Problem when trying to activate bioinfo

[2tesla2]

Hello!

When I try to run the command
micromamba activate bioinfo

This is returned to me
-bash: syntax error near unexpected token '('
(bioinfo)

How do I fix this?

Thanks!

[ialbert]

that's a weird error for sure.

you have some sort of invalid command in your .bashrc or .bash_profile

but since you also have the (bioinfo) displayed it looks like the environment is activate correctly

see if command line tools still work, bwa, samtools

then you would need to check the syntax of your .bashrc or .bash_profile

[2tesla2]

What would I be looking for in the syntax of .bashrc or .bash_profile?

Thank you!

[ialbert]

see how even the code above when pasted complains about unclosed parentheses? though to be honest I don't what the quick solution is here.

[2tesla2]

Upon playing around with the script, I have discovered that if I change the path from

export path=~/bin:~/edirect:$PATH

into

export path='~/bin:~/edirect:$PATH'

There is no more syntax error. However, I am now faced with the problem that commands such as mkdir are now not found:

Command 'mkdir' is available in the following places

• /bin/mkdir
• /usr/bin/mkdir
  The command could not be located because '/usr/bin:/bin' is not included in the PATH environment variable.
  mkdir: command not found

Should I continue using this line in the script?

export path='~/bin:~/edirect:$PATH'

[ialbert]

you set your path to something invalid, there is a difference between single quotes and double quotes,

when you use double quotes the value of the $PATH variable is expanded to what it contains,

when you use single quotes then the path will be set to literally the word $PATH

But, that being said, it is an interesting and meaningful information, it seems that it is the contents of the $PATH variable that is invalid and incorrect.

Thus my recommendation is to look at what the $PATH contains with echo $PATH (when set in the original way) to see what might go bad there.

I expect that you have some sort of invalid directory listed there that is valid under Windows but not under Linux

[2tesla2]

/home/slchua/bin/sratoolkit.3.0.0-ubuntu64/bin:/home/slchua/bin:/home/slchua/edirect:/home/slchua/micromamba/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/Program Files/dotnet/:/mnt/c/Program Files/Geneious Prime:/mnt/c/Users/Sean's Laptop/AppData/Local/Microsoft/WindowsApps:/snap/bin

This is what is showing as my directory when I run echo $PATH. Are the paths with WINDOWS the invalid paths? I've been looking for what may be setting this in my .bashrc and .biostar but can't find any code that sets path other than export PATH=/bin:/edirect:$PATH.

What could I do?

[ialbert]

I think your problem may be (but I am not entire sure) that your computer is called Sean's Laptop, and Unix really does not like names that include apostrophes + spaces and it is probably not escaped quite right.

I would edit the .bashrc or wherever that PATH is set and remove the lines where it adds weird windows paths and see what happens. Also I would recommend the computer name to be set to a simple word with no punctuation of any kind, streambeam, darkstar, laptoppy, pixelpal :-) so that you don't run the risk of invalid unix symbols messing it up