SPAdes 3.9.0 will not run on Mac (10.10.5)

Question

[danni_lynne]

Hello everyone,

I'm trying to download and run SPAdes 3.9.0 on a Mac OS (10.10.5). I've downloaded the gunzipped file with the command: curl http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Darwin.tar.gz -o SPAdes-3.9.0-Darwin.tar.gz

then tar -xzf SPAdes-3.9.0.tar.gz

changed directory to SPAdes-3.9.0-Darwin

According to the manual, it is supposed to be good to go. I have tried testing it in the SPAdes directory using spades.py --test, but it says command not found.

I have no idea what I am doing wrong or why this is not working. It it executable when I look at ls -l.

Please help me!

Answer 1

[GenoMax]

Since the directory you are in is not in your $PATH you are not able to run the program the way you tried it. Instead try this (if you are in the spades directory):

./spades.py --test

It would be best if you at least familiarize yourself with the basics of unix command line using this tutorial. This will save you a lot of heartache down the road.

Answer 2

[danni_lynne]

I did try to put the directory in the $PATH and run the program but it still did not work... Thank you for your answer and the tutorial.

[GenoMax]

Did you run the command the way I showed above (while you were in the SPAdes directory)? What did that produce (an error or some other message)?

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