AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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January 18, 2021 08:25PM
Hi, Ann-

For *some* reason I don't understand, conda folks make finishing their installation a pain with tcsh. It boggles my mind.

First, a grumble: Conda just sets up bash shell by default on installation, putting necessary pointer information in ~/bashrc on your system. In theory, the conda folks eventually "helped" make installations in non-bash shells easier by making the following command available (among a similar one for other shells):
conda init tcsh
This puts necessary path information into your ~/.*rc file for a given shell, so it knows where to find conda on your computer. The text it creates contains an if-condition between some comment lines with "conda initialize" in them, like this:
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
[if condition stuff, syntax based on particular shell]
# <<< conda initialize <<<
.... however, this does not set up your ~/.cshrc (which is what we use for tcsh setup) but instead goes for your ~/.tcshrc file (creating it if it doesn't exist already). Why they don't have "conda init csh", I cannot say (tcsh and csh have essentially the same syntax, one derived from the other).

OK, what you can do to set things up:
See if you have ~/.tcshrc already, by copy+pasting:
\ls ~/.tcshrc
If that file does not exist, you will get an error message like "ls: cannot access ...". If it *does* exist, you will just see that file shown with full path. (This will slightly affect the steps taken, below.)

Now, run this:
conda init tcsh
... to create the conda path information in ~/.tcshrc.

*If* the file *did* exist from the start (from check above), then open it up (e.g., "afni_open -e ~/.tcshrc"), as well as the ~/.cshrc file (e.g., "afni_open -e ~/.cshrc"); copy just the lines that conda has created in ~/.tcshrc between the "# >>> conda initialize >>>" and "# <<< conda initialize <<<" comments---including those comments themselves---and paste them in your ~/.cshrc file. Then, open a new terminal and see if things work.

*If* the file did *not* exist from the start (from check above) then open it up, because it exists now (e.g., "afni_open -e ~/.tcshrc"), as well as the ~/.cshrc file (e.g., "afni_open -e ~/.cshrc"); copy the lines that conda has created in ~/.tcshrc between the "# >>> conda initialize >>>" and "# <<< conda initialize <<<" comments---including those comments themselves---and paste them in your ~/.cshrc file. Then, close those two files, and copy+paste this in a terminal:
\mv ~/.tcshrc ~/.tcshrc_backup
(which just renames it, so it won't get sourced instead of ~/.cshrc). Now, open a new terminal and see if things work.

Wheeeeee.

--pt
Subject Author Posted

tcsh vs. Miniconda

annschoe January 18, 2021 04:33PM

Re: tcsh vs. Miniconda

ptaylor January 18, 2021 08:25PM

Re: tcsh vs. Miniconda

annschoe January 18, 2021 11:59PM

Re: tcsh vs. Miniconda

ptaylor January 19, 2021 09:09AM

Re: tcsh vs. Miniconda

annschoe January 19, 2021 11:33AM

Re: tcsh vs. Miniconda

ptaylor January 19, 2021 04:25PM