added receipe for bdgenomics.mango

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

recipes/mango/meta.yaml

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+{% 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