CRAFT cannot detect input data #2 #7
Description
Hi,
I have an issue running an analysis. I prepared the necessary files in the following directory structure:
.
└── test
├── input
│ ├── backsplice_gene_name.txt
│ ├── hg38.fa
│ ├── hg38.ndb
│ ├── hg38.nhr
│ ├── hg38.nin
│ ├── hg38.njs
│ ├── hg38.not
│ ├── hg38.nsq
│ ├── hg38.ntf
│ ├── hg38.nto
│ ├── hg38.shd
│ ├── Homo_sapiens.GRCh38.dna.primary_assembly.fa
│ ├── Homo_sapiens.GRCh38.104.gtf
│ ├── hg38.00.idx
│ ├── hg38.01.idx
│ ├── hg38.02.idx
├── list_backsplice.txt
├── params.txt
└── path_files.txt
which lies inside C:\test. Then I paste the command: docker run -it -v C:\test :/data annadalmolin/craft:v1.0 to WIndows command prompt, but then I get an error:
Quitting from lines 90-153 (functional_predictions_all_circRNAs.Rmd)
Error in read.table(file_parameters, header = F) :
no lines available in input
Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> read.table
In addition: Warning message:
package(s) not installed when version(s) same as current; use force = TRUE to
re-install: 'grid'
As far as I understand, it cannot detect input data or/and some packages in R are not appropriate version. But maybe I just should run it in Linux or directly in Docker?
I'm new to bioinformatics, so I might be making some basic mistakes. I find your analysis process so cool though, I would really like to make it work :)