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Conda/Container documentation and option naming improvements. #684

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Jun 2, 2017
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Conda/Container documentation and option naming improvements. #684

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2 changes: 1 addition & 1 deletion docs/_writing_dependencies_conda.rst
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Expand Up @@ -248,7 +248,7 @@ all the software and all the versions available matching that search term - incl

Alternatively the Anaconda_ website can be used to search for packages. Typing ``seqtk``
into the search form on that page and clicking the top result will bring on to `this page
https://anaconda.org/bioconda/seqtk`__ with information about the Bioconda package.
<https://anaconda.org/bioconda/seqtk>`__ with information about the Bioconda package.

When using the website to search though, you need to aware of what channel you are using. By
default, Planemo and Galaxy will search a few different Conda channels. While it is possible
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14 changes: 7 additions & 7 deletions docs/_writing_dependencies_docker.rst
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Expand Up @@ -47,7 +47,7 @@ tool from the introductory tutorial.

::

$ planemo lint --biocontainer seqtk_xml
$ planemo lint --biocontainers seqtk_seq.xml
Linting tool /home/planemo/workspace/planemo/project_templates/seqtk_complete/seqtk_seq.xml
Applying linter tests... CHECK
.. CHECK: 1 test(s) found.
Expand Down Expand Up @@ -79,11 +79,11 @@ BioConda_ recipes are packaged into containers and registered on quay.io_
as part of the BioContainers_ project.

This tool can be tested using ``planemo test`` in its BioContainer
Docker container using the flag ``--mulled_containers`` as shown (in part) next.
Docker container using the flag ``--biocontainers`` as shown (in part) next.

::

$ planemo test --mulled_containers seqtk_seq.xml
$ planemo test --biocontainers seqtk_seq.xml
...
2017-03-01 08:18:19,669 INFO [galaxy.tools.actions] Handled output named output1 for tool seqtk_seq (22.145 ms)
2017-03-01 08:18:19,683 INFO [galaxy.tools.actions] Added output datasets to history (14.604 ms)
Expand Down Expand Up @@ -123,7 +123,7 @@ This line indicates that Galaxy was able to find a container for this tool and
executed the tool in that container.

For interactive testing, the ``planemo serve`` command also implements the
``--mulled_containers`` flag.
``--biocontainers`` flag.

In this seqtk example the relevant BioContainer already existed on quay.io_,
this won't always be the case. For tools that contain multiple ``requirement``
Expand Down Expand Up @@ -247,11 +247,11 @@ Docker command ``images`` and explore the new container interactively with
/usr/local/bin/bwa

As before, we can test running the tool inside its container in Galaxy using
the ``--mulled_containers`` flag.
the ``--biocontainers`` flag.

::

$ planemo test --mulled_containers bwa_and_samtools.xml
$ planemo test --biocontainers bwa_and_samtools.xml
...
2017-03-01 10:20:58,077 INFO [galaxy.tools.actions] Handled output named output_2 for tool bwa_and_samtools (17.443 ms)
2017-03-01 10:20:58,090 INFO [galaxy.tools.actions] Added output datasets to history (12.935 ms)
Expand Down Expand Up @@ -305,7 +305,7 @@ Planemo doesn't yet expose options that make it possible to build mulled
containers for local packages that have yet to be published to anaconda.org
but the mulled toolkit allows this. See mulled_ documentation for more
information. However, once a container for a local package is built with
``mulled-build-tool`` the ``--mulled_containers`` command should work to test
``mulled-build-tool`` the ``--biocontainers`` command should work to test
it.

----------------------------------------------------------------
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2 changes: 2 additions & 0 deletions planemo/commands/cmd_lint.py
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Expand Up @@ -34,7 +34,9 @@
help="Check tool requirements for availability in best practice Conda channels.",
)
@click.option(
"biocontainer",
"--biocontainer",
"--biocontainers",
is_flag=True,
default=False,
help="Check best practice BioContainer namespaces for a container definition applicable for this tool.",
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2 changes: 2 additions & 0 deletions planemo/options.py
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Expand Up @@ -343,7 +343,9 @@ def job_config_option():

def mulled_containers_option():
return planemo_option(
"mulled_containers",
"--mulled_containers",
"--biocontainers",
is_flag=True,
help="Test tools against mulled containers (forces --docker).",
)
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