Mercurial > repos > jpayne > seqsero2s

annotate misc/bioconda-recipes-seqsero2s-meta.yml @ 9:4c4899031795 draft

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planemo upload commit fcafae43456eb929e62b5c879ac954f75745bbf8
author galaxytrakr
date Fri, 15 May 2026 11:44:48 +0000
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1 {% set name = "SeqSero2S" %}
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2 {% set version = "1.1.4" %}
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3 {% set release = "89f1f5aca7a8819ee96239592fedd2e737036ada" %}
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4 {% set sha256 = "995f1815cc6cee7b8e37604b068bbec673e2ee8880e41adf6df0350966fe4c65" %}
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5
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6 package:
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7 name: {{ name|lower }}
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8 version: {{ version }}
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9
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10 source:
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11 url: https://github.com/LSTUGA/SeqSero2S/archive/refs/tags/v{{ version }}.tar.gz
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12 sha256: {{ sha256 }}
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13
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14 build:
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15 number: 2
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16 noarch: python
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17 script:
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18 - {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
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19 # patch stringMLST.py log path: replace dbPrefix reference with cwd to avoid
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20 # patches ALL occurrences (at line 1464 and predict section at line 1478).
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21 - bash $RECIPE_DIR/patch_stringmlst.sh
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22 run_exports:
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23 - {{ pin_subpackage(name|lower, max_pin="x.x") }}
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24
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25 requirements:
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26 host:
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27 - python >=3
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28 - pip
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29 - setuptools
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30 - stringmlst >=0.6
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31 run:
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32 - python >=3
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33 - blast >=2.2
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34 - zstd # libzstd.so.1 required by blastn binary
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35 - samtools
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36 - bedtools >=2.17
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37 - sra-tools >=2.8
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38 - spades >=3.9
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39 - salmid
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40 - bwa >=0.7
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41 - seqtk >=1.3
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42 - stringmlst >=0.6
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43 - mlst >=2.32.2
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44
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45 test:
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46 commands:
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47 - SeqSero2S.py -h
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48 - blastn -help
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49 - SalmID.py -h
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50 - mlst -h
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51
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52 about:
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53 home: "https://github.com/LSTUGA/{{ name }}"
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54 license: "GPL-2.0-or-later"
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55 license_family: GPL
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56 license_file: 'LICENSE'
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57 summary: "Simplified Salmonella serotype prediction from genome sequencing data"
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58 dev_url: "https://github.com/LSTUGA/{{ name }}"
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59
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60 extra:
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61 recipe-maintainers:
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62 - LSTUGA
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63 - crashfrog
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64 - biocoder
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65 identifiers:
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66 - doi:10.1128/aem.02600-24
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67