Add vsearch to the image

v1.3.2--6

Fix typo

Tolerate failure of gene abundance

For samples where no species meet the minimum abundance threshold to quantify the genes present, skip that step without failing.

This release will not have different results from the previous release, but it will prevent failure for some edge cases (no highly abundant organisms).

Add ENA for SRA download

All of the failures observed so far have been when downloading data from SRA via fastq-dump. This adds the ability to download from ENA when available, which helps by not using the fastq-dump cache directory (which is located on the docker OS partition, and therefore fills up quickly).

Process each sample in its own folder

The previous release was inadvertently deleting the reference database after the first sample. This release will process each sample in its own folder, and only delete the reference database once the entire process is complete.

Also clear the fastq-dump cache after each sample

Working wrapper script

Computes the species summary and gene abundance, along with functional gene annotations. The SNP quantification is not currently implemented (mostly due to the extremely large amount of output it produces)

MIDAS v1.3.2

MIDAS v1.3.2 is installed, but none of the supporting infrastructure and dependencies.

Made for development purposes.