I have downloaded and installed the Biostars Bioinformatics-recipes according to the directions here: https://bioinformatics-recipes.readthedocs.io/en/latest/index.html
OS = Ubuntu 18, anaconda python
I am unable to get a simple script to work.
I created a new project -> uploaded a data file (filelist.txt) which is a text file just listing the full path to some files
The data tab shows:
Data:filelist.txt
Data List
Files contained in the dataset
filelist.txt
Data Content
/home/test/biorecipes/trimFastq/Y12_R1.fastq
/home/test/biorecipes/trimFastq/Y12_R2.fastq
Table of Contents filelist.txt
Then I added a data field to the recipe: [data]
label = 'Pick data'
source = 'PROJECT'
help = 'Pick data from this project.'
choices = [ ['A','Default'] ]
This allows me to choose my filelist.txt on the run tab.
In the code tab I have:
echo 'List my files'
echo $PWD
cat filelist.txt
When I run I get the following error:
cat: filelist.txt: No such file or directory
Command 'bash recipe.sh' returned non-zero exit status 1.
when I run only:
echo 'List my files'
echo $PWD
I get the expected result.
Suggestions would be helpful.
Thank you
