Question: How to change the path so that screen can take the default python path?
0
gravatar for saadleeshehreen
10 months ago by
saadleeshehreen70 wrote:

I am using a python script from GitHub to do some of my analysis. To run the script, I required some other programs which are also installed in our server. I linked the software with those programs by the following command.

ln -s /usr/local/bin/clustalo\
ln -s /usr/bin/blastn

The script behaves properly when I run it in our server and taking the python from the following path.

/usr/bin/python

But I can't run the program on screen because the python path is now as following and all the dependencies are not in this path.

userdata/student_users/X/software/miniconda2/bin/python

How can I change the path of the screen so that it takes this path?

/usr/bin/python
script issue python • 301 views
ADD COMMENTlink modified 10 months ago by Jeffin Rockey1.1k • written 10 months ago by saadleeshehreen70

Try providing the python executable path at the top of python script? (#!/usr/bin/python)

ADD REPLYlink modified 10 months ago • written 10 months ago by cpad011212k
1
gravatar for Jeffin Rockey
10 months ago by
Jeffin Rockey1.1k
Karimannoor
Jeffin Rockey1.1k wrote:

While installing Miniconda, towards the end, the script would have asked whether to add the path entries in ~/.bashrc and probably you would have given a yes. No problem with that. But this prefixing of miniconda path in ~/.bashrc is by which it gets its precedence.

Easiest fix to make system take the path you want is,

vi ~/.bashrc

then go to the bottom of entries and add

export PATH=/usr/bin:$PATH

This is not the cleanest method but it will work.

Other option is to comment the entries made by miniconda in ~/.bashrc.

Usually the entries will be demarcated with a informing comment line (# added by Miniconda2 installer) above.

Either case, please exit the terminal and login again for the changes to take effect.

ADD COMMENTlink modified 10 months ago • written 10 months ago by Jeffin Rockey1.1k
1

And remember

source ~/.bashrc

to make it work.

ADD REPLYlink written 10 months ago by MatthewP260

Thanks.I shall add that.

ADD REPLYlink written 10 months ago by Jeffin Rockey1.1k
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