src/run/salmon.mk info.json file had to be renamed to refInfo.json

[njbowen]

in the current src/run/salmon.mk file
I had to rename info.json on line 40 to refInfo.json to get the salmon.mk to find the index files.

[ialbert]

thanks for the report, might be that they renamed the index file, I will investigate

[ialbert]

Which version of salmon is this, I tried with version 1.10.3 and the index file was still info.json

[njbowen]

$ salmon -v
salmon 0.14.1
(bioinfo)

$which salmon
/Users/myusername/micromamba/envs/bioinfo/bin/salmon

[njbowen]

Yes, we’ve used the stats env as well. But it installs R 4.3 I believe. I suppose that I could set up an env and try to install a previous version of R there, if that’s the salmon issue.

[ialbert]

Since Bioconductor is tied to R>=4, we cannot install a previous version of R unfortunately.

[njbowen]

Ok, thanks, salmon is not an R package, so I can make something work in a separate env, correct?

[ialbert]

yes, I found that salmon works best if it lives in its own environment. It makes use of C++ libraries that are also used in numerous other software - and with that creates a lot of conflicts.

best to run salmon from its own env which is not much trouble, though a bit annoying as the command line grows:

micromamba run -n salmonenv salmon

[njbowen]

Yes, full circle, you did recommended that initially above. I should remember to scroll up! Thank you.