Question: How to run locuszoom in Ubuntu 16.04
0
gravatar for sjunlee89
4 months ago by
sjunlee890
sjunlee890 wrote:

I would like to run locuszoom in Ubuntu 16.04

the code as I ran is below.

mkdir locuszoom && cd locuszoom
wget https://statgen.sph.umich.edu/locuszoom/download/locuszoom_1.4_srconly.tgz
tar -zxvf locuszoom_1.4_srconly.tgz
cd locuszoom_1.4_srconly.tgz/
cp locuszoom /usr/local/bin/ && chmod a+x /usr/local/bin/locuszoom

On the other hand, after installation process, locuszoom was not running and I only saw this message.

locuszoom: commnad not found

How can I install locuszoom well and run this program in Ubuntu.

Thanks advanced.

software error • 218 views
ADD COMMENTlink modified 4 months ago by ATpoint15k • written 4 months ago by sjunlee890
3
gravatar for ATpoint
4 months ago by
ATpoint15k
Germany
ATpoint15k wrote:

If you copy the entire folder to bin, then the binary you call with locuszoom is still in the locuszoom/bin folder and therefore not in PATH. Either add locuszoom/bin to PATH or do cp locuszoom/bin/locuszoom /usr/bin.

ADD COMMENTlink modified 4 months ago • written 4 months ago by ATpoint15k

Thank you for your reply. It works very well.

ADD REPLYlink written 4 months ago by sjunlee890

is it normal when i run locuszoom? i saw error locuszoom +-------------------------------------------+ | LocusZoom 1.4 (05/01/2017) | | Plot regional association results | | from GWA scans or candidate gene studies | +-------------------------------------------+

Traceback (most recent call last): File "./locuszoom", line 28, in <module> main(); File "/home/XinkaiTong/software/locuszoom/bin/../src/m2zfast.py", line 2102, in main conf = getConf() File "/home/XinkaiTong/software/locuszoom/bin/../src/m2zfast.py", line 130, in getConf conf = Conf(conf_file) File "/home/XinkaiTong/software/locuszoom/bin/../src/m2zfast.py", line 119, in __init__ self._load(conf_file) File "/home/XinkaiTong/software/locuszoom/bin/../src/m2zfast.py", line 123, in _load execfile(file,conf_dict) TypeError: must be string, not None

ADD REPLYlink written 4 months ago by xinkaitong0
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