From 44cf1b3c408261a29defe8d3265372ccc9aa3e9f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fa=CC=81bio=20Madeira?= Date: Mon, 16 Jun 2025 17:41:45 +0100 Subject: [PATCH] chore: syntax fixes --- docs/HowToInstall.rst | 2 +- docs/HowToRun.rst | 10 +++++----- docs/ImprovingPerformance.rst | 2 +- docs/Introduction.rst | 10 +++++----- docs/UnderTheHood.rst | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/HowToInstall.rst b/docs/HowToInstall.rst index 50f9d9b..75f62e4 100644 --- a/docs/HowToInstall.rst +++ b/docs/HowToInstall.rst @@ -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 diff --git a/docs/HowToRun.rst b/docs/HowToRun.rst index 0b8eb3d..bb780ca 100644 --- a/docs/HowToRun.rst +++ b/docs/HowToRun.rst @@ -11,7 +11,7 @@ Running InterProScan --input \ --datadir -If ``InterProScan`` was `installed from source <`__, please use the following +If ``InterProScan`` was `installed from source `__, please use the following command: .. code-block:: bash @@ -97,9 +97,9 @@ To analyse nucleic acid sequences please see the `"How to Analyse Nucleic Sequences" documentation `_ .. 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 ------------------ @@ -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 diff --git a/docs/ImprovingPerformance.rst b/docs/ImprovingPerformance.rst index 4d4166d..16357ac 100644 --- a/docs/ImprovingPerformance.rst +++ b/docs/ImprovingPerformance.rst @@ -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 diff --git a/docs/Introduction.rst b/docs/Introduction.rst index 49b50b0..0470681 100644 --- a/docs/Introduction.rst +++ b/docs/Introduction.rst @@ -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 `__, and for setting up a local installation ``InterProScan`` please see the @@ -85,10 +85,10 @@ This distribution of InterProScan includes: - `SMART `__ (unlicensed components only) - `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 `__ diff --git a/docs/UnderTheHood.rst b/docs/UnderTheHood.rst index 24b8c57..5b35795 100644 --- a/docs/UnderTheHood.rst +++ b/docs/UnderTheHood.rst @@ -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 `_ within the IPS6-CDD docker image.