Version numbers about stag-sis

[AroArz]

Hey, sorry for the sparse documentation I've been intending to expand upon it. The --develop branch of StaG is the only branch that can run Snakemake with Singularity images. master and dnbseq-prerpoc uses conda, however, we noticed there was a problem with the conda compiled version of Kraken2 and so decided to transition into singularity.

The dependencies you likely are missing if you're running StaG-SIS would be the databases as they are not included in the images.

1. fork https://github.com/AroArz/stag-mwc
2. In your fork edit config.yaml in the develop branch to accurately reflect the databases on your server.
3. Assumming all your databases share the same mount point edit following lines startscript.sh

Database=/path/to/databases


-B $PWD,$Input:/input,$Output:/output_dir,$Workdir:/workdir,$Database:/path/to/databases

4. Then edit the following lines in runscript.sh

Database=/path/to/databases

git clone --branch develop YourForkedStaG .

Note: I've only tested StaG-SIS with the following config settings, you may run into unexpected errors if you choose to employ other steps.

#########################
# Pipeline steps included
#########################
qc_reads: True
host_removal: True
naive:
    assess_depth: False
    sketch_compare: False
taxonomic_profile:
    kaiju: False
    kraken2: True
    metaphlan2: False
functional_profile:
    humann2: False
antibiotic_resistance: False
mappers:
    bbmap: False
    bowtie2: False
assembly: False
binning: False
multiqc_report: True

Thus far the only side-effect we've noticed of singularity in singularity as root is permission changes to /tmp, /proc, /sys, and /dev.