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robmaz / distmap

Sequence alignment on Hadoop
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Remove executables/popoolation #32

Closed magicDGS closed 6 years ago

magicDGS commented 6 years ago

The whole popoolation toolkit is linked into the executables, which is bad because it is only used for the trim-fastq.pl.

Because nowadays nobody uses the trim-fastq.pl, but ReadTools, I do not think that it should be bundled anymore into the repo.

Removing this executable is part of #7 and also deletes a lot of unused files (part of #6), but it makes easier things like #26

magicDGS commented 6 years ago

@robmaz - I think that you should have a look to this one for remove a bunch of unused files that makes even more difficult to cleanup the file structure.

robmaz commented 6 years ago

I am not sure this trim-fastq.pl script is currently unused. It appears to me that the --only-trim option in fact does use it.

magicDGS commented 6 years ago

The only place where it appears after checking in the repo is in bin/cluster_trimming.pl and bin/cluster_trimming-1.pl. But I guess that it is uploaded into the hadoop files if not provided by the user.

Thus, I will revert both trimming scripts in this branch (trim-fastq.pl and trim-fastq_gz.pl) and add a READMEto the popoolation folder indicating the origin of the files.

robmaz commented 6 years ago

They appear to use the "Test" and trim-fastq_gz.pl also the "Pileup" module. Tracking down these internal dependencies now seems like a bit of a waste, though, since we want to remove the whole dependency anyway. Maybe we should just leave it in for now?

magicDGS commented 6 years ago

True, it has wierd dependencies - I'll close for now, until we remove the trimming from the cluster. I just realize that if the user provides a custom trim script from popoolation, it requires that its folder is complete too, so it is again a bad idea to continue supporting that...