justincbagley
commented
4 years ago Hola Juan,
First, in terms of generalities, I have not been able to replicate your issue on my MacBook Pro, but I noticed that you are running Linux and have installed PIrANHA through linuxbrew, so this is likely a Linux- or Linux distribution-specific issue, which means that other Linux users could be experiencing something similar. However, Mac users should be fine.
The main problem is a bad substitution syntax error, which is means the wrong shell is being called. You should not have to manually change SCRIPT_PATH, UTILS_LOCATION, etc. Notice that trimSeqs is a shell script thus uses the shell shebang (#!/bin/sh). So sh is not getting called; instead your trimSeqs function is either being run by bash or dash.
If you are running on Ubuntu, the default shell used to be (prob still is) dash. Check this with
echo $SHELL
Check available shells on your machine with:
cat /etc/shells
So the best solution would be to reconfigure your machine to use bash as the default shell instead (e.g. see solutions here and here).
Another solution: you may also try changing the trimSeqs shebang from #!/bin/sh to #!/bin/bash, but not sure this will work.
Let me know if the above resolves your issue, or if you have any further questions.
Best, ~J
biologistico
I'm having trouble getting trimSeqs to work. Here's the error I get:
I tried updating the paths to utils.sh, sharedFunctions.sh, and sharedVariables.sh files in the trimSeqs.sh file but it still gives me the same error. Is it because I also have to specify something on the SCRIPT_PATH line of the trimSeqs.sh script? Here's what I modified in that script so far shown in bold (2 asterisks):
I'm sure it's something minor but I can't seem to figure it out.