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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
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pip installation corrupt #26

Closed schellt closed 4 years ago

schellt commented 5 years ago

When installing tigmint via pip3 install tigmint the shebangs of the python scripts are hard coded (and obviously not working on every system).

$ head -1 /usr/bin/tigmint*
==> /usr/bin/tigmint <==
#!/bin/sh

==> /usr/bin/tigmint-arcs-tsv <==
#!/usr/local/opt/python/bin/python3.7

==> /usr/bin/tigmint-cut <==
#!/usr/local/opt/python/bin/python3.7

==> /usr/bin/tigmint-make <==
#!/usr/bin/make -rRf

==> /usr/bin/tigmint-molecule <==
#!/usr/local/opt/python/bin/python3.7
stale[bot] commented 4 years ago

This issue has been automatically marked as stale because it has not had any recent activity. It will be closed in 7 days if no further activity occurs. Thank you for your interest in Tigmint!

aakashsur commented 2 years ago

I had the same issue, I ostensibly need to change the shebangs. Not sure where this could be remedied. Running without changing it leads to the following error - /usr/local/opt/python/bin/python3.7: bad interpreter: No such file or directory

lcoombe commented 2 years ago

Hi @aakashsur,

Could you try installing Tigmint using conda or brew? The pip distribution is not up to date, unfortunately.

aakashsur commented 2 years ago

Thanks for the heads up, I've gone ahead and installed from source since I'm working on a cluster and already had a python virtual environment with most of the things I need. I'll let you know if I run into any issues, at the very least, the python shebangs are now /usr/bin/env python3 which appear to circumvent the issue with the pip install.

lcoombe commented 2 years ago

Great, I'm glad you found that workaround! I will remove the pip3 install tigmint instructions from the README for now, since as I mentioned it still has an older version and as you reported, doesn't work for all systems.