diff --git a/recipes/mango/build.sh b/recipes/mango/build.sh new file mode 100644 index 0000000000000..14d7462e70205 --- /dev/null +++ b/recipes/mango/build.sh @@ -0,0 +1,36 @@ +#!/bin/bash + +BINARY_HOME=$PREFIX/bin +PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM + +mkdir -p $BINARY_HOME +mkdir -p $PACKAGE_HOME + +ls $PACKAGE_HOME +cp -R core/* $PACKAGE_HOME + +for f in $PACKAGE_HOME/bin/* ; do + if [[ -f $f ]] ; then + ln -s $f $BINARY_HOME/ + fi +done + +# modin +$PYTHON -m pip install python_modin/.[dask] --no-deps --ignore-installed -vv + +# adam +$PYTHON -m pip install python_adam/. --no-deps --ignore-installed -vv + +# mangos +$PYTHON -m pip install python/. --no-deps --ignore-installed -vv + +$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 + +mkdir -p $PREFIX/mango-assembly/target +for f in $PACKAGE_HOME/repo/*.jar ; do + ln -s $f $PREFIX/mango-assembly/target/ +done diff --git a/recipes/mango/meta.yaml b/recipes/mango/meta.yaml new file mode 100644 index 0000000000000..19a109ac1bc88 --- /dev/null +++ b/recipes/mango/meta.yaml @@ -0,0 +1,87 @@ +{% set name = "bdgenomics.mango" %} +{% set pileup_name = "bdgenomics.mango.pileup" %} +{% set adam_name = "bdgenomics.adam" %} + +{% 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" %} + +# 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 + +package: + name: "mango" + version: "{{ version }}" + +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 + +build: + number: 0 + noarch: python + +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 + +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 + +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" + +extra: + recipe-maintainers: + - akmorrow13