Hello, I got the same error as #209, is it fixed?

@SolMiele Did you try installing this pull request?
e.g.

pip uninstall ncbi-genome-download
pip install git+https://github.com/chasemc/ncbi-genome-download@4c5c24e27aa8123c7995890046b17b815da3571b

Note: I haven't fully tested it but it did work with ncbi-genome-download -s refseq --assembly-accessions GCF_000525635.1 bacteria

It works for me and downloaded 40,000 bacterial genomes from genbank and refseq

Hello! I tried this :

pip uninstall ncbi-genome-download

pip install git+https://github.com/chasemc/ncbi-genome-download@4c5c24e27aa8123c7995890046b17b815da3571b

and my command like this:

ncbi-genome-download --assembly-accessions "GCA_001951075.2" bacteria,archaea -l "complete" --section genbank --formats fasta --flat-output -o ./

but it does not work. So , what should I do ? Can you hepl me ? The same error as #209, is it fixed?

Hello, I tried the pip uninstall ncbi-genome-download pip install git+https://github.com/chasemc/ncbi-genome-download@4c5c24e27aa8123c7995890046b17b815da3571b

and then tried ncbi-genome-download --genera Streptomyces bacteria --dry-run | head

Seems to be working to some point but I also get an error message at the end. @ialbert Please see the following. Using NCBI-genome-download --genera Streptomyces bacteria --dry-run | head - capital letters for NCBI as in the handbook still says command not found.

Considering the following 2815 assemblies for download:
GCF_003208035.1 Streptomyces actuosus   ATCC 25421
GCF_016921115.1 Streptomyces actuosus   VRA1
GCF_000156475.1 Streptomyces albidoflavus       J1074
GCF_000359525.1 Streptomyces albidoflavus       J1074
GCF_000719495.1 Streptomyces albidoflavus       NRRL F-5621
GCF_000719435.1 Streptomyces albidoflavus       NRRL F-5618
GCF_000719955.1 Streptomyces albidoflavus       NRRL B-1271
GCF_000717375.1 Streptomyces albidoflavus       NRRL B-2307
GCF_001509565.1 Streptomyces albidoflavus       NRRL WC-3066
Traceback (most recent call last):
  File "/home/bstarnush/miniconda3/bin/ncbi-genome-download", line 8, in <module>
    sys.exit(main())
  File "/home/bstarnush/miniconda3/lib/python3.10/site-packages/ncbi_genome_download/__main__.py", line 26, in main
    ret = args_download(args)
  File "/home/bstarnush/miniconda3/lib/python3.10/site-packages/ncbi_genome_download/core.py", line 184, in args_download
    return config_download(config)
  File "/home/bstarnush/miniconda3/lib/python3.10/site-packages/ncbi_genome_download/core.py", line 212, in config_download
    print(entry['assembly_accession'], entry['organism_name'], get_strain(entry), sep="\t")
BrokenPipeError: [Errno 32] Broken pipe

The proposed fix should work, so it's likely that it's an issue with installing the PR.

Python is pretty notoriously difficult when dealing with package versions and I'm no expert pip's installation details but that's likely why it seems it's not working.

Change the my_directory variable below to point to a path on your computer

my_directory='/home/chase/Downloads/ncbi-genome-download'

python3 -m venv dl $my_directory
source $my_directory
pip install git+https://github.com/chasemc/ncbi-genome-download@4c5c24e27aa8123c7995890046b17b815da3571b 

Then $my_directory will have a bin directory containing ncbi-genome-download
Use the activated environment to run it or by using the path directly
e.g. $my_directory/bin/ncbi-genome-download

@nush320 that is a different issue related to implementation (without the pipe to head should work)
see https://docs.python.org/3/library/signal.html#note-on-sigpipe

@chasemc as a temporary solution I used your changes to patch the Bioconda recipe

Thanks for this, I ended up solving it slightly different in bd46071. Should be fixed in 0.3.2