search

sanger-pathogens / iva

de novo virus assembler of Illumina paired reads
http://sanger-pathogens.github.io/iva/
Other
53 stars 18 forks source link

Set smalt's random seed #95

Closed donkirkby closed 3 years ago

donkirkby commented 4 years ago

This change just hard codes the -r option to 1 when you run smalt map, as discussed in #93. If you prefer, I can add a --smalt_random option to the SMALT mapping options group so users can specify the random seed when they call IVA. Can you think of a scenario where users would actually want the possibility of different results each time it runs? Would someone test to see if an assembly is stable by rerunning it 100 times?

I also switched the Dockerfile to building from the local IVA source code, because that let me test my changes in Docker. If you really prefer building from GitHub's master branch every time, I'll switch that back. I think the other changes in the Docker file are necessary to make it run after a year and a half of dependency upgrades.

puethe commented 3 years ago

Reverted the changes in the Dockerfile as that has been fixed in the meantime in another PR. Thanks for setting the smalt seed, important to make runs repeatable. I don't think that it'll be necessary for the user to specify the value. Sorry for the long delay, IVA is not really maintained anymore, just discovered your PR.