Unverified Commit 1fedac75 authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Fix ``mulled-update-singularity-containers`` documentation 

The `mulled-singularity-testing` command was never added to the
`galaxy-tool-util` package.
parent 95c6e4b7

doc/source/admin/special_topics/mulled_containers.rst

+7 −5
Original line number Diff line number Diff line
@@ -153,8 +153,6 @@ Multiple containers can be installed simultaneously by giving ``--containers`` m 


   $ mulled-update-singularity-containers --containers samtools:1.6--0 bamtools:2.4.1--0 --filepath /tmp/sing/ --installation /usr/local/bin/singularity



.. code-block:: bash



For a large number of containers, it may be more convenient to employ the ``--container-list`` option:



.. code-block:: bash
@@ -163,15 +161,19 @@ For a large number of containers, it may be more convenient to employ the ``--co 


Here ``list.txt`` should contain a list of containers, each on a new line.



In order to generate the list file the ``mulled-list`` command may be useful. The following command returns a list of all Docker containers available on the quay.io biocontainers organization, excluding those already available as Singularity containers via https://depot.galaxyproject.org/singularity/.:: bash

In order to generate the list file the ``mulled-list`` command may be useful. The following command returns a list of all Docker containers available on the quay.io biocontainers organization, excluding those already available as Singularity containers on https://depot.galaxyproject.org/singularity/ .



.. code-block:: bash



   $ mulled-list --source docker --not-singularity --blacklist blacklist.txt --file output.txt



The list of containers will be saved as ``output.txt``. The (optional) ``--blacklist`` option may be used to exclude containers which should not included in the output; ``blacklist.txt`` should contain a list of the 'blacklisted' containers, each on a new line.



Containers, once generated, should be tested. This can be achieved by affixing ``--testing test-output.log`` to the command, or alternatively, by use of the dedicated ``mulled-singularity-testing`` tool.:: bash

The generated containers should also be tested. This can be achieved by affixing ``--testing test-output.log`` to the ``mulled-update-singularity-containers`` command:



.. code-block:: bash



   $ mulled-singularity-testing --container-list list.txt --filepath /tmp/sing/ --installation /usr/local/bin/singularity --logfile test-output.txt

   $ mulled-update-singularity-containers --container-list list.txt --filepath /tmp/sing/ --installation /usr/local/bin/singularity --testing test-output.log



.. _IUC: https://galaxyproject.org/iuc/

.. _container annotation:  https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/catDocker.xml#L4