Hey @amojarro ! This may not be a PR that is necessary to merge, however I've done some really cool work with the updated SCIF (Scientific Filesystem, what Singularity was using a previous version of to install the various pipeline steps here). In a nutshell, I got back really fantastic reviews for SCIF and one of the reviewers had this amazing insight that it didn't just have to be for one particular container technology, or containers at all! So the revised scientific filesystem is agnostic to the host or container. This means that the same recipe can install to Docker or Singularity or (if someone wanted) a host. Or another container technology I haven't shown. Because it just comes down to writing a recipe, then installing like:
pip install scif
scif install recipe.scif
Anyway, I've completely redone the Singularity examples, and added a Docker example (containers provided in their respective hubs) to show how CarrierSeq can be run with both. A good "side by side comparison" is here --> https://github.com/vsoch/carrierseq/blob/master/docs/README.md, and the detailed version here --> https://sci-f.github.io/apps/examples/carrierseq.scif The comparison is also going to be featured (with CarrierSeq!) in the upcoming manuscript - the response to reviewers is done and we are sending it around for a round of edits from the various community members.
Hey @amojarro ! This may not be a PR that is necessary to merge, however I've done some really cool work with the updated SCIF (Scientific Filesystem, what Singularity was using a previous version of to install the various pipeline steps here). In a nutshell, I got back really fantastic reviews for SCIF and one of the reviewers had this amazing insight that it didn't just have to be for one particular container technology, or containers at all! So the revised scientific filesystem is agnostic to the host or container. This means that the same recipe can install to Docker or Singularity or (if someone wanted) a host. Or another container technology I haven't shown. Because it just comes down to writing a recipe, then installing like:
Anyway, I've completely redone the Singularity examples, and added a Docker example (containers provided in their respective hubs) to show how CarrierSeq can be run with both. A good "side by side comparison" is here --> https://github.com/vsoch/carrierseq/blob/master/docs/README.md, and the detailed version here --> https://sci-f.github.io/apps/examples/carrierseq.scif The comparison is also going to be featured (with CarrierSeq!) in the upcoming manuscript - the response to reviewers is done and we are sending it around for a round of edits from the various community members.