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FRED2 as a conda package #11469

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merged 4 commits into from
Oct 22, 2018
Merged

FRED2 as a conda package #11469

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66aa4e4
Attempt to get FRED2 as a conda package
apeltzer Oct 21, 2018
cebbe32
SHA update
apeltzer Oct 21, 2018
58dc4a9
99 little bugs in the code
apeltzer Oct 21, 2018
bed0300
Fix things Björn mentioned
apeltzer Oct 22, 2018
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3 changes: 3 additions & 0 deletions recipes/fred/build.sh
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Original file line number Diff line number Diff line change
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#Patch away the install requires, we're getting these through conda directly
sed -i 's/install_requires/#install_requires/g' setup.py
$PYTHON setup.py install
49 changes: 49 additions & 0 deletions recipes/fred/meta.yaml
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{% set name = "fred" %}
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should that be fred2?

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Hm, could be - should I rename it ?

{% set version = "2.0.2" %}
{% set sha256 = "223f139b35357e25d98644eb2668b9140f1489f4befd1e337a83fa6253cc0d54" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://github.com/FRED-2/Fred2/archive/{{ version }}.tar.gz
sha256: '{{ sha256 }}'

build:
noarch: python
number: 0
skip: True # [not py27]

requirements:
host:
- python
- setuptools
- pyomo
- pandas
- pyvcf
- biopython
- mysql-python
run:
- python
- setuptools
- pyomo
- pandas
- pyvcf
- biopython
- mysql-python

test:
commands:
- python -c "from Fred2.Core import Allele, Peptide, Protein,generate_peptides_from_proteins"

about:
home: http://nf-co.re/
license: MIT
summary: 'Python package with helper tools for the nf-core community.'

extra:
container:
# click requires a unicode locale when used with Python 3
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But you are not using click here isn't it?

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Whoops, thats a relict of my template. I'll remove it.

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Changed it, renamed the package as well to fred2

# extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly
extended-base: true