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jfnavarro / st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
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problem installing #98

Open Pinolinoo opened 2 years ago

Pinolinoo commented 2 years ago

Dear all,

Sadly I am not able to install the stpipeline. When using pip in a fresh conda env I get the following error:

` Preparing metadata (setup.py) ... error error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [6 lines of output] Traceback (most recent call last): File "", line 2, in File "", line 34, in File "/private/var/folders/z4/dc80cgy93pj6rgjpx46mnh680000gn/T/pip-install-9dekewms/taggd_cbeca8e7f968423694db01796dba5096/setup.py", line 4, in import numpy ModuleNotFoundError: No module named 'numpy' [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details.`

When using git clone, also I get an error when running the setup.py. It says it can't find the file in stpipeline/common/cdistance.c which is also not in this directory!

Happy for your help, philipp

thinkzink commented 1 year ago

You should just run pip install numpy (with the caveat of this being the latest numpy version rather than any particular one that may be depended upon) before re-executing