Install didn't work

[wqhf]

Hello dariober, I try to install cnv_facets on centos7.2 but it doesn't work. I just followed your readme file. the error message like:

Error: bin directory requested by -b/--bin_dir '/root/bin' is not on PATH

I also try several ways but it failed too

[root@wulab cnv_facets-src]# bash setup.sh -b ../
Error: bin directory requested by -b/--bin_dir '../' is not on PATH
[root@wulab cnv_facets-src]# bash setup.sh -b ../cnv_facets
Error: bin directory requested by -b/--bin_dir '../cnv_facets' is not on PATH
[root@wulab cnv_facets-src]# bash setup.sh -b /data2/database/opt/common/cnv_facets/cnv_facets
Error: bin directory requested by -b/--bin_dir '/data2/database/opt/common/cnv_facets/cnv_facets' is not on PATH

[dariober]

Hi- As the error message says, it appears the directory you chose to install to via the -b option is not on your PATH.

To see what directories are on your PATH execute echo $PATH and either choose a directory where you can write or create a new directory and add it to your PATH.

A common directory for installing custom programs like cnv_facets.R is $HOME/bin or /usr/local/bin (but this latter requires admin rights to write to).

I would suggest working as regular user not as root, as it seems from your code blocks.

Putting it all together, what you can do as regular user (not root):

• Create a personal bin directory

mkdir -p $HOME/bin  

• Add this directory to your PATH (it may be already on your PATH, check the output of echo $PATH, maybe post the output of echo $PATH here)

echo 'export PATH=$HOME/bin:$PATH' >> ~/.bash_profile
source ~/.bash_profile

• Install cnv_facets:

bash setup.sh -b $HOME/bin

Let me know how you get on and feel free to report back any further issues you may have...

[dariober]

Hi- If still interested, cnv_facets can be installed now with bioconda. I recommend this route rather the setup.sh script.