Installation failed using Ubuntu 18.04.5

SCT
1

I tried to install SCT5.5 on my server, however, it was failed.
OS I’m using is Ubuntu 18.04.5.
I created a conda env using:
conda create -n name python==3.6
and then I simply unzip the zip file of SCT5.5 and run the install_sct.
But it seems like some package could not be installed right, please see the install_log if you are interested in the detail.
Thanks so much for your help :slight_smile:
install_sct_log.txt (38.8 KB)

2

Hi Kinny,

Could you try again, but using
conda create -n name python==3.7
to create then conda env?

It looks like SCT switched from Python 3.6 to Python 3.7 for SCT5.5, because Python 3.6 has reached end-of-life status. Also, I see from your install log that it’s failing to install the Python module coverage with version 6.3, which makes sense because the coverage module dropped support for Python 3.6 in that version.

If that still doesn’t work, please reply in this thread again, and I’ll give you instructions on how to install SCT5.5 without the coverage module, which is really only needed for SCT developers.

3

Also, if you don’t mind, where did you get the suggestion to use
conda create -n name python==3.6?
If it’s somewhere in our documentation, we should update it.

4

Thanks for your advice! I tried python==3.7 before, but it seems like there is an authority problem when I using python3.7, but I think it is caused by my server, I will check again

5

I did not find the suggested version of python in the installment page, so I thought it may work with python3.6. Maybe you can highlight it on the page? :smiley:

6

Hi! Considering the last issue is caused by the version of python, I tried SCT5.4 and I guess it works with python3.6, I successfully installed spinalcordtoolbox-5.4, however, then I get another problem:

Creating launchers for Python scripts...
./install_sct: line 662: no match: /home/liuyan/sct_5.4/python/envs/venv_sct/bin/*sct*
 Installation failed!

This really confuses me, can u give me some advice? Thank you so much!
The log txt-file is provided and hopefully be helpful.
sct5.4log.txt (49.3 KB)

7

Actually, it seems that the recommended way to install SCT is without using a conda env, because the installer will create a correct conda env by itself. According to the Linux install instructions, you should be able to just:

  1. Download 5.5.zip from the Releases page;
  2. Unzip in a temporary directory;
  3. In the terminal, go to the extracted directory spinalcordtoolbox-5.5/ and run the command ./install_sct

The installer should work with (I think) any version 3.x of Python, and it will create a conda env called venv_sct with the correct version of Python installed.

1 Like
8

Thanks for your advice!