Question: SPAdes 3.9.0 will not run on Mac (10.10.5)
0
gravatar for danni_lynne
3.3 years ago by
danni_lynne0 wrote:

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!

assembly • 1.4k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by danni_lynne0
0
gravatar for genomax
3.3 years ago by
genomax75k
United States
genomax75k wrote:

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.

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by genomax75k
0
gravatar for danni_lynne
3.3 years ago by
danni_lynne0 wrote:

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.

ADD COMMENTlink written 3.3 years ago by danni_lynne0

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)?

Note: In future please use ADD COMMENT/ADD REPLY to respond to existing posts. SUBMIT ANSWER should only be used for new answers for original question.

ADD REPLYlink written 3.3 years ago by genomax75k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 723 users visited in the last hour