output directory

[plantman8]

I am trying to run your program but seem to be failing at a quite early step. For some reason I get the error below when I try and run the program. A new directory is created when this runs but I still get an error. My guess is it is something small and stupid I am missing/doing.

tormes --metadata /home/user/Agro/samples_metadata.txt --output /home/user/Agro/output

Thanks for using tormes version 1.3.0
Let's check that all software are properly installed and all the data included in the metadata file is correct

/home/user/anaconda3/envs/tormes-1.3.0/bin/tormes: line 590: /home/user/Agro//home/user/Agro/output/temp1: No such file or directory

ERROR: files could not be generated in the selected output directory (-o/--output option):
/home/user/Agro//home/user/Agro/output
Please check!

[biobrad]

Hi Plantman,

Try just using the directory name on its own for the output. (same for the meta data)
Tormes will create the output directory for you as well.

So if you are running tormes from the directory where your metadata folder is and where you want your output folder you just have to run the following:

tormes -m samples_metadata.txt -o temp1

As you can see with the error, the tormes script has code in it that knows where you currently are in your directory structure, so if you tell tormes to output to /home/user/Agro/output then tormes is going to think that you want your output folder called '/home/user/Agro/output', which is why you get that error.

Good luck!

cheers
Brad

[nmquijada]

Hi @plantman8

@biobrad is correct. How tormes is built right now, there's a bug that it does not accept full but relative paths for the -o/--output option. This issue has been corrected in the ongoing development version of the tool.

In the meantime, you can simply run tormes as:

tormes --metadata /home/user/Agro/samples_metadata.txt --output output

Best,
Narciso