I am running Trinity for my transcriptome assembly using the Cluster of our University. I got the the following error: ./runMe.sh: line 18: ../../Trinity: Permission denied. Any one could suggest a solution for this error.
Thanks
I see three options:
1. The script runMe.sh looks for Trinity binary two levels above the current folder. Perhaps you are trying to read any other folder on the server for which you do not have permission.
2. More likely, you have to add the executable permission to Trinity binary. You can do this by navigating to the folder with Trinity binary and executing a command chmod 700 Trinity. Then run again the runMe.sh.
3. Also likely, the system does not allow execution of local binaries. This is quite common on uni clusters. You'll need to ask the admin to install Trinity on the cluster.
Hope that helps.
Your best bet is to ask your local cluster admin. They will have a better idea what is or isn't possible.
Although having said that, my guess is that you've not set the 'current working directory' flag in your job submission therefore the relative path you have given in your script is no longer valid. Either define the working directory appropriately or use an absolute path e.g. /home/username/path/to/Trinity
1. Obtain the admin permission
2. Add the 'Trinity' program to your directory
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