularity in which LSF
will split the jobs/per node. In this example we ask for each machine
to be allocated a multiple of 4 cores. This might affect queuing
......
......@@ -12,7 +12,7 @@ eHive is great, and the user manual is great.
The code is open source, and `available on GitHub`_.
.. _available on GitHub: http://github.com/Ensembl/ensembl-hive
.. _available on GitHub: https://github.com/Ensembl/ensembl-hive
The main documentation for eHive is organized into a couple sections:
......
......@@ -20,12 +20,12 @@ download and install first:
At the moment, the following database options are available:
- MySQL 5.1 `or higher <http://dev.mysql.com/downloads/>`__.
- MySQL 5.1 `or higher <https://dev.mysql.com/downloads/>`__.
**Warning:** eHive is not compatible with MysQL 5.6.20 but is
with versions 5.6.16 and 5.6.23. We suggest avoiding the
5.6.[17-22] interval
- SQLite 3.6 `or higher <http://www.sqlite.org/download.html>`__
- PostgreSQL 9.2 `or higher <http://www.postgresql.org/download/>`__
- PostgreSQL 9.2 `or higher <https://www.postgresql.org/download/>`__
The database has to be accessible from all the machines you want to
run pipelines on, so make sure the SQLite database is on a shared
......@@ -61,7 +61,7 @@ Check out the repository by cloning it from GitHub:
All eHive pipelines will require the ensembl-hive repository, which can
be found on `GitHub <https://github.com/Ensembl/ensembl-hive>`__. As
such it is assumed that `Git <http://git-scm.com/>`__ is installed on
such it is assumed that `Git <https://git-scm.com/>`__ is installed on
your system, if not follow the instructions
`here <https://help.github.com/articles/set-up-git/>`__
......
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