Make fails after cloning

[termithorbor]

Hi all,

the make command fails after cloning with this error:

bonsai/include/bonsai/entropy.h:2:10: fatal error: hll/circularqueue/cq.h: No such file or directory
2 | #include "hll/circularqueue/cq.h"

So what is missing here?

Thanks in advance :)

[dnbaker]

Hi there --

It looks like there might be an issue about include paths and submodules. I'll check in on this and get it fixed soon.

Thanks,

Daniel

[dnbaker]

Update: there's one change in the bonsai repository, which I've updated for main here. You could update main and then update recursively, or you can edit the file in question (bonsai/include/bonsai/entropy.h) and remove the "hll/" on line 2, reflecting this change if you don't want to bother with updating dashing and its submodules.

Let me know if you run into any more issues. Thanks!

Daniel

[termithorbor]

I tryed it and now make works but when I want to run dashing my system says that it can not find the command dashing. However I am in the dashing folder so it should be there, or?

dashing: command not found

I have now installed it via bioconda but there is only an older version available.

[dnbaker]

Your options are to add the folder the Dashing executable is in to your $PATH variable, or copy the executable into a folder that is in your path, such as /usr/local/bin. or your conda bin folder.

I'm hoping to get a more recent version into conda in the near future. Thanks,

Daniel