Problem with examples

[WizardPanther]

I try to install GARFIELD successfully with output like this:

$perl INSTALL.pl force = TRUE use cpanm at: /home/yanglab/software/Garfield-1.0/scripts/cpanminus local::lib is up to date. (2.000029) Perl module Benchmark is already installed. Perl module FindBin is already installed. Perl module File::Spec is already installed. Perl module Pod::Usage is already installed. Perl module Getopt::Long::Subcommand is already installed. Perl module Fcntl is already installed. Perl module Parallel::ForkManager is already installed. Rscript found in the PATH. Installing R libraries Bioconductor version 3.18 (BiocManager 1.30.25), R 4.3.1 (2023-06-16) Warning message: package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: 'logicFS' Required R packages have been successfully installed!

All dependencies have been satisfied. Now you can take Garfield on your journey!

██████╗ █████╗ ██████╗ ███████╗██╗███████╗██╗ ██████╗ ██╔════╝ ██╔══██╗██╔══██╗██╔════╝██║██╔════╝██║ ██╔══██╗ ██║ ███╗███████║██████╔╝█████╗ ██║█████╗ ██║ ██║ ██║ ██║ ██║██╔══██║██╔══██╗██╔══╝ ██║██╔══╝ ██║ ██║ ██║ ╚██████╔╝██║ ██║██║ ██║██║ ██║███████╗███████╗██████╔╝ ╚═════╝ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚══════╝╚══════╝╚═════╝

/_/\ ~ MEOW ~ ( o.o )

^ <

And then, when I test the example file with this command: $Garfield Gene --genotype ./example/test.genotype --trait ./example/test.trait.txt --bed ./example/test.geneAnno.bed --extension 20000 --outdir ./test --temporary ./tmp --prefix test --threads 1

Which print several Error message:

Error in nrow(vim.result) == 0 || unique(factor(predicted_genotype$predict)) == : 'length = 2' in coercion to 'logical(1)' Calls: Garfield_main Execution halted Use of uninitialized value $result_TPED in pattern match (m//) at /home/yanglab/software/Garfield-1.0/lib/Garfield/Gene.pm line 148, <$bed_fh> line 1. Error in nrow(vim.result) == 0 || unique(factor(predicted_genotype$predict)) == : 'length = 2' in coercion to 'logical(1)' Calls: Garfield_main Execution halted

with printing several times it goes to :DONE! running time: 22 wallclock secs ( 0.01 usr 0.00 sys + 23.17 cusr 10.74 csys = 33.92 CPU)

And there is nothing in output files.

[heroalone]

Hey. I'm not sure of the exact reason, but we have made it run with Docker directly. Could you please try again with something like: docker run -it garfield Gene --genotype ...

[WizardPanther]

Hey. I'm not sure of the exact reason, but we have made it run with Docker directly. Could you please try again with something like: docker run -it garfield Gene --genotype ...

Yes I install it with docker. $ sudo docker pull wenjiewei9908/garfield:1.0 1.0: Pulling from wenjiewei9908/garfield Digest: sha256:df4fff544f6b6a1d19b7ce13f9b2f3314c7932e88a78eb5470fc96c56e23bf8f Status: Image is up to date for wenjiewei9908/garfield:1.0 docker.io/wenjiewei9908/garfield:1.0

But, $ sudo docker run -i garfield Unable to find image 'garfield:latest' locally docker: Error response from daemon: pull access denied for garfield, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.

I don't know much about docker, I would try.