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some RST syntax fixes #21

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2 changes: 1 addition & 1 deletion docs/HowToInstall.rst
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Expand Up @@ -128,7 +128,7 @@ To test ``InterProScan``, run the following command:
Explanation of parameters:


* ``profile test,docker```:
* ``profile test,docker``:
* ``test``: use an included example FASTA file
* ``docker``: execute tasks in Docker containers
* ``--datadir`` data: use data as the directory for storing all required databases; created automatically if needed
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10 changes: 5 additions & 5 deletions docs/HowToRun.rst
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Expand Up @@ -11,7 +11,7 @@ Running InterProScan
--input <FASTA> \
--datadir <DATADIR>

If ``InterProScan`` was `installed from source <<HowToInstall.html>`__, please use the following
If ``InterProScan`` was `installed from source <HowToInstall.html>`__, please use the following
command:

.. code-block:: bash
Expand Down Expand Up @@ -97,9 +97,9 @@ To analyse nucleic acid sequences please see the
`"How to Analyse Nucleic Sequences" documentation <HowToNucleic.html>`_

.. NOTE::
The ``--datadir``` flag is not needed when only running member databases that do not require additional data files.
This only applies to ``mobidblite`` and ``coils``` (which do not require additional datafiles) and the
licensed software (``SignalP``, ``Phobius``, and ``TMHMM```).
The ``--datadir`` flag is not needed when only running member databases that do not require additional data files.
This only applies to ``mobidblite`` and ``coils`` (which do not require additional datafiles) and the
licensed software (``SignalP``, ``Phobius``, and ``TMHMM``).

Optional arguments
------------------
Expand Down Expand Up @@ -311,7 +311,7 @@ for the process can be found (useful for trouble shooting).

The second column (e.g. ``process > SCAN_SEQUENCES:RUN_ANTIFAM``) identifies the type of
task (e.g. ``process``), and the name
of the task (e.g. ``SCAN_SEQUENCES:RUN_ANTIFAM```). The number
of the task (e.g. ``SCAN_SEQUENCES:RUN_ANTIFAM``). The number
in parenthesises identifies the total number of spawned instances of that process.

The third column (e.g. ``[100%] 1 of 1 ✔``) indicates the percentage of the currently spawned instances
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2 changes: 1 addition & 1 deletion docs/ImprovingPerformance.rst
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Expand Up @@ -20,7 +20,7 @@ Consider chunking large input files
If your FASTA input files contains a large number of sequences say over 160,0000 protein sequences,
then you may consider splitting your input into smaller chunks (thus depends on resources, but batches of
100,000 protein sequences is a suggested starting point). You can then submit the smaller input files to
``InterProScan``` and process the results afterwards.
``InterProScan`` and process the results afterwards.

For DNA/RNA sequences a much smaller number is suggested (e.g. 12,000 sequences).
However for improved performance you could translate these using an external tool
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10 changes: 5 additions & 5 deletions docs/Introduction.rst
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Expand Up @@ -53,9 +53,9 @@ After completion, you’ll find three output files in your working directory:
* ``test.faa.xml``: full annotations (XML)

.. NOTE::
The ``--datadir``` flag is not needed when only running member databases that do not require additional data files.
This only applies to ``mobidblite`` and ``coils``` (which do not require additional datafiles) and the
licensed software (``SignalP``, ``Phobius``, and ``TMHMM```).
The ``--datadir`` flag is not needed when only running member databases that do not require additional data files.
This only applies to ``mobidblite`` and ``coils`` (which do not require additional datafiles) and the
licensed software (``SignalP``, ``Phobius``, and ``TMHMM``).

For using alternative executors (e.g. Azure and AWS Batch) and container runtimes (e.g. Podman) please
see the `profiles page <Profiles.html>`__, and for setting up a local installation ``InterProScan`` please see the
Expand Down Expand Up @@ -85,10 +85,10 @@ This distribution of InterProScan includes:
- `SMART <http://smart.embl-heidelberg.de/>`__ (unlicensed components only)
- `SUPERFAMILY <http://supfam.cs.bris.ac.uk/SUPERFAMILY/>`__

A number of other analyses are available in ``InterProScan```. These
A number of other analyses are available in ``InterProScan``. These
analyses use licensed components provided by third parties. If you
wish to run these analyses it will be necessary for you to obtain a
license from the vendor and configure your local ``InterProScan```
license from the vendor and configure your local ``InterProScan``
installation to use these:

- `Phobius <http://phobius.sbc.su.se/>`__
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2 changes: 1 addition & 1 deletion docs/UnderTheHood.rst
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Expand Up @@ -301,7 +301,7 @@ with a set of conserved domains, Hidden Markov Models (HMMs), or pre-algined pro
rspbproc
^^^^^^^^

A wrapper for ``RPS-BLAST``` which aims to provide results that match those computed by NCBI's on-line
A wrapper for ``RPS-BLAST`` which aims to provide results that match those computed by NCBI's on-line
search services, including site annotation and the location of conserved domain superfamily
footprints. It is downloaded from the `CDD ftp server <https://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/>`_
within the IPS6-CDD docker image.
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