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8 changes: 4 additions & 4 deletions docs/advanced_topics.rst
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ Docker useful tips
Bash interactive script
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block::
.. code-block:: bash

$ docker run -t -i ubuntu /bin/bash
root@af8bae53bdd3:/#
Expand All @@ -36,7 +36,7 @@ In this example:

Let’s try running some commands inside the container:

.. code-block::
.. code-block:: bash

root@af8bae53bdd3:/# ls
bin boot dev etc home lib lib64 media mnt opt proc root run sbin srv sys tmp usr var
Expand All @@ -51,7 +51,7 @@ Start a daemonized Hello world

Let’s create a container that runs as a daemon.

.. code-block::
.. code-block:: bash

$ docker run -d ubuntu /bin/sh -c "while true; do echo hello world; sleep 1; done"
1e5535038e285177d5214659a068137486f96ee5c2e85a4ac52dc83f2ebe4147
Expand All @@ -60,7 +60,7 @@ Let’s create a container that runs as a daemon.

We can use this container ID to see what’s happening with our hello world daemon. First, let’s make sure our container is running. Run the ``docker ps`` command. The docker ``ps`` command queries the Docker daemon for information about all the containers it knows about.

.. code-block::
.. code-block:: console

$ docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
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2 changes: 1 addition & 1 deletion docs/best_practices.rst
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Expand Up @@ -155,7 +155,7 @@ General


* ADD vs COPY: Both ADD and COPY adds local files when building a container but ADD does some additional magic like adding remote files and ungzipping and untaring archives. Only use ADD if you understand this difference.
* WORKDIR and ENV: Each command will create a new temporary image and runs in a new shell hence if you do a cd :raw-html-m2r:`<directory>` or export :raw-html-m2r:`<var>`\ =\ :raw-html-m2r:`<value>` in your Dockerfile it won't work. Use WORKDIR to set your working directory across multiple commands and ENV to set environment variables.
* WORKDIR and ENV: Each command will create a new temporary image and runs in a new shell hence if you do a `cd <directory>` or `export <var>=<value>` in your Dockerfile it won't work. Use WORKDIR to set your working directory across multiple commands and ENV to set environment variables.
* CMD and ENTRYPOINT: CMD is the default command to execute when an image is run. The default ENTRYPOINT is /bin/sh -c and CMD is passed into that as an argument. We can override ENTRYPOINT in our Dockerfile and make our container behave like an executable taking command line arguments (with default arguments in CMD in our Dockerfile).
* ADD your code last: ADD invalidates your cache if files have changed. Don't invalidate the cache by adding frequently changing stuff too high up in your Dockerfile. Add your code last, libraries and dependencies first. For node.js apps that means adding your package.json first, running npm install and only then adding your code.
* USER in Dockerfiles: By default docker runs everything as root but you can use USER in Dockerfiles. There's no user namespacing in docker so the container sees the users on the host but only uids hence you need the add the users in the container.
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8 changes: 4 additions & 4 deletions docs/conda_integration.rst
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Expand Up @@ -97,7 +97,7 @@ We utilize `mulled <https://github.com/mulled/mulled>`_ with `involucro <https:/
Here is a short introduction:

Search for conda-based containers
~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This will search for containers in the biocontainers organisation.

Expand All @@ -106,7 +106,7 @@ This will search for containers in the biocontainers organisation.
$ mulled-search -s vsearch -o biocontainers

Build all packages from bioconda from the last 24h
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The BioConda community is building a container for every package they create with a command similar to this:

Expand All @@ -117,7 +117,7 @@ The BioConda community is building a container for every package they create wit
--involucro-path ./involucro --recipes-dir ./bioconda-recipes --diff-hours 25 build

Building Docker containers for local Conda packages
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Conda packages can be tested with creating a busybox-based container for this particular package in the following way.
This also demonstrates how you can build a container locally and on-the-fly.
Expand Down Expand Up @@ -148,7 +148,7 @@ The ``--0`` indicates the build version of the conda package. It is recommended
you will override already existing images. For Python Conda packages this extension might look like this ``--py35_1``.

Build, test and push a conda-forge package to biocontainers
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. note:: You need to have write access to the biocontainers repository

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8 changes: 4 additions & 4 deletions docs/examples.rst
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Expand Up @@ -6,14 +6,14 @@ BioContainers in Examples
In this section we provide a set of examples about how to use BioContainers in your analysis. Please feel free to contribute to this help with your own examples.

Peptide MS search engine (Tide)
-------------------------
-------------------------------

Let’s run a proteomics search engine to identified proteins using `Tide <http://crux.ms/commands/tide-index.html>`_. Proteomics data analysis is dominated by database-based search engines strategies. Amount Search Engines, **Tide** is one of the most popular nowadays.

Get the docker container
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block::
.. code-block:: bash

$ docker pull biocontainers/crux:v3.2_cv3

Expand All @@ -34,7 +34,7 @@ I'm placing all these files inside a folder in your machine, in my case I will u
Start searching
~~~~~~~~~~~~~~~~~~~~~~

.. code-block::
.. code-block:: bash

$ docker run -v /Users/yperez/workplace/:/data/ biocontainers/crux:v3.2_cv3 crux tide-index small-yeast.fasta yeast-index

Expand All @@ -43,7 +43,7 @@ Start searching
After running this command you will see a new folder called yeast-index in your path (``/Users/yperez/workplace``).


.. code-block::
.. code-block:: bash

$ docker run -v /Users/yperez/workplace/:/data/ biocontainers/crux:v3.2_cv3 crux tide-search --compute-sp T --mzid-output T demo.ms2 yeast-index

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4 changes: 2 additions & 2 deletions docs/getting_started.rst
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Expand Up @@ -4,7 +4,7 @@ Getting started with Docker
============================

Docker Configuration
---------------
--------------------

`Docker <https://www.docker.com/>`__ is the world’s leading platform for software containerization. Docker includes multiple tools and components such as: `docker <https://docs.docker.com/>`__, `docker engine <https://docs.docker.com/engine/installation/>`__, `docker hub <https://docs.docker.com/docker-hub/>`__.

Expand Down Expand Up @@ -76,7 +76,7 @@ In many cases the software you are using requires an input or an output file to

After setting the folder and necessary files inside we can execute the image we want. In the example bellow we are running an image built from an example container:

.. code-block::
.. code-block:: bash

$ docker run -v /home/user/docker/:/data/ biocontainers/program:version -input /data/prot.fa -output /data/result.txt`

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35 changes: 0 additions & 35 deletions docs/index.rst
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Expand Up @@ -13,49 +13,14 @@ Contents
:maxdepth: 1

introduction
.. toctree::
:maxdepth: 3

what_is_container
.. toctree::
:maxdepth: 3

what_is_biocontainers
.. toctree::
:maxdepth: 3

getting_started
.. toctree::
:maxdepth: 3

running_example
.. toctree::
:maxdepth: 3

conda_integration
.. toctree::
:maxdepth: 3

biocontainers_registry
.. toctree::
:maxdepth: 3

examples
.. toctree::
:maxdepth: 3

best_practices
.. toctree::
:maxdepth: 3

citations
.. toctree::
:maxdepth: 3

advanced_topics
.. toctree::
:maxdepth: 3

contributing
.. toctree::
:maxdepth: 3
2 changes: 1 addition & 1 deletion docs/presentations.rst
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Expand Up @@ -3,5 +3,5 @@ Presentations and Training Materials
==============================================


* Introduction to BioContainers at EBI Campus, November 2016: :raw-html-m2r:`<a href="http://biocontainers.pro/docs/presentations/presentations/November-EBI-2016/">Presentation Slides</a>`
* Introduction to BioContainers at EBI Campus, November 2016: `Presentation Slides <http://biocontainers.pro/docs/presentations/presentations/November-EBI-2016/>`_
* ELIXIR Webinar: Bioconda and BioContainers, March 2017: `get the PDF <https://github.com/BioContainers/BioContainers.github.io/raw/master/docs/img/ELIXIR-Webinar-BioConda-BioContainers.pdf>`_
2 changes: 1 addition & 1 deletion docs/running_example.rst
Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ Now that you have enough information to start comparing sequences using BLAST, y
We hope that this short example can shed some light on how important and easy it is to run containerized software.

Run everything in one go
~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: bash

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2 changes: 1 addition & 1 deletion docs/singularitycontainers.rst
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
.. _singularitycontainers

Using Singularity containers
=========================
============================

6 changes: 3 additions & 3 deletions docs/what_is_biocontainers.rst
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ When a container is deployed and the developer closes the issue in GitHub, the u
.. note:: You can read other sections about :doc:`conda_integration` and :doc:`singularitycontainers`

Reporting a problem with a container
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If the user finds a problem with a container an issue should be opened in
the `container repository <https://github.com/BioContainers/containers/issues>`__, the user should use the **broken tag** (`see tags <https://github.com/BioContainers/containers/labels>`_). Developers of the project will pick-up the issue and deploy a new version of the container. A message will be delivered when the container has been fixed.
Expand All @@ -74,7 +74,7 @@ BioContainers build the docker containers from two different sources the `Docker
In order to be able to contribute to BioContainers you should be able to create a BioConda recipe or a Dockerfile recipe.

Create a BioConda recipe
~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~

.. note:: Before you start please read the Conda documentation and `how to setup conda in your machine <https://conda.io/projects/conda-build/en/latest/source/user-guide/tutorials/index.html>`__

Expand All @@ -87,7 +87,7 @@ In summary should follow these steps:
After the PR gets merged, a Conda package gets created and the corresponding docker container get pushed into `Quay.io Registry <https://quay.io/organization/biocontainers>`__ and the `BioContainers Registry <https://biocontainers.pro/#/registry>`__

Create a Dockerfile recipe
~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~

This is a standard template for creating a new Dockerfile for BioContainers:

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1 change: 1 addition & 0 deletions docs/what_is_container.rst
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Expand Up @@ -32,6 +32,7 @@ In the next video you can check out what you can achieve by using docker contain
<iframe width="100%" height="600px" src="https://www.youtube.com/embed/aLipr7tTuA4" frameborder="0"></iframe>

.. raw:: html

</b>

Container technologies
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