Mercurial > repos > jpayne > seqsero2s

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit fcafae43456eb929e62b5c879ac954f75745bbf8
author galaxytrakr
date Fri, 15 May 2026 11:44:48 +0000
parents
children
comparison
equal deleted inserted replaced
8:e3b5ed54af18 9:4c4899031795
1 {% set name = "SeqSero2S" %}
2 {% set version = "1.1.4" %}
3 {% set release = "89f1f5aca7a8819ee96239592fedd2e737036ada" %}
4 {% set sha256 = "995f1815cc6cee7b8e37604b068bbec673e2ee8880e41adf6df0350966fe4c65" %}
5
6 package:
7 name: {{ name|lower }}
8 version: {{ version }}
9
10 source:
11 url: https://github.com/LSTUGA/SeqSero2S/archive/refs/tags/v{{ version }}.tar.gz
12 sha256: {{ sha256 }}
13
14 build:
15 number: 2
16 noarch: python
17 script:
18 - {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
19 # patch stringMLST.py log path: replace dbPrefix reference with cwd to avoid
20 # patches ALL occurrences (at line 1464 and predict section at line 1478).
21 - bash $RECIPE_DIR/patch_stringmlst.sh
22 run_exports:
23 - {{ pin_subpackage(name|lower, max_pin="x.x") }}
24
25 requirements:
26 host:
27 - python >=3
28 - pip
29 - setuptools
30 - stringmlst >=0.6
31 run:
32 - python >=3
33 - blast >=2.2
34 - zstd # libzstd.so.1 required by blastn binary
35 - samtools
36 - bedtools >=2.17
37 - sra-tools >=2.8
38 - spades >=3.9
39 - salmid
40 - bwa >=0.7
41 - seqtk >=1.3
42 - stringmlst >=0.6
43 - mlst >=2.32.2
44
45 test:
46 commands:
47 - SeqSero2S.py -h
48 - blastn -help
49 - SalmID.py -h
50 - mlst -h
51
52 about:
53 home: "https://github.com/LSTUGA/{{ name }}"
54 license: "GPL-2.0-or-later"
55 license_family: GPL
56 license_file: 'LICENSE'
57 summary: "Simplified Salmonella serotype prediction from genome sequencing data"
58 dev_url: "https://github.com/LSTUGA/{{ name }}"
59
60 extra:
61 recipe-maintainers:
62 - LSTUGA
63 - crashfrog
64 - biocoder
65 identifiers:
66 - doi:10.1128/aem.02600-24
67