Can't install scirpy on Apple Silicon about scirpy

[a-munoz-rojas]

Thanks for reminding me to follow up. Yes, that's exactly the fix I found as well. Here is the thread on parasail that describes it: jeffdaily/parasail-python#24. To summarize:

1. brew install automake libtool autoconf
2. pip install scirpy

Should work to install on apple silicon. Installing via conda doesn't work because currently there is no bioconda recipe for parasail available for osx-arm64. Hopefully this helps.

[grst]

I'm afraid bioconda does currently not compile packages for ARM64. See also these issues:

bioconda/bioconda-utils#706
bioconda/bioconda-recipes#23454

You should still be able to install scirpy using pip install.

[djlisko01]

Hello, I had the same issue on my Apple M2 Pro and fixed it by running the following code before installing scirpy:
brew install automake libtool autoconf

[grst]

Now, with the numba implementation of TCRdist merged, we could consider making parasail an optional dependency and suggesting TCRdist as the standard alignment metric.

[a-munoz-rojas]

Thanks for the info. I think now there are several packages available on the bioconda/osx-arm64 channel (even scirpy itself), it's just parasail that's not there. I can open an issue there, but based on the links you sent seems like it might be a while.

I also tried installing scirpy via pip but it also fails - seems to be an issue with parasail:

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for parasail
  Running setup.py clean for parasail
Failed to build parasail
ERROR: Could not build wheels for parasail, which is required to install pyproject.toml-based projects

I can open an issue with parasail, but thought you'd want to know installation is failing

[grst]

Thanks for the heads-up! Creating an issue in parasail sounds good! If you do, please tag me that I'm kept in the loop!

[FvdBre]

I am quite new to python, so my apologies if I miss the obvious ;-) .
I have tried this approach as well using conda to install the dependencies.

1. conda install automake libtool autoconf
2. pip install scirpy

However, I get the same error:

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for parasail Running setup.py clean for parasail Failed to build parasail ERROR: Could not build wheels for parasail, which is required to install pyproject.toml-based projects

Even when I manually download the parasail source code, compiled it, and then installed the Python bindings.

Versions:

• m4 1.4.18 h1230e6a_1
• libtool 2.4.6 h313beb8_1009
• autoconf 2.71 pl5340h80987f9_0
• automake 1.16.5 pl5340hca03da5_1

Thanks in advance!

[grst]

In jeffdaily/parasail-python#24, there's also mentioned libtools (with s) additionally.

If you can't make it work, please comment in the linked issue -- ultimately, this is an issue with parasail, not scirpy.

[FvdBre]

Thanks, I will contact them.

[a-munoz-rojas]

As a user, I think this is a good idea - would greatly simplify installation, and the numba implementation of TCRdist seems to be a better and faster metric anyways. Really excited to hear it was implemented, thanks!