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robmaz / distmap

Sequence alignment on Hadoop
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Decide if samtools or picard is required #9

Closed magicDGS closed 6 years ago

magicDGS commented 6 years ago

Currently, both picard and samtools are required. Most of the functionality of samtools is included already in picard, so I suggest to require only picard for DistMap.

In addition, I don't know if after the ReadTools integration Picard is still required, so maybe both of them may be removed...

magicDGS commented 6 years ago

This can be done easily after remove support for separate picard files (see #39) and requiring picard.jar

magicDGS commented 6 years ago

Requirements can be found in this experimental branch: https://github.com/robmaz/distmap/tree/dgs_rm_samtools

magicDGS commented 6 years ago

I can also bundle the required tools from Picard into ReadTools, which is what actually GATK is doing in its toolkit in version 4.0.0.0 - like that, only the ReadTools binary should be distributed around the workers instead of the Picard one.

Nevertheless, the ReadTools binary is much larger, so maybe there is some problem in that respect.

robmaz commented 6 years ago

I am not sure why we need either now. It seems to me that readtools handles everything now. I don't think the workers need picard either?

magicDGS commented 6 years ago

In that case I can also have a look to the branch for remove samtools/picard, between today and tomorrow.

magicDGS commented 6 years ago

Samtools is already removed. Closing this in favor of #78