Question: Can not make folder under /usr/local/bin in order to use FASTX-toolkit in Galaxy
gravatar for chchl7
3.2 years ago by
United States
chchl70 wrote:

Dear all,

I want to use FASTX-toolkit to split a large FASQ file into small ones based on barcodes. I need to make a folder fastx_bin in /usr/local/bin. However, I got this error, "mkdir: cannot create directory `fastx_bin': Permission denied". Anyone can help?  Thanks!


ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by chchl70
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This is a unix permission error. If sudo works, try that. Or, do one of the following: choose a different location that you have read/write permission to or modify this area so that you have read/write. Worry about execute permissions at the end of the install.

Once done, be sure that if there is an executable installed, and you want Galaxy to use it, that the "Galaxy user" knows where to find it ($PATH) and has permissions to run it (executable "x" is set). 

More about directory permissions can be found many places around the internet with a simple search. Permissions in any computer are a global function, unrelated to Galaxy, and even often unrelated to the shell (or rather, how permissions function are common between modern unix shells).

Take care, Jen, Galaxy team

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k
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