How to run and debug the viral-ngs docker?

cd ~/DATA/Data_Huang_Human_herpesvirus_3/viralngs
cp -r /home/jhuang/Tools/viral-ngs/bin .
cp /home/jhuang/Tools/viral-ngs/Snakefile .

#BUG_1: FileNotFoundError: [Errno 2] No such file or directory: '/home/jhuang/Tools/samtools-1.9/samtools': '/home/jhuang/Tools/samtools-1.9/samtools'
#DEBUG_1 (DEPRECATED):
        # - In docker install independent samtools
        conda create -n samtools-1.9-env samtools=1.9 -c bioconda -c conda-forge
        # - persistence the modified docker, next time run own docker image
        docker ps
        #CONTAINER ID   IMAGE                              COMMAND   CREATED         STATUS         PORTS     NAMES
        #881a1ad6a990   quay.io/broadinstitute/viral-ngs   "bash"    8 minutes ago   Up 8 minutes             intelligent_yalow
        docker commit 881a1ad6a990 own_viral_ngs
        docker image ls
        docker run -it own_viral_ngs bash
        #Change the path as "/opt/miniconda/envs/samtools-1.9-env/bin/samtools" in /work/bin/tools/samtools.py
        #         If another tool expect for samtools could not be installed, also use the same method above to install it on own_viral_ngs!
#DEBUG_1_BETTER_SIMPLE: TOOL_VERSION = '1.6' --> '1.9' in ~/DATA/Data_Huang_Human_herpesvirus_3/viralngs/bin/tools/samtools.py

#BUG_2:
        bin/taxon_filter.py deplete data/00_raw/2040_04.bam tmp/01_cleaned/2040_04.raw.bam tmp/01_cleaned/2040_04.bmtagger_depleted.bam tmp/01_cleaned/2040_04.rmdup.bam data/01_cleaned/2040_04.cleaned.bam --bmtaggerDbs /home/jhuang/REFs/viral_ngs_dbs/bmtagger_dbs_remove/hg19 /home/jhuang/REFs/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3 /home/jhuang/REFs/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA --blastDbs /home/jhuang/REFs/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters /home/jhuang/REFs/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus --threads 15 --srprismMemory 14250 --JVMmemory 50g --loglevel DEBUG
        #2025-05-23 09:58:45,326 - __init__:445:_attempt_install - DEBUG - Currently installed version of blast: 2.7.1-h4422958_6
        #2025-05-23 09:58:45,327 - __init__:448:_attempt_install - DEBUG - Expected version of blast:            2.6.0
        #2025-05-23 09:58:45,327 - __init__:449:_attempt_install - DEBUG - Incorrect version of blast installed. Removing it...
#DEBUG_2: TOOL_VERSION = "2.6.0" --> "2.7.1" in ~/DATA/Data_Huang_Human_herpesvirus_3/viralngs/bin/tools/blast.py

#BUG_3:
        bin/read_utils.py bwamem_idxstats data/01_cleaned/1762_04.cleaned.bam /home/jhuang/REFs/viral_ngs_dbs/spikeins/ercc_spike-ins.fasta --outStats reports/spike_count/1762_04.spike_count.txt --minScoreToFilter 60 --loglevel DEBUG
#DEBUG_3: TOOL_VERSION = "0.7.15" --> "0.7.17" in ~/DATA/Data_Huang_Human_herpesvirus_3/viralngs/bin/tools/bwa.py

#BUG_4: FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/bin/trimmomatic': '/usr/local/bin/trimmomatic'
#DEBUG_4: TOOL_VERSION = "0.36" --> "0.38" in ~/DATA/Data_Huang_Human_herpesvirus_3/viralngs/bin/tools/trimmomatic.py

#BUG_5: FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/spades.py': '/usr/bin/spades.py'
#DEBUG_5:  TOOL_VERSION = "0.36" --> "0.38" in ~/DATA/Data_Huang_Human_herpesvirus_3/viralngs/bin/tools/trimmomatic.py
#                def install_and_get_path(self):
#                        # the conda version wraps the jar file with a shell script
#                        return 'trimmomatic'


docker run -it -v /mnt/md1/DATA/Data_Huang_Human_herpesvirus_3/viralngs:/work -v /home/jhuang/REFs:/home/jhuang/REFs -v /home/jhuang/Tools/GenomeAnalysisTK-3.6:/home/jhuang/Tools/GenomeAnalysisTK-3.6 -v /home/jhuang/Tools/novocraft_v3:/home/jhuang/Tools/novocraft_v3    own_viral_ngs bash
cd /work
snakemake --directory /work --printshellcmds --cores 40

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