Question: cutadapt installation location
1
gravatar for jolin0701-dy
2.5 years ago by
jolin0701-dy60
jolin0701-dy60 wrote:

I followed the manual to install cutadapt

It should be installed in /usr/local/bin

But it shows

Requirement already up-to-date: cutadapt in /Users/yc/Library/Python/2.7/lib/python/site-packages

Any suggestions??

Thanks so much~~

rna-seq • 1.0k views
ADD COMMENTlink modified 2.5 years ago by ablanchetcohen1.2k • written 2.5 years ago by jolin0701-dy60

If you don't have root privileges then you would not be able to install in /usr/local/bin/. If there is a cutadapt in that directory you can use it from there.
Note: If you are on OS X (which I think is the case) then a /usr/local/bin directory may not exist by default (generally present on linux). If you do have root/sudo then you could create that directory and then cutadapt can be installed there.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax56k
1
gravatar for ablanchetcohen
2.5 years ago by
ablanchetcohen1.2k
Canada
ablanchetcohen1.2k wrote:

The documentation on the installation of cutadapt is just a bit misleading, as far as I'm concerned. Cutadapt was just installed as a Python package. The cutadapt executable is probably in /Users/yc/Library/Python/2.7/bin.

If that folder is already in your PATH you can just type cutadapt to run the program. Otherwise, you'll have to type the full path. /Users/yc/Library/Python/2.7/bin/cutadapt

As long as you're the only user using the program, it will work fine.

ADD COMMENTlink written 2.5 years ago by ablanchetcohen1.2k
1

Documentation seems to clearly indicate that to install in /usr/local/bin you would need root privileges.

ADD REPLYlink written 2.5 years ago by genomax56k
1

Of course, without root privileges, you could never install to /usr/local/bin. I just find the documentation somewhat misleading because it indicates that cutadapt would be installed to $HOME/.local/bin, without root privileges. This is not the case for my installation. The program is installed to the bin subdirectory of Python. I did some more research, and found that pip will install executables to the path returned by sysconfig.get_path("scripts"), which in my case is the bin subdirectory of Python.

ADD REPLYlink written 2.5 years ago by ablanchetcohen1.2k
1

That is good to know. The original question may have arisen because of OS X (at least that is my guess).

ADD REPLYlink written 2.5 years ago by genomax56k
1

Thanks~~ I'll choose to type the full path….. Not much pain...

ADD REPLYlink written 2.5 years ago by jolin0701-dy60
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