About building the index

[Pedramto89]

Hi. I setup the pipeline and followed the procedure. However, when I wanted to build the index, I got an error:

This is the command: scsnv index -g genes.gtf -r genome.fa index_prefix

And this is the error: zsh: command not found: scsnv

It seems the scsnv is not activated. My directory is: ~/CNV analysis/scsnv And I was doing all these on mac terminal.

[GWW]

Hi,

You need to include the full path to the exectuable:

/your/path/scsnv/build/src/scsnv index ...

[Pedramto89]

I still get an error but a different one: zsh: permission denied

[GWW]

You may need to give the scsnv binary execute permissions.

chmod +x /your/path/scsnv/build/src/scsnv
ls -alh /your/path/scsnv/build/src/scsnv

You should see something like:

-rwxr-xr-x 1 gww gww 5.3M Mar 14  2022 scsnv

[Pedramto89]

It did not work: This is what I get: `(base) pedram@Pedrams-MacBook-Air scsnv % ls -alh total 112

drwxr-xr-x 17 pedram staff 544B 7 Feb 22:50 . drwxr-xr-x 6 pedram staff 192B 7 Feb 22:41 .. -rw-r--r--@ 1 pedram staff 6.0K 7 Feb 22:50 .DS_Store drwxr-xr-x 13 pedram staff 416B 7 Feb 22:41 .git -rwxr-xr-x 1 pedram staff 1.3K 7 Feb 22:41 .gitignore -rw-r--r-- 1 pedram staff 316B 7 Feb 22:41 .gitmodules -rw-r--r-- 1 pedram staff 740B 7 Feb 22:41 CMakeLists.txt -rw-r--r-- 1 pedram staff 1.0K 7 Feb 22:41 LICENSE -rw-r--r-- 1 pedram staff 17K 7 Feb 22:41 OLDDOC -rw-r--r-- 1 pedram staff 12K 7 Feb 22:41 README.md drwxr-xr-x 2 pedram staff 64B 7 Feb 22:41 build drwxr-xr-x 6 pedram staff 192B 7 Feb 22:41 data drwxr-xr-x 5 pedram staff 160B 7 Feb 22:41 external drwxr-xr-x 49 pedram staff 1.5K 7 Feb 22:41 include drwxr-xr-x 4 pedram staff 128B 7 Feb 22:50 sample drwxr-xr-x 8 pedram staff 256B 7 Feb 22:44 scsnvpy drwxr-xr-x 35 pedram staff 1.1K 7 Feb 22:41 src`

[GWW]

You aren't using the full path from the directory you are in the executable is at:

./build/src/scsnv 

[Pedramto89]

I am in the directory. scsnv at the terminal shows this

[GWW]

That isn't the correct directory the scsnv executable is in a different path relative to the scsnv directory. For example, on my computer my scsnv directory is:

/home/gww/projects/scsnv/

But the executable is at:

/home/gww/projects/scsnv/build/src/scsnv

You need to use the path of the executable to run scsnv.

[Pedramto89]

So, maybe the problem is this: I do not have a scsnv folder in my build. This is what I have: `(base) pedram@Pedrams-MacBook-Air scsnv % ls

CMakeLists.txt LICENSE OLDDOC README.md build data external include sample scsnvpy src`

And in the build folder, there is no file.

[GWW]

You need to compile and build scsnv as per the build instructions on the main github page.