Add GenoFLU dependencies

[joverlee521]

Description of proposed changes

Add dependencies for GenoFLU to run in avian-flu:

• ncbi-blast+
• openpyxl (for pandas.read_excel)

Related issue(s)

Resolves #242

Checklist

• Checks pass

[jameshadfield]

Awesome! I haven't tested, but I can if it'd be helpful.

[joverlee521]

Awesome! I haven't tested, but I can if it'd be helpful.

Thanks! I left the example command in nextstrain/avian-flu#127 (comment).

[joverlee521]

Ah, just caught up on conversation in #127.

Worth noting this is installing https://packages.debian.org/bookworm/ncbi-blast+ which is v2.12.0.

[jameshadfield]

Tested this via the nextstrain/base:branch-genoflu-deps image and all works. As a bonus it's faster than the homebrew MacOS blast!

LGTM

[joverlee521]

Re: whether this significantly increases the image size:

os/arch	latest size	branch size
linux/amd64	704.38 MB	728.54 MB
linux/arm64	686.68 MB	710.64 MB

[jameshadfield]

Pasting here the error you get if you try to run GenoFLU (which needs the blast tools added in this PR) with an older docker image:

        python ./vendored-GenoFLU-multi/bin/genoflu-multi.py             -f fauna/data/genoflu/             -n 1 > fauna/logs/run_genoflu.txt
        
cat: write error: Broken pipe
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/usr/local/lib/python3.10/multiprocessing/pool.py", line 51, in starmapstar
    return list(itertools.starmap(args[0], args[1]))
  File "/nextstrain/build/ingest/./vendored-GenoFLU-multi/bin/genoflu-multi.py", line 41, in run_genoflu
    genoflu.blast_hpai_genomes()
  File "/nextstrain/build/ingest/vendored-GenoFLU-multi/bin/genoflu.py", line 202, in blast_hpai_genomes
    blast_hpai_genotyping = Blast_Fasta(
  File "/nextstrain/build/ingest/vendored-GenoFLU-multi/bin/genoflu.py", line 70, in __init__
    with open(blastout_file, 'r') as blast_file:
FileNotFoundError: [Errno 2] No such file or directory: 'fauna/data/genoflu/temp/1/temp_blast_out.txt'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/nextstrain/build/ingest/./vendored-GenoFLU-multi/bin/genoflu-multi.py", line 197, in <module>
    pool_data = pool.starmap(run_genoflu, zip(split_strain_records, range(1,cores+1)))
  File "/usr/local/lib/python3.10/multiprocessing/pool.py", line 375, in starmap
    return self._map_async(func, iterable, starmapstar, chunksize).get()
  File "/usr/local/lib/python3.10/multiprocessing/pool.py", line 774, in get
    raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'fauna/data/genoflu/temp/1/temp_blast_out.txt'
[Sun Feb 23 22:23:03 2025]
Error in rule run_genoflu:
    jobid: 20
    input: fauna/data/genoflu/sequences_pb2.fasta, fauna/data/genoflu/sequences_pb1.fasta, fauna/data/genoflu/sequences_pa.fasta, fauna/data/genoflu/sequences_ha.fasta, fauna/data/genoflu/sequences_np.fasta, fauna/data/genoflu/sequences_na.fasta, fauna/data/genoflu/sequences_mp.fasta, fauna/data/genoflu/sequences_ns.fasta
    output: fauna/data/genoflu/results/results.tsv
    log: fauna/logs/run_genoflu.txt (check log file(s) for error details)
    shell:
        
        python ./vendored-GenoFLU-multi/bin/genoflu-multi.py             -f fauna/data/genoflu/             -n 1 > fauna/logs/run_genoflu.txt
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)