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
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
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