Closed Pedramto89 closed 1 year ago
Hi,
You need to include the full path to the exectuable:
/your/path/scsnv/build/src/scsnv index ...
I still get an error but a different one:
zsh: permission denied
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
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`
You aren't using the full path from the directory you are in the executable is at:
./build/src/scsnv
I am in the directory. scsnv at the terminal shows this
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.
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.
You need to compile and build scsnv as per the build instructions on the main github page.
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.