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CMU-SAFARI / RawAlign

RawAlign is a real-time raw nanopore read mapper based on the Seed-Filter-Align paradigm as described by Lindegger et al. (https://arxiv.org/abs/2310.05037)
https://arxiv.org/abs/2310.05037
GNU General Public License v3.0
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Make: missing Dependencies: hdf5 and slow5lib #1

Closed Cuypers-Wim closed 11 months ago

Cuypers-Wim commented 11 months ago

Thank you for your efforts on this project, looks really cool! I'm genuinely interested in utilizing RawAlign for my microbial genomics & nanopore work. However, while attempting to set it up, I encountered a few challenges that I hope can be addressed.

Description

While attempting to build RawAlign from source, I encountered errors indicating that the hdf5 and slow5lib dependencies are missing from the extern directory.

What I did

  1. I cloned the RawAlign repository.
  2. Navigated to the RawAlign directory and ran make.

Actual Behavior

The build process fails with errors indicating that it cannot find the hdf5 and slow5lib directories within the extern directory. Here are some relevant snippets of the error messages:

/bin/sh: 1: cd: can't cd to ../extern/hdf5
/bin/sh: 3: ./configure: not found
...
make[3]: *** /mnt/[drive]/[project_name]/[subproject]/[tool_name]/RawAlign/src/../extern/slow5lib/: No such file or directory. Stop.

Possible Solution

It seems that the required submodules or external dependencies for hdf5 and slow5lib are not included in the repository. Including instructions on how to obtain these dependencies or adding them as submodules might help resolve the issue.

Thank you for looking into this issue. I'm looking forward to a solution!

joellindegger commented 11 months ago

Hi Wim

Thanks for reporting this issue. These dependencies were supposed to be available as submodules and were missing in the prior commit. ee59c4e Should address the problem.

To use these changes in your cloned repository, please run git pull and git submodule update --init.

Best, Joel

Cuypers-Wim commented 10 months ago

Seems to work, thank you!