Issue with bootstrapping mikado

[martinjvickers]

mikado-1.1.1.def works fine as install steps but boot strapping never seems to work correctly.

• [ ] One of the earlier dependencies (bioconda?) appears to download some of the later dependencies for Trinity (bowtie2) for it's only /opt/conda/bin (I think) PATH.
• [ ] Installing portcullis/bioconda usually works but then occasionally complains about there being a more recent version....despite using the Miniconda3-latest-Linux-x86_64.sh script. https://github.com/martinjvickers/install_scripts/blob/7541975706c8995baee8b5123af8b5a8da544b59/singularity/mikado-1.1.1.def#L46
• [ ] I may need to check to see if there are any env variable issues.

[martinjvickers]

Resolved by installing the whole pipeline using bioconda in the daijin recipe.