Yesod - updated database hosting

As the original database files were no longer publicly accessible on BioShare, we have shifted them over to make them available from Zenodo. Additionally, database files are now compressed for faster download, and can be unpacked either manually or automatically at their local destination.

2.2.01 - Yesod - minor fixes

This is 2.2.0, but with several minor fixes, including one bug in the RefSeq_reduce_to_genus.py script that dropped several of the most high-prevalence results.

2.2.0 - Yesod

Decent sized update, includes some improvements courtesy of Sebastian Renaut (seb951):

• Multithreading added for Trimmomatic, PEAR, SortMeRNA
• The script automatically creates a checkpoint file. Once a step is finished, it writes the name of that specific step in checkpoint and that step is skipped on a rerun of the master_script. This is done to avoid re-running CPU-intensive steps if unnecessary.
• A new version of the master script now exists, called "master_script_preserving_unmerged.sh". In this script, in the merging step, unmerged reads are concatenated and added to a single file. The forward read and the reverse (complement) read are concatenated with a string of 20 Ns in the middle: This is done through a new R script entitled: combining_umerged.R
• Extra care is taken to remove unnecessary files once a step is performed to keep disk usage at a minimum.
• Each step contains an exit statement to be printed if the master script dies due to an unforseen error.
  Trimmomatic removes adapter contamination according to a specific fasta file.
• All options, read & program location are to be specified in the first section of the script.
• The script is formated to be run on a HPC using a SLURM job scheduler, but this can be easily changed / removed.
• The flag --num_alignments 0 in the ribosomal sortmrna step has been removed. This caused problems and slowed things down a lot. Plus, we don't care about the rRNA alignments - whether a sequence aligns to 1 or 1,000 rRNA, it's out anyways...

2.1.0 - Malkuth

Significant overhaul since previous version of SAMSA2 (alpha). Improvements include:

• Better installation and automated pathing for programs/scripts/features, with thanks to user Kaedenn for building software-focused improvements
• New R scripts for generating raw and normalized counts tables.
• Correction to PEAR to properly select files through the automated pipeline.
• Many, many bug fixes.
• Recursions blocked.
• Improved Python3 compatibility.
• Improved heatmap script.
• Better elimination of duplicates when dealing with finnicky Subsystems database.
• Slightly more coherent print statements.

Updated alpha - bug fixes

Fixed several typos and other issues. Major update coming soon to improve installation and pathing, but for now, this should be stable and solve some minor problems that were caught by users.

SAMSA v2.0.0-alpha

This is the alpha release version of SAMSA2, intended mainly for testing purposes and final polishing before the release of the software paper. This version of SAMSA includes:

• Currently working versions of programs and dependencies used by SAMSA2, to avoid later issues with later releases of these programs no longer being compatible.
• Currently used Python and R scripts in the pipeline.
• Documentation.

Note that this is still an alpha release; as such, there may still be errors and issues that will need to be addressed in patches.