MaSuRCA Assembler runCA Error

[rafaykhan]

Successfuly install MaSuRCA

tar xfz MaSuRCA-3.2.1.tar.gz

cd MaSuRCA-3.2.1

sudo ./install.sh

Configure and run config.txt

MaSuRCA-3.2.1/bin/masurca MaSuRCA-3.2.1/bin/config.txt
Verifying PATHS...
jellyfish OK
Error: runCA not found or failed to run

Help me to get through this error.

[sklages]

Please do not crosspost to Biostars if you want help here ..

jellyfish is in your PATH, runCA is not.

You could either use --path /PATH/TO/runCA with masurca or add the corresponding path to your PATH variable.

There is a bin folder in masurca installation directory which holds the common binaries. runCA and other programs are in one of the "neighbor" folders, in CA/bin or CA8/bin.

best,
Sven

[rafaykhan]

Thank you Sven, its work

PATH=~/tools/MaSuRCA-3.2.1_12062016/CA/Linux-i686/bin:$PATH
PATH=$PATH:~/tools/MaSuRCA-3.2.1_12062016/CA/Linux-i686/bin

sudo env "PATH=$PATH" ~/tools/MaSuRCA-3.2.1_12062016/bin/masurca ~/tools/MaSuRCA-3.2.1_12062016/bin/config.txt

[drunk_coder]

I also have a runCA issue, I installed MaSuRCA-3.2.1_01202017 successfully. I use CA8/bin in my PATH. During Assembly, MsSuRCA threw a runCA error:
"ERROR: the runCA option ovlHashBlockSize is not recognized.
This runCA functionality changed in CABOG version 7.
Try using ovlHashBlockLength instead."

I found masurca generated "assemble.sh" based on runCA6 command, but installed runCA version is 8.2. So how to fix this issue ?

best,
mjx