HCP installation on Mac Catalina about workbench HOT 20 CLOSED

from workbench.

Thank you for your reply! I have try the following command, but the terminal still cannot find wb?command:

(base) Renxis-Mac-mini:~ renxili$ cd /Users/renxili/
(base) Renxis-Mac-mini:~ renxili$ echo 'export PATH=$PATH:/Applications/workbench/bin_macosx64'  >>  ~/.bashrc
(base) Renxis-Mac-mini:~ renxili$ echo 'set PATH = ($PATH   /Applications/workbench/bin_linux64)' >> ~/.cshrc
(base) Renxis-Mac-mini:~ renxili$ wb_command
-bash: wb_command: command not found
(base) Renxis-Mac-mini:~ renxili$ 

from workbench.

I think GitHub changes my scripts when posting. Let me attach a screen shoot.

from workbench.

Github's markdown formatting got applied to your text and ate all the "~" characters, I will fix it with "code" sections.

Adding the lines to your shell startup file doesn't change your active terminal.  You need to open a new terminal window and try the command there.

By the way, the full command is "wb_command -file-information", the "-file-info" bit is from the optional tab completion instructions, which will not work by default on mac (you must use a newer version of bash than Apple provides to have the prerequisites for our tab completion).

from workbench.

Note that the echo lines append to files that your shell executes when it starts up, and it looks like you may have executed them more than once. You may want to use a text editor to make sure ~/.bashrc and ~/.cshrc don't contain repeated lines.

from workbench.

Do you mean deleting the ">>" before the ~/.bashrc and ~/.cshrc?

from workbench.

No. Do nano -w ~/.bashrc (the -w disables auto line wrapping), use the down arrow key or page down key to get to the bottom of the file, and see if there are multiple lines that say the same thing. Use the arrow keys to put the cursor on one of the duplicate lines, use control-k to delete the line the cursor is on, until there is only one of the line that was duplicated. If you mess up, press control-x to quit, and press n to not save the changes. Once you have fixed it correctly, press control-o to save, press enter to accept saving to the same filename, then press control-x to quit (these commands are shown in the bottom of the editor screen, ^ means control). Do the same for ~/.cshrc.

You could try textedit, but you would need to be very careful to use plain text mode, not introduce any unicode characters, and you might need to disable autocorrect - if the file is saved with problems in it, new terminal windows will complain and may not have the correct PATH and may behave strangely. If you know someone who uses linux or the command line a lot, you might ask them to help you.

from workbench.

I have deleted the duplicated file in both ~/.bashrc and ~/.cshrc. I also updated the bash to 5.0 via homebrew. However, when I put wb_command -file-info in a new terminal, it still says wb_command is not found. Any suggestions?

from workbench.

what is your env

from workbench.

You mean the duplicate lines in ~/.bashrc and ~/.cshrc, and not deleting files, right?

Do echo $PATH in a new terminal window and tell us what it says. It is possible that bash is only reading .profile or .bash_profile, and that it doesn't source .bashrc - shell startup is always an adventure.

from workbench.

This is when I entered echo $PATH:

(base) Renxis-Mac-mini:~ renxili$ echo $PATH
/Library/Frameworks/Python.framework/Versions/3.8/bin:/Users/renxili/opt/anaconda3/bin:/Users/renxili/opt/anaconda3/condabin:/usr/local/fsl/bin:/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
(base) Renxis-Mac-mini:~ renxili$

from workbench.

This is when I entered "printenv SHELL"

(base) Renxis-Mac-mini:~ renxili$ printenv SHELL
/bin/bash

from workbench.

Yes, I only delete the duplicate lines in ~/.bashrc and ~/.cshrc, and leaving one line for each ~/.bashrc and ~/.cshrc

from workbench.

Do cat ~/.bashrc, cat ~/.bash_profile and cat ~/.profile and tell us what they say.

from workbench.

from workbench.

from workbench.

So, it looks like for other software you have been putting the lines in your .bash_profile. You also have a line for MSM in your .bashrc, which probably also doesn't work. I would probably solve this by making the .bash_profile source the .bashrc (like it often does on linux), by doing echo 'if [[ -f ~/.bashrc ]]; then source ~/.bashrc; fi' >> ~/.bash_profile (only once!). John's solution is similar, but uses old sh syntax.

Then, open a new terminal and try wb_command.

Our README.txt in the workbench zip distribution looks like it already says to do echo 'export PATH=$PATH:/Applications/workbench/bin_macosx64' >> ~/.bash_profile, not .bashrc, so you apparently followed instructions for a different OS?

from workbench.

I can get wb_command running under bash 5.0 now! Is wb_command only runnable under bash?

from workbench.

No, wb_command can be run by literally anything that wants to. The only thing specific to bash is the tab completion of wb_command operations, options, and file extension filtering. Other shells may still do naive filename tab completion.

from workbench.

Okay, now it works in zsh as well. Thank you all so much for your patience and help! You guys are amazing!

from workbench.