Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Help with paths
0
gravatar for tuto345
3.5 years ago by
tuto345 • 20
France
tuto345 • 20 wrote:

Hi all,

I have problems understanding how environment variables are used/modified in galaxy.

I have some tools like, for instance, bedtools installed in /usr/local/bin which is in the path on a cluster and I would like this binary to be used. Some tools that launch bedtools after a pipe (i.e. ... | bedtools genomecov) do not find it. Another example was the special case of samtools where I found that linking the 0.1.19 version to a directory named default solved my problems.

So how can I tell galaxy tools to look first or always in /usr/local/bin? How can I check which instance (or version) of a software is being used?

Thanks for your help!

Cristian
galaxy environment • 833 views
ADD COMMENT • link •
modified 3.5 years ago • written 3.5 years ago by tuto345 • 20

Hi Hanz-Rudolf

This worked perfectly!

I never thought of reading the run.sh file and the scripts launched from within. A very interesting read...

Thanks again,

Cristian

ADD REPLY • link written 3.5 years ago by tuto345 • 20

Please accept Hans-Rudolf's answer to help other people to identify answered posts. Thanks

ADD REPLY • link written 3.5 years ago by Martin Čech ♦♦ 4.9k
Sure! And how exactly do I do that?
ADD REPLY • link written 3.5 years ago by tuto345 • 20

I think you should see a 'tick' mark to the left of Hans-Rudolf's answer. Click that.

ADD REPLY • link written 3.5 years ago by Martin Čech ♦♦ 4.9k

Done! I was accessing the mobile version and didn't have the tick mark.

Cheers,

Cristian

ADD REPLY • link written 3.5 years ago by tuto345 • 20
4
gravatar for Hotz, Hans-Rudolf
3.5 years ago by
Hotz, Hans-Rudolf • 1.8k
Switzerland
Hotz, Hans-Rudolf • 1.8k wrote:

Hi Christian

Quick and dirty solution:  add the path to your 'run.sh' file,

eg:

PATH=$PATH:/usr/local/bin

 

Regards, Hans-Rudolf

 
ADD COMMENT • link written 3.5 years ago by Hotz, Hans-Rudolf • 1.8k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 181 users visited in the last hour