add pbipa #966
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add pbipa #966
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erinyoung
approved these changes
Apr 23, 2024
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Looks like the tests worked.
#11 101.5 config:{'advanced_options': '', 'coverage': 0, 'genome_size': 0, 'm4filt_high_copy_sample_rate': 1.0, 'max_nchunks': 40, 'nproc': 4, 'phase_run': 1, 'polish_run': 1, 'purge_dups_calcuts': '', 'purge_dups_run': 1, 'reads_fn': 'RUN/input.fofn', 'tmp_dir': '/tmp'}
#11 101.5 >ctg/b/l/000000/1 LN:i:13806 RC:i:74 XC:f:1.000000
#11 101.5 AACACTGGAGCATTACAAAATCTTGCAGACAGATACGATAACTTGAGCAACCTTTTAAACCAATACAATTACTTAAATTCCTTAGTCAATCTAGCCAGCACGCCTAGCGCGATTACCGGTGCGATTGACAATCTAAGCTCAAGCGCGATCAATCTCACTAGCGCTACCACCACTTCTCCGGCCTATCAAGCTGTGGCTTTAGCGCTCAATGCGGCTGTGGGCATGTGGCAAGTCATAGCCTTTGGCATCAGCTGTGGCCCTGGCCCCAATCTTGGCCCAGAACATTTAGAAAATGGGGGCGTTCGATCGTTTGACAACACGCCAAACTACAGCTACAACACCGGTAGCGGAACGACCACCACCACTTGTAATGGAGCCAGTAATGTAGGGCCCAATGGTATCCTATCTAGCAGCGAATACCAGGTTCTCAATACCGCTTATCAAACTATCCAAACCGCTTTAAACCAAAACCAAGGAGGCGGGATGCCTGCCTTGAATAGCTCCAAAAATATGGTAGTCAATATCAATCAAACTTTCACAAAAAACCCTACCACAGAATACACTTACCCCGATGGGAATGGCAATTATTATTCAGGCGGTTCATCAATCCCAATCCAGCTAAAGATTAGTAGCGTCAATGACGCTGAAAACCTTTTGCAACAAGCCGCTACTATCATCAATGTCCTTACCACCCAAAACCCGCATGTGAATGGTGGCGGTGGGGCATGGGGGTTTGGCGGTAAGACCGGGAATGTGATGGATATTTTTGGCGATAGTTTTAACGCTATTAACGAAATGATCAAAAACGCTCAAGCCGTTTTAGAAAAAACCCAACAGCTTAACGCTAATGAAAACACCCAAATCACGCAACCAGACAATTTCAACCCCTACACTTCTAAAGACACGCAGTTCGCTCAAGAAATGCTCAATAGAGCTAACGCTCAAGCAG
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I don't have any changes to recommend. I'm going to merge this PR and deploy pbipa to dockerhub and quay with the tags 1.8.0 and latest |
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Thank you for putting this together! You can check the status of the deploy here: https://github.com/StaPH-B/docker-builds/actions/runs/8803935182 |
erinyoung
reviewed
Apr 23, 2024
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| RUN micromamba install --name base -c conda-forge -c bioconda python=3.8 pbipa=${IPA_VER} && \ | ||
| eval "$(micromamba shell hook --shell bash)" &&\ |
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This line indicates that this was painful to install. Thank you for your hard work!
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Related #926
After a lot of iteration, I finally found a working recipe.
PacBio distributes the program as pbipa on conda, although its name is ipa. We can deploy as pbipa too. So I created its directory as pbipa.
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15)spades/3.12.0/Dockerfile)shigatyper/2.0.1/test.sh)spades/3.12.0/README.md)