Install help for others

[Phillip-a-richmond]

Not sure if this is much use, but I am eager to use the toolkit and am using it on a shared system where I don't have root privileges. With virtualenv, installing this toolkit is trivial.

Just a few extra commands on top of your existing install instructions can get this working on a shared system where the user has limited privileges:

Create virtualenv on system, then installing the toolkit:

My python loading from module system

module load python/3.7

Run virutalenv to create an environment, here I do it within a directory called ~/TOOLS/

virtualenv --no-download ~/TOOLS/STR_Tools_Environment

Activate your environment

source ~/TOOLS/STR_Tools_Environment/bin/activate

install scipy dependency

pip install scipy

Clone this repo

cd ~/TOOLS/
git clone https://github.com/gymreklab/STRTools
cd STRTools

Run your set-up

python setup.py --install --prefix=~/project/TOOLS/STR_Tools_Environment/

And Voila! you're done!

Using it

source ~/project/TOOLS/STR_Tools_Environment/bin/activate
dumpSTR -h

[bibb]

Hi, thanks for the instructions, but I'm still unable to run plinkSTR, I have tried many ways to install it and make it run but I always have the same error:

plinkSTR -h

Traceback (most recent call last):
File "/Users/bib0660/TOOLS/STR_Tools_Environment/bin/plinkSTR", line 11, in
load_entry_point('strtools==1.0.0', 'console_scripts', 'plinkSTR')()
File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 489, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 2843, in load_entry_point
return ep.load()
File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 2434, in load
return self.resolve()
File "/usr/local/lib/python3.7/site-packages/pkg_resources/init.py", line 2440, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/Users/bib0660/TOOLS/STRTools/plinkSTR/plinkSTR.py", line 48
print record.start, int(start), record.ID
^
SyntaxError: invalid syntax

It looks like this is a coding mistake, isn't it? Unfortunately I haven't received any help from the developers in orrder to fix this

Thanks

[nmmsv]

Hi @bibb
I believe plinkSTR only runs in python2.7 environments. Can you please confirm this @shubhamsaini ?

@Phillip-a-richmond thanks for detailed instructions!

[nmmsv]

I made some changes that should fix the plinkSTR issue. Thanks for reporting it!