Skip to content

Latest commit

 

History

History
101 lines (75 loc) · 4.54 KB

PLUGINSDEV.md

File metadata and controls

101 lines (75 loc) · 4.54 KB
Raw

SYNOPSIS

These are instructions on how to make a SneakerNet plugin. It does not matter which language the plugin is coded in. All that matters is that it is executable by the SneakerNet user and that it can accept certain parameters.

EXAMPLES

Please see below for language specific tips for Hello World examples.

How to make a plugin

Two major steps are described below for making a plugin.

Create the script.

  1. The first positional argument must be the MiSeq run directory
  2. The script must accept the following flags with the following example values (or no values). The flags must adhere to original meaning behind the flags. For example, --help must provide a help menu. The script does not necessarily need to use these flags however.
  3. Add any desired soft-coded variables such as the location of a blast database into config.bak/settings and config/settings. config.bak is tracked with git, and config is created upon SneakerNet installation.
  4. Inputs: the plugin can and should read sample names and properties from samples.tsv.
  5. If the plugin generates any files, please organize them into runDirectory/SneakerNet/customdirectory (where customdirectory is a name of your choice), and add any results for the resulting email to runDirectory/SneakerNet/forEmail. Any files under this directory will be emailed with the SneakerNet email.
  6. List your results in runDirectory/SneakerNet/properties.tsv. This will ensure that your results will be in the email report.
    1. properties.tsv is three columns: plugin name, key, value
    2. You should include version
Flag Default value description
--help generate a help menu
--numcpus 1 Parallelization
--debug generate more messages or any other debugging
--tempdir automatically generated, e.g., with File::Temp or mktemp Where temporary files are located
--force This is loosely defined but can be used for many things like overwriting output files
--version Print a version in the format of X.Y or X.Y.Z
--citation Print a citation statement to give yourself credit.
--check-dependencies check all executable dependencies. Print executable dependencies to stdout and version information to stderr.

Available inputs

How do you specify where the input assemblies are? Or where the kraken inputs are? After all, the only parameter is the input directory right?

Never fear! Here are some basic inputs that you have access to as a developer. The most important input is samples.tsv. Here are the most common inputs you might want to have access to:

What path from root input folder [^1] Common source script or plugin [^2] For more information
Sample information samples.tsv SneakerNet.roRun.pl --createsamplesheet or sn_createSampleSheet.pl SneakerNetInput.md under the samples.tsv section
Assemblies and genbank files SneakerNet/assemblies/[samplename]/ assembleAll.pl
Assembly and predicted gene metrics SneakerNet/forEmail/assemblyMetrics.tsv assembleAll.pl
Kraken output SneakerNet/kraken/[samplename] sn_kraken.pl
read metrics SneakerNet/forEmail/readMetrics.tsv addReadMetrics.pl

[^1] [samplename] is the name of the sample in samples.tsv.
[^2] It is possible that other sources would generate this information and so these are the most common sources.

Activate the script as a plugin

  1. Place it in the SneakerNet.plugins folder
  2. chmod the script to be executable
  3. Add the plugin to the list of plugins in config.bak/plugins and config/plugins

Unit tests

Create a file under t/ and copy a previous example unit test from that directory.

To run all unit tests:

perl Makefile.PL
make
make test

language-specific tips

There are three Hello World example plugins. For perl, there is an API. However, I would kindly take any help in other languages.

perl

Please see the perl hello world plugin. Also, please run perldoc lib/perl5/SneakerNet.pm for help on the library API.

python

Please see the python hello world plugin

shell

Please see the hello world shell plugin