eggnog_proteins.dmnd needed for tmpfs

[yanhui09]

Placing eggnog db in memory is unbeliveably fast for the annotations step. 👍
The eggnog_proteins.dmnd seems also to be included. I need this for our clusters, also eggnogdb/eggnog-mapper#277 (comment)

A flaw for putting the eggnog db in memory:
The cp will cause crashes if two/more qsub jobs run in the same computing node. In this case, the jobs use the same /dev/shm, and the cp (except in the first job) will collapse if the files are already there.
It's a bit tricky to solve it. You can't re-write the db file, if one job's using it. Also, the jobs in one node/cluster didn't finish in the same time.

Maybe just leave it as it is. At least, it's easily controlled to place annotation rule in separate nodes if we choose approriate number of threads. Or repeat the pipeline several times.

[SilasK]

I think we need to optimize this. The new eggnog mapper doesn't use the shm anymore. But thank you I got the same error

[yanhui09]

Just being curious. What would be a better solution if tempsf is not allowed anymore?
The speed of homology search is acceptabl, annotation steps takes forever is the db is not in the memory.
Will MMseqs search faster than the default diamond mode?

[SilasK]

If I'm not mistaken the new eggnog maoper has an option to do this step on memory. It's more or less the same. I also prefer mmseqs.