Question: unable to access executable in PATH from remote server
0
gravatar for deman23
3 months ago by
deman230
deman230 wrote:

I have an web application hosted with Django-gUnicorn-Nginx. The web app is working mostly fine and is accessible except for one functionality.

Recently, I added pybedtools, a python wrapper package for bedtools. I have the binary executables of bedtools in the PATH variable. However, the server is unable to access this executable.

The error just reports intersectBed does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method

I have tested/reinstalled the latest versions locally and it works, but not in the server.

Any ideas? Thanks in advance.

ADD COMMENTlink modified 3 months ago • written 3 months ago by deman230

I have the binary executables of bedtools in the PATH variable. However, the server is unable to access this executable.

Please show code how you did that. PATH should contain the directory where binaries are stored in, not the binary itself.

So if bedtools executable is in a folder bin then set PATH to export PATH=$PATH:/path/to/bin

ADD REPLYlink modified 3 months ago • written 3 months ago by ATpoint36k

Thanks. Yes, I've done it as you mentioned

export PATH=$PATH:/home/xxxxxx/miniconda3/bin

This is where I've the bedtools executables

ADD REPLYlink written 3 months ago by deman230
1
gravatar for deman23
3 months ago by
deman230
deman230 wrote:

Good old print statements came to rescue!

The path variable passed on to the server instance somehow had only the defaults /usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin.

I couldn't manage to export the location where bedtools is installed to the PATH. So I simply created a symlink of bedtools executable in my /usr/local/bin

Thanks for the suggestions @ATpoint.

ADD COMMENTlink written 3 months ago by deman230

Thanks a lot for this! very helpful and easiest to do.

ADD REPLYlink written 6 weeks ago by alhafidzhamdan0
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