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galaxyproject / tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.
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deprecate broken samtools pileup #574

Closed bernt-matthias closed 3 years ago

bernt-matthias commented 3 years ago

samtools mpileup is now at IUC

seems to be the last tool in the devteam repo that fails the weekly tests.

bgruening commented 3 years ago

ping @wm75

nsoranzo commented 3 years ago

pileup is different from mpileup (both as a tool and as a format), but the former has been deprecated since samtools 0.1.17 (6 July, 2011), so I think it's still fine to deprecate it.

Can you please move the sam_pileup directory in the tools/ subdirectory of deprecated/ ?

bernt-matthias commented 3 years ago

Can you please move the sam_pileup directory in the tools/ subdirectory of deprecated/ ?

Yep. Also moved sam_merge -- which I misplaced as well :(

nsoranzo commented 3 years ago

Can you please move the sam_pileup directory in the tools/ subdirectory of deprecated/ ?

Yep. Also moved sam_merge -- which I misplaced as well :(

I already did that on master yesterday, can be removed from here.

bernt-matthias commented 3 years ago

fixed