Hello again, Galaxyans! Long time no see…
Bug on NCBI Datasets Genomes tool
Seems like the - - force option broke the wrapper after the new version of the tool
New version of client (18.25.1) available at https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets.
Error: field(s) [--force] not recognized.
Use dataformat tsv genome <command> --help for detailed help about a command.
Tool:
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_genome/18.24.0+galaxy0
Command:
[ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem"; datasets download genome accession 'GCF_904425465.1' --assembly-version latest --include genome,rna,protein,cds,gff3,gtf,gbff,seq-report --no-progressbar --dehydrated && dataformat tsv genome --package ncbi_dataset.zip --fields --force > genome_data_report.tsv && unzip ncbi_dataset.zip && datasets rehydrate --directory ./ --gzip --max-workers ${NCBI_DATASETS_MAX_WORKERS:-10} && find ncbi_dataset \( -name "*.faa" -o -name "*.fna" -o -name "*.faa.gz" -o -name "*.fna.gz" \) -exec sh -c 'mv {} $(echo {} | sed "s/.f[an]a\(.gz\)\?$/.fasta\1/")' \; && find ncbi_dataset -name "*.jsonl.gz" -exec sh -c 'mv {} $(dirname {})/$(basename {} .gz)' \; && find ncbi_dataset \( -name "*.gz" ! -name "*fasta.gz" \) -exec gunzip {} \; && find ncbi_dataset -name "*fasta.gz" -exec gunzip {} \; && find ncbi_dataset -name sequence_report.jsonl -exec sh -c 'dataformat tsv genome-seq --inputfile {} > $(dirname {})/$(basename {} .jsonl).tsv' \; && true
Thanks!