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Colab Install Help

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Colab Install Help

I'm trying to install Pyrosetta using Colab with the workshop notebooks but I keep getting errors. The main error is locating the tar file in My Drive. The code I'm running is: 

#sys.path.insert(0, google_drive_packages_path)


# installing PyRosetta

if sys.version_info.major != 3 or sys.version_info.minor != 6:

    print('Need Python-3.6 to run!')



import_start_time = time.time()


# upload PyRosetta Linux package into your google drive and put it path here

pyrosetta_distr_path = google_drive.replace(' ', '\\ ') + '/PyRosetta/*'


!tar xjf $pyrosetta_distr_path -C PyRosetta --strip-components=1

!cd PyRosetta/setup && python install --install-lib=$pyrosetta_install_prefix_path

!rm -rf PyRosetta


import_end_time = time.time()


print(f'PyRosetta setup took: {import_end_time - import_start_time:.1f}s...')

I have a folder called Pyrosetta in My Drive as directed. I think the problem lies here pyrosetta_distr_path = google_drive.replace(' ', '\\ ') + '/PyRosetta/*' 


tar (child): /content/google_drive/My Drive/PyRosetta/*: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now /bin/bash: line 0: cd: PyRosetta/setup: No such file or directory PyRosetta setup took: 2.2s...

When I go to put the path for the tar file instead I get an invalid syntax error. 

Not really sure how to solve this. 

Post Situation: 
Wed, 2020-06-03 07:26

Nevermind. I just simplied the code of the tutorial and was able to get it to work.

Thu, 2020-06-04 08:07

Hi I get this same problem. Could you explain how you resolved this issue? Thank you! 

Thu, 2021-01-14 13:21

It may be that the glob pattern (/PyRosetta/*) is not being properly expanded with the Notebook environment. (Normally it's the shell which does the expansion.) What you can try is to pass the tar command the full explicit path to the file, rather than using wildcards.

Tue, 2021-02-09 08:57