From 68c3cbdbcce34aa2241a68c3bf20abb325ddd137 Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Tue, 8 Oct 2019 11:29:32 -0700
Subject: [PATCH 01/10] added receipe for bdgenomics.mang

---
 recipes/mango/build.sh  | 14 ++++++++++++++
 recipes/mango/meta.yaml | 38 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+)
 create mode 100644 recipes/mango/build.sh
 create mode 100644 recipes/mango/meta.yaml

diff --git a/recipes/mango/build.sh b/recipes/mango/build.sh
new file mode 100644
index 0000000000000..7b2e56cc41db0
--- /dev/null
+++ b/recipes/mango/build.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+BINARY_HOME=$PREFIX/bin
+PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+
+mkdir -p $BINARY_HOME
+mkdir -p $PACKAGE_HOME
+
+cp -R * $PACKAGE_HOME
+
+ln -s $PACKAGE_HOME/bin/mango-notebook $BINARY_HOME
+ln -s $PACKAGE_HOME/bin/mango-submit $BINARY_HOME
+ln -s $PACKAGE_HOME/bin/make_genome $BINARY_HOME
+
diff --git a/recipes/mango/meta.yaml b/recipes/mango/meta.yaml
new file mode 100644
index 0000000000000..538bb8db79333
--- /dev/null
+++ b/recipes/mango/meta.yaml
@@ -0,0 +1,38 @@
+{% set version="0.0.5" %}
+
+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: f438bdbe93e855db1dae077fa28ff3f7
+
+build:
+  number: 0
+  noarch: generic
+
+requirements:
+  host:
+    - python >3
+    - pip
+  run:
+    - python
+    - bdgenomics.mango =={{ version }}
+    - bdgenomics.mango.pileup =={{ version }}
+    - openjdk >=8,<9
+    - pyspark
+
+test:
+  # Python imports
+  imports:
+    - bdgenomics.mango
+    - bdgenomics.mango.pileup
+  commands:
+    - mango-submit --help
+    - mango-notebook --help
+    - make_genome --help
+about:
+  home: https://github.com/bigdatagenomics/mango
+  license: Apache 2
+  summary: Scalable genomics visualization tool built on Apache Spark

From ac7a8e75fc6ace1cd6527795503b3e9862c0ad80 Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Tue, 8 Oct 2019 14:32:59 -0700
Subject: [PATCH 02/10] updated mango recipe

---
 recipes/mango/meta.yaml | 55 ++++++++++++++++++++++++++++++-----------
 1 file changed, 41 insertions(+), 14 deletions(-)

diff --git a/recipes/mango/meta.yaml b/recipes/mango/meta.yaml
index 538bb8db79333..fe6e8a54d3836 100644
--- a/recipes/mango/meta.yaml
+++ b/recipes/mango/meta.yaml
@@ -1,38 +1,65 @@
-{% set version="0.0.5" %}
+{% set name = "bdgenomics.mango" %}
+{% set version = "0.0.5" %}
 
 package:
-  name: mango
-  version: {{ version }}
+  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: f438bdbe93e855db1dae077fa28ff3f7
+  - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+    sha256: 12dc1b334597481b2caa3988417cb6742569585fd1f056c02adfce2b1f208467
+  - url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/mango/mango-distribution/{{ version }}/mango-distribution-{{ version }}-bin.tar.gz
+    md5: f438bdbe93e855db1dae077fa28ff3f7
+
 
 build:
-  number: 0
   noarch: generic
+  number: 0
+  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv "
 
 requirements:
   host:
-    - python >3
+    - bdgenomics.adam ==0.30.0a0
+    - bdgenomics.mango.pileup ==0.0.4
+    - cigar ==0.1.3
+    - ipython ==7.8.0
+    - ipywidgets ==7.0.0
+    - jupyter ==1.0.0
+    - matplotlib ==2.0.2
     - pip
-  run:
+    - psutil
     - python
-    - bdgenomics.mango =={{ version }}
-    - bdgenomics.mango.pileup =={{ version }}
+  run:
     - openjdk >=8,<9
     - pyspark
+    - bdgenomics.adam ==0.30.0a0
+    - bdgenomics.mango.pileup ==0.0.4
+    - cigar ==0.1.3
+    - ipython ==7.8.0
+    - ipywidgets ==7.0.0
+    - jupyter ==1.0.0
+    - matplotlib ==2.0.2
+    - psutil
+    - python
 
 test:
-  # Python imports
   imports:
+    - bdgenomics
     - bdgenomics.mango
+    - bdgenomics.mango.test
     - bdgenomics.mango.pileup
   commands:
     - mango-submit --help
     - mango-notebook --help
     - make_genome --help
+
 about:
-  home: https://github.com/bigdatagenomics/mango
-  license: Apache 2
-  summary: Scalable genomics visualization tool built on Apache Spark
+  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

From 6087fe9a10b5f593a300171e5de821d3540dd8fd Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@users.noreply.github.com>
Date: Wed, 9 Oct 2019 10:20:07 +0200
Subject: [PATCH 03/10] Update meta.yaml

---
 recipes/mango/meta.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/recipes/mango/meta.yaml b/recipes/mango/meta.yaml
index 538bb8db79333..3f00f220935b5 100644
--- a/recipes/mango/meta.yaml
+++ b/recipes/mango/meta.yaml
@@ -13,9 +13,6 @@ build:
   noarch: generic
 
 requirements:
-  host:
-    - python >3
-    - pip
   run:
     - python
     - bdgenomics.mango =={{ version }}

From 5d20ead6478958d56ece504381f6234e98219d05 Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Wed, 16 Oct 2019 12:00:17 -0700
Subject: [PATCH 04/10] update

---
 recipes/mango/build.sh  | 23 ++++++++++++-
 recipes/mango/meta.yaml | 73 ++++++++++++++++++++++++++++-------------
 recipes/ray/build.sh    | 11 -------
 recipes/ray/meta.yaml   | 36 --------------------
 4 files changed, 73 insertions(+), 70 deletions(-)
 delete mode 100644 recipes/ray/build.sh
 delete mode 100644 recipes/ray/meta.yaml

diff --git a/recipes/mango/build.sh b/recipes/mango/build.sh
index 7b2e56cc41db0..e934f3992c7fd 100644
--- a/recipes/mango/build.sh
+++ b/recipes/mango/build.sh
@@ -6,9 +6,30 @@ PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $BINARY_HOME
 mkdir -p $PACKAGE_HOME
 
-cp -R * $PACKAGE_HOME
+ls $PACKAGE_HOME
+cp -R core/* $PACKAGE_HOME
 
 ln -s $PACKAGE_HOME/bin/mango-notebook $BINARY_HOME
 ln -s $PACKAGE_HOME/bin/mango-submit $BINARY_HOME
 ln -s $PACKAGE_HOME/bin/make_genome $BINARY_HOME
 
+echo "PYTHON VERSION----"
+$PYTHON --version
+echo $PY_VER
+which $PYTHON
+which python3.7
+
+# modin
+$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
diff --git a/recipes/mango/meta.yaml b/recipes/mango/meta.yaml
index fe6e8a54d3836..62e9f388720ab 100644
--- a/recipes/mango/meta.yaml
+++ b/recipes/mango/meta.yaml
@@ -1,56 +1,85 @@
 {% 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: noarch not working for either python or generic
+## noarch generic uses a different python version in test, so imports will fail
+## noarch python makes symlinks not work from build script
+# 2: 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
+    patches:
+      - mango-notebook.patch
+      - mango-submit.patch
+      - make_genome.patch
   - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
     sha256: 12dc1b334597481b2caa3988417cb6742569585fd1f056c02adfce2b1f208467
-  - url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/mango/mango-distribution/{{ version }}/mango-distribution-{{ version }}-bin.tar.gz
-    md5: f438bdbe93e855db1dae077fa28ff3f7
-
+    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:
-  noarch: generic
   number: 0
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv "
+  noarch: python
 
 requirements:
   host:
-    - bdgenomics.adam ==0.30.0a0
-    - bdgenomics.mango.pileup ==0.0.4
-    - cigar ==0.1.3
-    - ipython ==7.8.0
-    - ipywidgets ==7.0.0
-    - jupyter ==1.0.0
-    - matplotlib ==2.0.2
     - pip
     - psutil
-    - python
+    - python >3
+    - jupyter ==1.0.0
   run:
+    - dask
+    - distributed
     - openjdk >=8,<9
-    - pyspark
-    - bdgenomics.adam ==0.30.0a0
-    - bdgenomics.mango.pileup ==0.0.4
+    - pyspark ==2.4.4
+    - psutil
+    - python >3
     - cigar ==0.1.3
     - ipython ==7.8.0
     - ipywidgets ==7.0.0
-    - jupyter ==1.0.0
     - matplotlib ==2.0.2
-    - psutil
-    - python
+    - 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.test
-    - bdgenomics.mango.pileup
+    # - bdgenomics.mango.io needs modin fix in conda
+    # - bdgenomics.mango.pileup needs modin fix
   commands:
     - mango-submit --help
-    - mango-notebook --help
+    - SPARK_HOME=$SP_DIR/pyspark mango-notebook --help
     - make_genome --help
 
 about:
diff --git a/recipes/ray/build.sh b/recipes/ray/build.sh
deleted file mode 100644
index 495a4945daec0..0000000000000
--- a/recipes/ray/build.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-
-mkdir -p $PREFIX/bin
-
-mkdir build
-cd build
-export MPICXX=$PREFIX/bin
-export OMPI_MCA_mpi_show_handle_leaks=1
-cmake . -DCMAKE_INSTALL_PREFIX=$PREFIX/bin ..
-make
-cp Ray $PREFIX/bin
diff --git a/recipes/ray/meta.yaml b/recipes/ray/meta.yaml
deleted file mode 100644
index 8fbc238c2987f..0000000000000
--- a/recipes/ray/meta.yaml
+++ /dev/null
@@ -1,36 +0,0 @@
-{% set name = "ray" %}
-{% set version = "2.3.1" %}
-
-package:
-  name: {{ name }}
-  version: {{ version }}
-
-source:
-  url: https://downloads.sourceforge.net/project/denovoassembler/Ray-{{ version }}.tar.bz2
-  md5: 82f693c4db60af4328263c9279701009
-
-build:
-  number: 1
-  skip: False
-
-requirements:
-  build:
-    - {{ compiler('c') }}
-    - openmpi >=2.0.2
-    - cmake
-
-  run:
-    - openmpi >=2.0.2
-
-test:
-  commands:
-    - which Ray # Ray -help requires ssh
-
-about:
-  home: 'http://denovoassembler.sourceforge.net/index.html'
-  license: GPL3
-  summary: "Parallel genome assemblies for parallel DNA sequencing"
-extra:
-  identifiers:
-    - biotools:ray
-    - doi:10.1186/gb-2012-13-12-r122

From ea0d8b619de78ab81762d39f7aaa5602ed5b0879 Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Wed, 16 Oct 2019 12:01:07 -0700
Subject: [PATCH 05/10] added patches

---
 recipes/mango/make_genome.patch    | 31 ++++++++++++++++++++++++++
 recipes/mango/mango-notebook.patch | 35 ++++++++++++++++++++++++++++++
 recipes/mango/mango-submit.patch   | 33 ++++++++++++++++++++++++++++
 3 files changed, 99 insertions(+)
 create mode 100644 recipes/mango/make_genome.patch
 create mode 100644 recipes/mango/mango-notebook.patch
 create mode 100644 recipes/mango/mango-submit.patch

diff --git a/recipes/mango/make_genome.patch b/recipes/mango/make_genome.patch
new file mode 100644
index 0000000000000..0146b94a470f2
--- /dev/null
+++ b/recipes/mango/make_genome.patch
@@ -0,0 +1,31 @@
+--- a/bin/make_genome
++++ b/bin/make_genome
+@@ -20,12 +20,20 @@
+ # Runs MakeGenome, which generates a .genome file containing reference, genes, cytoband, and chromsizes.
+ # Requires 2 arguments: genome name and output file to save .genome file to.
+
+-SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})
++# Find original directory of this script, resolving symlinks
++# https://stackoverflow.com/questions/59895/get-the-source-directory-of-a-bash-script-from-within-the-script-itself/246128#246128
++SOURCE="${BASH_SOURCE[0]}"
++while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
++  DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
++  SOURCE="$(readlink "$SOURCE")"
++  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
++done
++SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
+
+ # get Mango jar
+-MANGO_CLI_JAR=$(${SOURCE_DIR}/find-mango-assembly.sh)
++MANGO_CLI_JAR=$(${SCRIPT_DIR}/find-mango-assembly.sh)
+
+-SPARK_SUBMIT=$(${SOURCE_DIR}/find-spark.sh)
++SPARK_SUBMIT=$(${SCRIPT_DIR}/find-spark.sh)
+
+ # submit the job to Spark
+ "$SPARK_SUBMIT" \
+@@ -34,4 +42,3 @@
+   --conf spark.kryo.registrator=org.bdgenomics.mango.serialization.MangoKryoRegistrator \
+   $MANGO_CLI_JAR \
+   "MakeGenome" "$@" \
+-
diff --git a/recipes/mango/mango-notebook.patch b/recipes/mango/mango-notebook.patch
new file mode 100644
index 0000000000000..2ac93184cd938
--- /dev/null
+++ b/recipes/mango/mango-notebook.patch
@@ -0,0 +1,35 @@
+--- a/bin/mango-notebook
++++ b/bin/mango-notebook
+@@ -62,6 +62,16 @@
+   echo ${path}
+ }
+
++# Find original directory of this script, resolving symlinks
++# https://stackoverflow.com/questions/59895/get-the-source-directory-of-a-bash-script-from-within-the-script-itself/246128#246128
++SOURCE="${BASH_SOURCE[0]}"
++while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
++  DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
++  SOURCE="$(readlink "$SOURCE")"
++  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
++done
++SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
++
+ # Retrieve the path of py4j zip archive used by current spark
+ get_py4jzip(){
+   local -a py4j_zip_all_versions
+@@ -112,14 +122,13 @@
+ # variable declarations
+ trap 'err_report ${LINENO} $?' ERR
+ declare -r PY4J_ZIP=$(get_py4jzip)
+-declare -r SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})
+ declare mango_cli_jar=""
+ declare wrapper_path
+ declare pyspark=""
+ parse_args "$@"
+
+ # get Mango jar
+-mango_cli_jar=$(${SOURCE_DIR}/find-mango-assembly.sh)
++mango_cli_jar=$(${SCRIPT_DIR}/find-mango-assembly.sh)
+
+ # get pyspark path
+ if [[ -z "${SPARK_HOME}" ]]; then
diff --git a/recipes/mango/mango-submit.patch b/recipes/mango/mango-submit.patch
new file mode 100644
index 0000000000000..2c4b1c96e6d79
--- /dev/null
+++ b/recipes/mango/mango-submit.patch
@@ -0,0 +1,33 @@
+--- a/bin/mango-submit
++++ b/bin/mango-submit
+@@ -20,7 +20,15 @@
+ # usage: mango-submit [<spark-args> --] <mango-args>
+ set -e
+
+-SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})
++# Find original directory of this script, resolving symlinks
++# https://stackoverflow.com/questions/59895/get-the-source-directory-of-a-bash-script-from-within-the-script-itself/246128#246128
++SOURCE="${BASH_SOURCE[0]}"
++while [ -L "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
++  DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
++  SOURCE="$(readlink "$SOURCE")"
++  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
++done
++SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
+
+ # Split args into Spark and ADAM args
+ DD=False  # DD is "double dash"
+@@ -52,10 +60,11 @@
+
+
+ # get Mango jar
+-MANGO_CLI_JAR=$(${SOURCE_DIR}/find-mango-assembly.sh)
++MANGO_CLI_JAR=$(${SCRIPT_DIR}/find-mango-assembly.sh)
+
+-SPARK_SUBMIT=$(${SOURCE_DIR}/find-spark.sh)
++SPARK_SUBMIT=$(${SCRIPT_DIR}/find-spark.sh)
+ echo "Using spark-submit=$SPARK_SUBMIT" 1>&2
++ls "$(dirname "$( dirname "$SPARK_SUBMIT" )" )"
+
+ # submit the job to Spark
+ "$SPARK_SUBMIT" \

From 8ab8b68a64ca4e520e3ebd94a1884ea91768e619 Mon Sep 17 00:00:00 2001
From: dpryan79 <dpryan79@gmail.com>
Date: Thu, 17 Oct 2019 10:32:54 +0200
Subject: [PATCH 06/10] some adjustments

---
 recipes/mango/build.sh | 28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/recipes/mango/build.sh b/recipes/mango/build.sh
index e934f3992c7fd..3db291748c6c2 100644
--- a/recipes/mango/build.sh
+++ b/recipes/mango/build.sh
@@ -9,15 +9,20 @@ mkdir -p $PACKAGE_HOME
 ls $PACKAGE_HOME
 cp -R core/* $PACKAGE_HOME
 
-ln -s $PACKAGE_HOME/bin/mango-notebook $BINARY_HOME
-ln -s $PACKAGE_HOME/bin/mango-submit $BINARY_HOME
-ln -s $PACKAGE_HOME/bin/make_genome $BINARY_HOME
-
-echo "PYTHON VERSION----"
-$PYTHON --version
-echo $PY_VER
-which $PYTHON
-which python3.7
+for f in $PACKAGE_HOME/bin/* ; do
+    if [[ -f $f ]] ; then
+        ln -s $f $BINARY_HOME/
+    fi
+done
+#ln -s $PACKAGE_HOME/bin/mango-notebook $BINARY_HOME
+#ln -s $PACKAGE_HOME/bin/mango-submit $BINARY_HOME
+#ln -s $PACKAGE_HOME/bin/make_genome $BINARY_HOME
+
+#echo "PYTHON VERSION----"
+#$PYTHON --version
+#echo $PY_VER
+#which $PYTHON
+#which python3.7
 
 # modin
 $PYTHON -m pip install python_modin/.[dask] --no-deps --ignore-installed -vv
@@ -33,3 +38,8 @@ $PYTHON -m pip install python_pileup/. --no-deps --ignore-installed -vv
 # 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/*.jar ; do
+    ln -s $f $PREFIX/mango-assembly/target/
+done

From 628f5fe98c53ef0e83366adba264a9bf0a6497a5 Mon Sep 17 00:00:00 2001
From: dpryan79 <dpryan79@gmail.com>
Date: Thu, 17 Oct 2019 10:43:33 +0200
Subject: [PATCH 07/10] oops

---
 recipes/mango/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/mango/build.sh b/recipes/mango/build.sh
index 3db291748c6c2..efed721736e13 100644
--- a/recipes/mango/build.sh
+++ b/recipes/mango/build.sh
@@ -40,6 +40,6 @@ $PYTHON -m pip install python_pileup/. --no-deps --ignore-installed -vv
 # jupyter nbextension enable bdgenomics.mango.pileup --user --py
 
 mkdir -p $PREFIX/mango-assembly/target
-for f in $PACKAGE_HOME/*.jar ; do
+for f in $PACKAGE_HOME/repo/*.jar ; do
     ln -s $f $PREFIX/mango-assembly/target/
 done

From 0eb359ed4fd5c21c034e940e36f314e941db2928 Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Thu, 17 Oct 2019 09:46:49 -0700
Subject: [PATCH 08/10] remove patches and cleanup

---
 recipes/mango/build.sh             |  9 --------
 recipes/mango/make_genome.patch    | 31 --------------------------
 recipes/mango/mango-notebook.patch | 35 ------------------------------
 recipes/mango/mango-submit.patch   | 33 ----------------------------
 recipes/mango/meta.yaml            |  9 +-------
 5 files changed, 1 insertion(+), 116 deletions(-)
 delete mode 100644 recipes/mango/make_genome.patch
 delete mode 100644 recipes/mango/mango-notebook.patch
 delete mode 100644 recipes/mango/mango-submit.patch

diff --git a/recipes/mango/build.sh b/recipes/mango/build.sh
index efed721736e13..14d7462e70205 100644
--- a/recipes/mango/build.sh
+++ b/recipes/mango/build.sh
@@ -14,15 +14,6 @@ for f in $PACKAGE_HOME/bin/* ; do
         ln -s $f $BINARY_HOME/
     fi
 done
-#ln -s $PACKAGE_HOME/bin/mango-notebook $BINARY_HOME
-#ln -s $PACKAGE_HOME/bin/mango-submit $BINARY_HOME
-#ln -s $PACKAGE_HOME/bin/make_genome $BINARY_HOME
-
-#echo "PYTHON VERSION----"
-#$PYTHON --version
-#echo $PY_VER
-#which $PYTHON
-#which python3.7
 
 # modin
 $PYTHON -m pip install python_modin/.[dask] --no-deps --ignore-installed -vv
diff --git a/recipes/mango/make_genome.patch b/recipes/mango/make_genome.patch
deleted file mode 100644
index 0146b94a470f2..0000000000000
--- a/recipes/mango/make_genome.patch
+++ /dev/null
@@ -1,31 +0,0 @@
---- a/bin/make_genome
-+++ b/bin/make_genome
-@@ -20,12 +20,20 @@
- # Runs MakeGenome, which generates a .genome file containing reference, genes, cytoband, and chromsizes.
- # Requires 2 arguments: genome name and output file to save .genome file to.
-
--SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})
-+# Find original directory of this script, resolving symlinks
-+# https://stackoverflow.com/questions/59895/get-the-source-directory-of-a-bash-script-from-within-the-script-itself/246128#246128
-+SOURCE="${BASH_SOURCE[0]}"
-+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
-+  DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-+  SOURCE="$(readlink "$SOURCE")"
-+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
-+done
-+SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-
- # get Mango jar
--MANGO_CLI_JAR=$(${SOURCE_DIR}/find-mango-assembly.sh)
-+MANGO_CLI_JAR=$(${SCRIPT_DIR}/find-mango-assembly.sh)
-
--SPARK_SUBMIT=$(${SOURCE_DIR}/find-spark.sh)
-+SPARK_SUBMIT=$(${SCRIPT_DIR}/find-spark.sh)
-
- # submit the job to Spark
- "$SPARK_SUBMIT" \
-@@ -34,4 +42,3 @@
-   --conf spark.kryo.registrator=org.bdgenomics.mango.serialization.MangoKryoRegistrator \
-   $MANGO_CLI_JAR \
-   "MakeGenome" "$@" \
--
diff --git a/recipes/mango/mango-notebook.patch b/recipes/mango/mango-notebook.patch
deleted file mode 100644
index 2ac93184cd938..0000000000000
--- a/recipes/mango/mango-notebook.patch
+++ /dev/null
@@ -1,35 +0,0 @@
---- a/bin/mango-notebook
-+++ b/bin/mango-notebook
-@@ -62,6 +62,16 @@
-   echo ${path}
- }
-
-+# Find original directory of this script, resolving symlinks
-+# https://stackoverflow.com/questions/59895/get-the-source-directory-of-a-bash-script-from-within-the-script-itself/246128#246128
-+SOURCE="${BASH_SOURCE[0]}"
-+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
-+  DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-+  SOURCE="$(readlink "$SOURCE")"
-+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
-+done
-+SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-+
- # Retrieve the path of py4j zip archive used by current spark
- get_py4jzip(){
-   local -a py4j_zip_all_versions
-@@ -112,14 +122,13 @@
- # variable declarations
- trap 'err_report ${LINENO} $?' ERR
- declare -r PY4J_ZIP=$(get_py4jzip)
--declare -r SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})
- declare mango_cli_jar=""
- declare wrapper_path
- declare pyspark=""
- parse_args "$@"
-
- # get Mango jar
--mango_cli_jar=$(${SOURCE_DIR}/find-mango-assembly.sh)
-+mango_cli_jar=$(${SCRIPT_DIR}/find-mango-assembly.sh)
-
- # get pyspark path
- if [[ -z "${SPARK_HOME}" ]]; then
diff --git a/recipes/mango/mango-submit.patch b/recipes/mango/mango-submit.patch
deleted file mode 100644
index 2c4b1c96e6d79..0000000000000
--- a/recipes/mango/mango-submit.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- a/bin/mango-submit
-+++ b/bin/mango-submit
-@@ -20,7 +20,15 @@
- # usage: mango-submit [<spark-args> --] <mango-args>
- set -e
-
--SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})
-+# Find original directory of this script, resolving symlinks
-+# https://stackoverflow.com/questions/59895/get-the-source-directory-of-a-bash-script-from-within-the-script-itself/246128#246128
-+SOURCE="${BASH_SOURCE[0]}"
-+while [ -L "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
-+  DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-+  SOURCE="$(readlink "$SOURCE")"
-+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
-+done
-+SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-
- # Split args into Spark and ADAM args
- DD=False  # DD is "double dash"
-@@ -52,10 +60,11 @@
-
-
- # get Mango jar
--MANGO_CLI_JAR=$(${SOURCE_DIR}/find-mango-assembly.sh)
-+MANGO_CLI_JAR=$(${SCRIPT_DIR}/find-mango-assembly.sh)
-
--SPARK_SUBMIT=$(${SOURCE_DIR}/find-spark.sh)
-+SPARK_SUBMIT=$(${SCRIPT_DIR}/find-spark.sh)
- echo "Using spark-submit=$SPARK_SUBMIT" 1>&2
-+ls "$(dirname "$( dirname "$SPARK_SUBMIT" )" )"
-
- # submit the job to Spark
- "$SPARK_SUBMIT" \
diff --git a/recipes/mango/meta.yaml b/recipes/mango/meta.yaml
index 62e9f388720ab..2fce39e52eda5 100644
--- a/recipes/mango/meta.yaml
+++ b/recipes/mango/meta.yaml
@@ -9,10 +9,7 @@
 {% set modin_version = "0.6.1" %}
 
 # Current issues:
-# 1: noarch not working for either python or generic
-## noarch generic uses a different python version in test, so imports will fail
-## noarch python makes symlinks not work from build script
-# 2: modin and ray are not on conda
+# 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
@@ -25,10 +22,6 @@ source:
   - url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/mango/mango-distribution/{{ version }}/mango-distribution-{{ version }}-bin.tar.gz
     md5: fb9c822dcc0ea1a13766d7faf3413af5
     folder: core
-    patches:
-      - mango-notebook.patch
-      - mango-submit.patch
-      - make_genome.patch
   - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
     sha256: 12dc1b334597481b2caa3988417cb6742569585fd1f056c02adfce2b1f208467
     folder: python

From dc38a37f24104cac7b89740370df5e07a5c48836 Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Thu, 17 Oct 2019 09:52:18 -0700
Subject: [PATCH 09/10] added back deleted recipe

---
 recipes/ray/build.sh  | 11 +++++++++++
 recipes/ray/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 47 insertions(+)
 create mode 100644 recipes/ray/build.sh
 create mode 100644 recipes/ray/meta.yaml

diff --git a/recipes/ray/build.sh b/recipes/ray/build.sh
new file mode 100644
index 0000000000000..495a4945daec0
--- /dev/null
+++ b/recipes/ray/build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+mkdir -p $PREFIX/bin
+
+mkdir build
+cd build
+export MPICXX=$PREFIX/bin
+export OMPI_MCA_mpi_show_handle_leaks=1
+cmake . -DCMAKE_INSTALL_PREFIX=$PREFIX/bin ..
+make
+cp Ray $PREFIX/bin
diff --git a/recipes/ray/meta.yaml b/recipes/ray/meta.yaml
new file mode 100644
index 0000000000000..8fbc238c2987f
--- /dev/null
+++ b/recipes/ray/meta.yaml
@@ -0,0 +1,36 @@
+{% set name = "ray" %}
+{% set version = "2.3.1" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://downloads.sourceforge.net/project/denovoassembler/Ray-{{ version }}.tar.bz2
+  md5: 82f693c4db60af4328263c9279701009
+
+build:
+  number: 1
+  skip: False
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - openmpi >=2.0.2
+    - cmake
+
+  run:
+    - openmpi >=2.0.2
+
+test:
+  commands:
+    - which Ray # Ray -help requires ssh
+
+about:
+  home: 'http://denovoassembler.sourceforge.net/index.html'
+  license: GPL3
+  summary: "Parallel genome assemblies for parallel DNA sequencing"
+extra:
+  identifiers:
+    - biotools:ray
+    - doi:10.1186/gb-2012-13-12-r122

From a01382088832405b17caae8f316a197d47d2a0a9 Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Tue, 22 Oct 2019 16:24:30 -0700
Subject: [PATCH 10/10] removed SP_DIR for mulled tests

---
 recipes/mango/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/mango/meta.yaml b/recipes/mango/meta.yaml
index 2fce39e52eda5..19a109ac1bc88 100644
--- a/recipes/mango/meta.yaml
+++ b/recipes/mango/meta.yaml
@@ -72,7 +72,7 @@ test:
     # - bdgenomics.mango.pileup needs modin fix
   commands:
     - mango-submit --help
-    - SPARK_HOME=$SP_DIR/pyspark mango-notebook --help
+    - SPARK_HOME=$(python -c "import site,os; print(os.path.join(site.getsitepackages()[0], \"pyspark\"))" ) mango-notebook --help
     - make_genome --help
 
 about: