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Simplify installation and user interface

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@TBradley27 TBradley27 released this 22 Sep 12:09
· 16 commits to master since this release
v1.3.0
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Learn about vigilant mode.

Major enhancements

  1. Installation and environment management is simplified. The user is now requested to install FilTar within its own standalone conda environment

  2. Modify how users specify dataset metadata. Previously users had to specify dataset metadata within nested YAML data structures. This is now simplified by requesting that users add this information in TSV format. This information is then processed by snakemake using the pandas module.

  3. Simplify dependency parameter configuration. FilTar utlilises a large number of dependency applications. These can now be more easily configured by the user within the config/dependencies.yaml file

  4. Use higher confidence miRNA annotations: Allow the user to use high-confidence miRNA annotations only, from miRBase. This option is set as default

Minor enhancements

  1. Update README to include URLs to the FilTar publications within Bioinformatics
  2. Throw an exception if the user specifies an invalid miRNA target prediction algorithm
  3. Use APAtrap binary files instead of script which reduces the number of dependencies to be installed by the user
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