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added receipe for bdgenomics.mango (#17960)
* added receipe for bdgenomics.mang * updated mango recipe * Update meta.yaml * update * added patches * some adjustments * oops * remove patches and cleanup * added back deleted recipe * removed SP_DIR for mulled tests
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#!/bin/bash | ||
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BINARY_HOME=$PREFIX/bin | ||
PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM | ||
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mkdir -p $BINARY_HOME | ||
mkdir -p $PACKAGE_HOME | ||
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ls $PACKAGE_HOME | ||
cp -R core/* $PACKAGE_HOME | ||
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for f in $PACKAGE_HOME/bin/* ; do | ||
if [[ -f $f ]] ; then | ||
ln -s $f $BINARY_HOME/ | ||
fi | ||
done | ||
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# modin | ||
$PYTHON -m pip install python_modin/.[dask] --no-deps --ignore-installed -vv | ||
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# adam | ||
$PYTHON -m pip install python_adam/. --no-deps --ignore-installed -vv | ||
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# mangos | ||
$PYTHON -m pip install python/. --no-deps --ignore-installed -vv | ||
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$PYTHON -m pip install python_pileup/. --no-deps --ignore-installed -vv | ||
# # Enable widget | ||
# jupyter nbextension enable --py widgetsnbextension | ||
# jupyter nbextension install --py --symlink --user bdgenomics.mango.pileup | ||
# jupyter nbextension enable bdgenomics.mango.pileup --user --py | ||
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mkdir -p $PREFIX/mango-assembly/target | ||
for f in $PACKAGE_HOME/repo/*.jar ; do | ||
ln -s $f $PREFIX/mango-assembly/target/ | ||
done |
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{% set name = "bdgenomics.mango" %} | ||
{% set pileup_name = "bdgenomics.mango.pileup" %} | ||
{% set adam_name = "bdgenomics.adam" %} | ||
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{% set version = "0.0.5" %} | ||
{% set pileup_version = "0.0.5" %} | ||
{% set adam_version = "0.30.0a0" %} | ||
{% set modin_name = "modin" %} | ||
{% set modin_version = "0.6.1" %} | ||
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# Current issues: | ||
# 1: modin and ray are not on conda | ||
## current issue in modin is that non-ray build still tries to pull | ||
## from ray modules, which causes an error because ray is not on conda | ||
## solution: need to wait until modin is on conda | ||
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package: | ||
name: "mango" | ||
version: "{{ version }}" | ||
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source: | ||
- url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/mango/mango-distribution/{{ version }}/mango-distribution-{{ version }}-bin.tar.gz | ||
md5: fb9c822dcc0ea1a13766d7faf3413af5 | ||
folder: core | ||
- url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz | ||
sha256: 12dc1b334597481b2caa3988417cb6742569585fd1f056c02adfce2b1f208467 | ||
folder: python | ||
- url: https://pypi.io/packages/source/{{ pileup_name[0] }}/{{ pileup_name }}/{{ pileup_name }}-{{ pileup_version }}.tar.gz | ||
sha256: bc35dae68a5541ba663d07f35ffdfb2534c33892e13a1dd8e68929a961b123d9 | ||
folder: python_pileup | ||
- url: https://pypi.io/packages/source/{{ adam_name[0] }}/{{ adam_name }}/{{ adam_name }}-{{ adam_version }}.tar.gz | ||
sha256: bfb9e5f0f2bf887a63eebc994d9d6c3d7606e1e9504b88426972b170b7d6f4a9 | ||
folder: python_adam | ||
- url: https://pypi.io/packages/source/{{ modin_name[0] }}/{{ modin_name }}/{{ modin_name }}-{{ modin_version }}.tar.gz | ||
sha256: 0b9b407ce9ba0907aae6c54d221e59e80d2d7a9b7a8510416625d5f4b9e83762 | ||
folder: python_modin | ||
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build: | ||
number: 0 | ||
noarch: python | ||
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requirements: | ||
host: | ||
- pip | ||
- psutil | ||
- python >3 | ||
- jupyter ==1.0.0 | ||
run: | ||
- dask | ||
- distributed | ||
- openjdk >=8,<9 | ||
- pyspark ==2.4.4 | ||
- psutil | ||
- python >3 | ||
- cigar ==0.1.3 | ||
- ipython ==7.8.0 | ||
- ipywidgets ==7.0.0 | ||
- matplotlib ==2.0.2 | ||
- ipykernel >=5.1.2 | ||
- widgetsnbextension >=3.5.0 | ||
- pandas ==0.25.1 # required by modin | ||
- traitlets >=4.3.0,<5.0 # required by jupyter widget | ||
- traittypes >=0.0.6 # required by jupyter widget | ||
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test: | ||
imports: | ||
- modin | ||
- bdgenomics | ||
- bdgenomics.adam | ||
- bdgenomics.mango | ||
# - bdgenomics.mango.io needs modin fix in conda | ||
# - bdgenomics.mango.pileup needs modin fix | ||
commands: | ||
- mango-submit --help | ||
- SPARK_HOME=$(python -c "import site,os; print(os.path.join(site.getsitepackages()[0], \"pyspark\"))" ) mango-notebook --help | ||
- make_genome --help | ||
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about: | ||
home: "https://github.com/bdgenomics/mango" | ||
license: "Apache 2" | ||
summary: "A scalable genomic visualization tool" | ||
doc_url: "https://bdg-mango.readthedocs.io/en/latest/" | ||
dev_url: "https://github.com/bigdatagenomics/mango" | ||
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extra: | ||
recipe-maintainers: | ||
- akmorrow13 |