Install error

[doeun99]

Hello,

I tried to install Ising to use it, but even with Docker, I couldn't install it. Can you please let me know if Ising is no longer available for use?

Thank you.

[szsctt]

Isling is still available - it runs ok in the docker container for me. Could you please provide some more information about the error you're getting?

[doeun99]

To provide you with more context, I am running the following command to execute the Isling:
snakemake --configfile /home/kde/PROJECTS/VirusIntegrationTools/download/isling/test/config/huH-1_bam.yml --cores 8 --use-conda

However, I am encountering an UnboundLocalError during the execution, and I wanted to seek your advice on how to address this error. The error message I am receiving is as follows:
UnboundLocalError in file /home/kde/PROJECTS/VirusIntegrationTools/download/isling/Snakefile, line 58: cannot access local variable 'bucket' where it is not associated with a value File "/home/kde/PROJECTS/VirusIntegrationTools/download/isling/Snakefile", line 58, in <module> File "/home/kde/PROJECTS/VirusIntegrationTools/download/isling/scripts/make_df.py", line 71, in make_df

I have provided the configuration file content (config/huH-1_bam.yml) below for your reference:
`test_huH1_bam_split:
read_folder: "/home/kde/PROJECTS/VirusIntegrationTools/huH-1_Bam/huH-1.sorted.dedup.bam"
out_dir: "/home/kde/PROJECTS/VirusIntegrationTools/isling_out/"
bam_suffix: ".bam"
read1-adapt: ""
read2-adapt: ""
mean-frag-len: "estimate"
merge: False
trim: False
host_name: "host_hg19"
host_fasta: "/home/kde/PROJECTS/VirusIntegrationTools/HBV_C/hg19.fa"
virus_name: "HBV"
virus_fasta: "/home/kde/PROJECTS/VirusIntegrationTools/HBV_C/AB033550.fa"
dedup: False
clip-cutoff: 10
min-mapq: 10
cigar-tol: 3
split: 3
post:
- filter
- dedup
merge-dist: 0
min-n-merge: 1

test_huH1_bam:
read_folder: "/home/kde/PROJECTS/VirusIntegrationTools/huH-1_Bam/huH-1.sorted.dedup.bam"
out_dir: "/home/kde/PROJECTS/VirusIntegrationTools/isling_out/"
bam_suffix: ".bam"
read1-adapt: ""
read2-adapt: ""
mean-frag-len: "estimate"
merge: False
trim: False
host_name: "host_hg19"
host_fasta: "/home/kde/PROJECTS/VirusIntegrationTools/HBV_C/hg19.fa"
virus_name: "HBV"
virus_fasta: "/home/kde/PROJECTS/VirusIntegrationTools/HBV_C/AB033550.fa"
dedup: False
clip-cutoff: 1
min-mapq: 10
cigar-tol: 3
split: 1
post:
- filter
- dedup
merge-dist: 0
min-n-merge: 1`

+I also wanted to provide the execution error using docker, but since I am a newbie my supervisor ran it for me with docker and I could not provide detailed information in this situation.

[szsctt]

Thanks for this! There was a bug in the way the config file is processed - I've fixed this so please pull the latest version and try again.