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Patch ncbi-genome-download recipe #41640

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Merged
merged 4 commits into from
Jun 23, 2023
Merged

Patch ncbi-genome-download recipe #41640

merged 4 commits into from
Jun 23, 2023

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rpetit3
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@rpetit3 rpetit3 commented Jun 22, 2023

There has been a recent change to a header in a file parsed by ncbi-genome-download.

This patch incorporates an open PR to ncbi-genome-download: kblin/ncbi-genome-download#210 which is related to this issue kblin/ncbi-genome-download#209

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@rpetit3 rpetit3 mentioned this pull request Jun 22, 2023
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rpetit3 commented Jun 22, 2023

@BiocondaBot please fetch artifacts

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Package(s) built on Azure are ready for inspection:

Arch Package Zip File
noarch ncbi-genome-download-0.3.1-pyh7cba7a3_1.tar.bz2 LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package Tag Install with docker
ncbi-genome-download 0.3.1--pyh7cba7a3_1
showgzip -dc LinuxArtifacts/images/ncbi-genome-download:0.3.1--pyh7cba7a3_1.tar.gz | docker load

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rpetit3 commented Jun 22, 2023

@BiocondaBot please fetch artifacts

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Package(s) built on Azure are ready for inspection:

Arch Package Zip File
noarch ncbi-genome-download-0.3.1-pyh7cba7a3_1.tar.bz2 LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package Tag Install with docker
ncbi-genome-download 0.3.1--pyh7cba7a3_1
showgzip -dc LinuxArtifacts/images/ncbi-genome-download:0.3.1--pyh7cba7a3_1.tar.gz | docker load

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rpetit3 commented Jun 23, 2023

@BiocondaBot please fetch artifacts

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Package(s) built on Azure are ready for inspection:

Arch Package Zip File
noarch ncbi-genome-download-0.3.1-pyh7cba7a3_1.tar.bz2 LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package Tag Install with docker
ncbi-genome-download 0.3.1--pyh7cba7a3_1
showgzip -dc LinuxArtifacts/images/ncbi-genome-download:0.3.1--pyh7cba7a3_1.tar.gz | docker load

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rpetit3 commented Jun 23, 2023

@BiocondaBot please fetch artifacts

@BiocondaBot
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Package(s) built on Azure are ready for inspection:

Arch Package Zip File
noarch ncbi-genome-download-0.3.1-pyh7cba7a3_1.tar.bz2 LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package Tag Install with docker
ncbi-genome-download 0.3.1--pyh7cba7a3_1
showgzip -dc LinuxArtifacts/images/ncbi-genome-download:0.3.1--pyh7cba7a3_1.tar.gz | docker load

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rpetit3 commented Jun 23, 2023

Testing

Current version build (0)

mamba create -n temp-ngd -c conda-forge -c bioconda ncbi-genome-download
...
+ ncbi-genome-download     0.3.1  pyh5e36f6f_0        bioconda/noarch          Cached
...
mamba activate temp-ngd
ncbi-genome-download \
     -s genbank -A GCA_029448725.1 --formats fasta all \
      \
     --output-folder ./ \
     --flat-output
Traceback (most recent call last):
  File "/home/robert_petit/miniconda3/envs/temp-ngd/bin/ncbi-genome-download", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/robert_petit/miniconda3/envs/temp-ngd/lib/python3.11/site-packages/ncbi_genome_download/__main__.py", line 26, in main
    ret = args_download(args)
          ^^^^^^^^^^^^^^^^^^^
  File "/home/robert_petit/miniconda3/envs/temp-ngd/lib/python3.11/site-packages/ncbi_genome_download/core.py", line 178, in args_download
    return config_download(config)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/robert_petit/miniconda3/envs/temp-ngd/lib/python3.11/site-packages/ncbi_genome_download/core.py", line 197, in config_download
    download_candidates = select_candidates(config)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/robert_petit/miniconda3/envs/temp-ngd/lib/python3.11/site-packages/ncbi_genome_download/core.py", line 308, in select_candidates
    for entry in filter_entries(entries, config):
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/robert_petit/miniconda3/envs/temp-ngd/lib/python3.11/site-packages/ncbi_genome_download/core.py", line 354, in filter_entries
    if not config.is_compatible_assembly_accession(entry['assembly_accession']):
                                                   ~~~~~^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'assembly_accession'

With patched version

conda activate
mamba create -n temp-ngd-patch -c conda-forge -c bioconda appdirs python 'requests>=2.4.3' tqdm
conda activate temp-ngd-patch
wget  -O LinuxArtifacts.zip https://artprodsu6weu.artifacts.visualstudio.com/A27bcc0f9-b22c-4418-83d8-514809b37fb2/25074ded-3133-43ca-af80-895ab87b53cb/_apis/artifact/cGlwZWxpbmVhcnRpZmFjdDovL2Jpb2NvbmRhL3Byb2plY3RJZC8yNTA3NGRlZC0zMTMzLTQzY2EtYWY4MC04OTVhYjg3YjUzY2IvYnVpbGRJZC8zNTM3Mi9hcnRpZmFjdE5hbWUvTGludXhBcnRpZmFjdHM1/content?format=zip
unzip LinuxArtifacts.zip
conda install LinuxArtifacts/packages/noarch/ncbi-genome-download-0.3.1-pyh7cba7a3_1.tar.bz2
conda env export | grep ncbi
  - ncbi-genome-download=0.3.1=pyh7cba7a3_1
  
ncbi-genome-download \
     -s genbank -A GCA_029448725.1 --formats fasta all \
      \
     --output-folder ./ \
     --flat-output

ls -lh GCA*
-rw-r--r-- 1 robert_petit robert_petit 639M Jun 23 01:17 GCA_029448725.1_ASM2944872v1_genomic.fna.gz

I think we are good here

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rpetit3 commented Jun 23, 2023

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Jun 23, 2023
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rpetit3 commented Jun 23, 2023

Thank you!

@rpetit3 rpetit3 merged commit 332d619 into bioconda:master Jun 23, 2023
@rpetit3 rpetit3 deleted the rp3-patch-ngd branch June 23, 2023 15:35
@matinnuhamunada matinnuhamunada mentioned this pull request Jun 27, 2023
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@taylorreiter taylorreiter mentioned this pull request Jun 29, 2023
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