Comments (5)
Sorry to leave this sit for so long- the long term intent here was always to use Docker for packaging tools, but security concerns have delayed adoption on the luna cluster.
We will be pursuing Singularity as a docker alternative on luna for portability in tandem with CWL for portable workflows. It still needs to be proven to play well with CWL, which has specific Docker hooks for some things, but we already have it installed on demo nodes and are actively evaluating it for this purpose.
Our goal is to have all versions of everything live for all users at all times, so conda doesn't fit that paradigm well.
This package and fireworks will remain live for prototyping and keeping in-house things as easy as possible, but production pipelines will be moving to CWL after its feasibility is proven. This package may or may not receive CWL writing support as our plans become more firm.
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@lordzappo Thanks for the update! I like the idea of going for CWL, mostly since it has much broader support in the bioinformatics community.
As a side note, you can still have versions of everything live for all users at all time using conda. You just need to create different virtual environments for each version. Sooner or later you run into problems of one program requiring a different version of another program. You can certainly handle this problem by manipulating PATH
variables, but it's a lot less structured imo.
Docker can solve this problem as well - you could still use anaconda within Docker though. The main issue with packaging software is that you need the community support. Otherwise you end up having to package everything yourself. Bioconda has a ton of packages already installed and quite a large following: https://github.com/bioconda/bioconda-recipes. There is BioContainers for docker, but the support is way smaller: https://github.com/BioContainers/containers. If one would set up a way to create Docker containers from bioconda packages, it would make a ton of bioinf packages readily available.
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Closing cuz of all reasons listed above against using conda.
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Related Issues (13)
- Minor fixes needed for maf2maf/vcf2maf wrappers HOT 2
- cmo_maf2maf spits out core dumps HOT 2
- Setuptools warning HOT 1
- Unable to install HOT 3
- Outdated cmo_resources.json HOT 1
- cmo_gdc tool bug in creating log folder HOT 2
- cmo_bwa_mem returns incorrect exit code HOT 2
- ValueError: Could not get next FW id! HOT 14
- StopIteration HOT 2
- Clone this repo at luna. HOT 5
- cmo.util.normalize_vcf crashes on duplicates HOT 2
- argparse does not allow multicharacter short args that overlap a shorter argument, e.g. "-R" and "-RMQT" conflict HOT 4
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