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Can't Bootstrap even after attempts to compile with cmake #382
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What does |
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HDF5 is not really being phased out -- it's just a pain to deal with that file structure and all the issues (including compilation issues) associated with it, but I don't think we'll deal with that problem anytime soon since it still works and I still use it all the time for sleuth analysis. It's kinda a pain to spend time rewriting parts of kallisto and sleuth for something that already works. But yeah, you need to get libtoolize working otherwise you cannot install kallisto from source. I haven't personally dealt with libtoolize so I'm not sure how to solve it. |
I guess you have your solution right there:
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I wanted to make sure I noted what "fixed" my problem; first I followed this:
Note I tried to run the next lines listed from that link, but those did not run in my terminal.
These gave me:
You still have to follow the instructions for ext/htslib to give HDF5 file capabilities. Sources: |
Amazing! Thanks for your contribution toward installing kallisto from source -- for htslib, I'm planning/hoping to make it an optional cmake option in the future, since it's been giving trouble (in part because the code base is based on an old version of HTSLIB; and honestly speaking, HTSLIB isn't really necessary for almost all use cases of kallisto anyway). |
@Yenaled: That's great news. Shameless plug: Don't forget to close my FR from seven years ago once you do so. 😜 |
kallisto version 48.0
OS: macOS Monterey Version 12.6.5
Issue: Unable to compile kallisto with -DUSE_HDF5=ON, kallisto ignores bootstrap option.
kallisto returns:
And attempting to compile kallisto without brew returns:
Attempting to compile CMake:
I also followed along with the instructions listed in Issue #303 and:
At this point, I am at a loss for how to get bootstrapping done for my files so I can pass them to sleuth. I do realize that hdf5 is being phased out, but don't we still require this capability to pass to sleuth?
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