Error with installing CrossMap
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Entering edit mode
13 months ago

I am having a hard time installing CrossMap from UCSC. I am VERY new to coding. I updated my Python to v.3.9.2 this morning.

I am using the commands given by UCSC on how to install and use Crossmap. The first line "pip3 install CrossMap" results in this large Error:

"ERROR: Command errored out with exit status 1: /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/9n/x6qkyx316jl0dbcmjxwhhjfc0000gn/T/pip-install-jxurijlf/pysam_4f7d7b6bde714233b1a7db1f1c017e48/setup.py'"'"'; __file__='"'"'/private/var/folders/9n/x6qkyx316jl0dbcmjxwhhjfc0000gn/T/pip-install-jxurijlf/pysam_4f7d7b6bde714233b1a7db1f1c017e48/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/9n/x6qkyx316jl0dbcmjxwhhjfc0000gn/T/pip-record-8er7rord/install-record.txt --single-version-externally-managed --compile --install-headers /Library/Frameworks/Python.framework/Versions/3.9/include/python3.9/pysam Check the logs for full command output."

This may be very basic but I honestly don't have enough experience with Python or Bash to udnerstand what the error is trying to say. Thanks in advance for your advice!

CrossMap • 1.0k views
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Entering edit mode
13 months ago

Installing into the main Python that comes with your Mac won't get you far.

Install miniconda, start a new environment with conda then install your bioinformatics software into those environments.

https://docs.conda.io/en/latest/miniconda.html

Once you have miniconda all you need to do is:

conda create --name bioinfo python=3.y -y

conda activate bioinfo

pip install CrossMap
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Entering edit mode
9 months ago

Bit late but this was the first google return that came up when I ran into the same issue on linux/ubuntu. For me it was due to not having libcurl installed in the environment I was using. Ran the following before installing Cross Map and it fixed the issue:

 sudo apt-get install libcurl4-openssl-dev
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Entering edit mode

You ran into the exact same error when libcurl was missing on Ubuntu? I find it hard to believe that the same error message occurred owing to a totally different cause on a different platform.

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