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Importing Cactus Alignments into vg: broken link to example data #2969

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egoltsman opened this issue Sep 2, 2020 · 1 comment
Open

Importing Cactus Alignments into vg: broken link to example data #2969

egoltsman opened this issue Sep 2, 2020 · 1 comment

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@egoltsman
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Hi,
The wiki page on importing from Cactus (https://github.com/vgteam/vg/wiki/Importing-Cactus-Alignments-into-vg) refers to a yeast data set that was used in the manuscript (?), but the link included is no longer valid as the contents of the hal2vg repo have changed and don't include the example_data directory. Having that data set would be very handy though! Is there another place it can be downloaded from?
Thanks!

@glennhickey
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That wiki is indeed pretty out of date. The broken link can be pulled out of an older hal2vg via https://github.com/ComparativeGenomicsToolkit/hal2vg/releases/download/v0.1/hal2vg-v0.1-src.tar.gz, but the sequence data it refers to isn't (and never was included). Until it's fixed, a better example would be to run the simulated example from cactus then use the suggested hal2vg invocation.

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