Oases python script can't find Velvet

[JakeBuehler]

Aloha,

So, I'm trying to run Oases to create a de novo transcriptome. I have the paired-end reads file ready to go, and the newest versions of Oases and Velvet downloaded and compiled on a Linux server. However, when I try to run the included script - oases_pipeline.py - using the command given in the manual (python oases_pipeline.py -m 17 -M 40 -o PairedEnd -d " -fastq reads.fastq" -p " -ins_length 300 ") it keeps returning the error message:

Could not find Velvet
Make sure that it is properly installed on your path

I've tried entering the full path names to everything and copying the executable files into the working directory, always the same error. Do I need to edit the script directly to find the right paths to the executables? Or am I just missing something?

Mahalo

[blancha]

velveth needs to be in your PATH environment variable.

If you're using the BASH shell, edit ~/.bash_profile to include velveth in your path.

PATH=$/pathTo/velveth:$PATH
export PATH

Once you've edited your .bash_profile file, logout and login for the new settings to take effect, or just type the following command, source ~/.bash_profile

You can check the path, just by typing echo $PATH, or you can just type velveth to check that velveth is in your path.

[Oyster_lab]

Hi all,

I'm facing a similar error at the moment., but for Oases. I've downloaded and compiled Velvet (version 1.2.09) using " $make " and also " $make 'MAXKMERLENGTH=64' ". Following that, I've downloaded and compiled Oases (version 0.2.08) using " $make " , " $make 'MAXKMERLENGTH=64' " and " $make 'VELVET_DIR=/home/manager/velvet' 'MAXKMERLENGTH=64' ". Velvet is running fine, but I can get Oases to work. I keep getting the following message when I try to run both "oases" and "oases_pipeline.py":

Could not find Oases
Make sure that it is properly installed on your path

What else should I do to get Oases running? I would really appreciate your help.

Kind regards,
Priscila

[blancha]

First, just try going to the oases folder and locating the oases file.
If the file is executable, just type:
./oases
If the file is not executable, make it executable first:
chmod u+x oases
You can check the file permissions with the following command:
ls -l oases

If you're able to execute the file when specifying the path to oases, you'll just need to edit your PATH environment variable to include the oases folder.
To see the folders currently included in your path, just type:
echo $PATH
To add the oases folder to your path, type:
export /path/to/oases/folder/:$PATH
To make the changes permanent, include the previous line in your .bash_profile file (if your shell is Bash).