From fe18549661c594c87fa094087f8aa6b4e1921b53 Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Tue, 19 Sep 2017 09:48:05 -0700
Subject: [PATCH 1/2] updated example to run locally with hdfs

---
 README.md                    | 2 +-
 example-files/run-example.sh | 9 +++++++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 2e7ab6f67..c40973623 100644
--- a/README.md
+++ b/README.md
@@ -28,7 +28,7 @@ $ mvn clean package -DskipTests
 ## Running mango
 mango is packaged via [appassembler](http://mojo.codehaus.org/appassembler/appassembler-maven-plugin/) and includes all necessary dependencies.
 
-Running an example script:
+Running an example script locally:
 ```
 From the main folder of mango, run ./example-files/run-example.sh to see a demonstration of chromosome 17, region 7500000-7515000.
 ```
diff --git a/example-files/run-example.sh b/example-files/run-example.sh
index a6640fc6f..c1c68bc70 100755
--- a/example-files/run-example.sh
+++ b/example-files/run-example.sh
@@ -1,7 +1,12 @@
-bin/mango-submit ./example-files/hg19.17.2bit \
+# get current local directory
+DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )
+
+# reference 2 bit does not need 'file:' because it is only read from the master
+bin/mango-submit ${DIR}/hg19.17.2bit \
 -genes http://www.biodalliance.org/datasets/ensGene.bb \
 -reads ./example-files/chr17.7500000-7515000.sam.adam \
 -variants ./example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf \
 -show_genotypes \
--discover
+-discover \
+-port 8080
 

From 832416db7bcaa9d02bced04a864a7ab6aaa3ce3c Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Tue, 19 Sep 2017 09:53:46 -0700
Subject: [PATCH 2/2] added hdfs example

3 added hdfs files
---
 README.md                                      |  8 +++++++-
 example-files/run-hdfs.sh                      | 11 +++++++++++
 example-files/{run-example.sh => run-local.sh} |  0
 3 files changed, 18 insertions(+), 1 deletion(-)
 create mode 100755 example-files/run-hdfs.sh
 rename example-files/{run-example.sh => run-local.sh} (100%)

diff --git a/README.md b/README.md
index c40973623..366da9ad9 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,7 @@ mango is packaged via [appassembler](http://mojo.codehaus.org/appassembler/appas
 
 Running an example script locally:
 ```
-From the main folder of mango, run ./example-files/run-example.sh to see a demonstration of chromosome 17, region 7500000-7515000.
+From the main folder of mango, run ./example-files/run-local.sh to see a demonstration of chromosome 17, region 7500000-7515000.
 ```
 For help launching the script, run `bin/mango-submit -h`
 ````
@@ -63,4 +63,10 @@ Using SPARK_SUBMIT=/Applications/spark-1.6.1-bin-hadoop2.4/bin/spark-submit
 View the visualization at: 8080
 Quit at: /quit
 ```
+
+Running an example script on hdfs:
+```
+From the main folder of mango, run ./example-files/run-hdfs.sh to see a demonstration of chromosome 17, region 7500000-7515000.
+```
+
 Note that for logging, you must use the /quit url for the log to be produced.
diff --git a/example-files/run-hdfs.sh b/example-files/run-hdfs.sh
new file mode 100755
index 000000000..84791d748
--- /dev/null
+++ b/example-files/run-hdfs.sh
@@ -0,0 +1,11 @@
+# get current local directory
+DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )
+hdfs dfs -put ${DIR}
+
+bin/mango-submit ${DIR}/hg19.17.2bit \
+-genes http://www.biodalliance.org/datasets/ensGene.bb \
+-reads example-files/chr17.7500000-7515000.bam.adam \
+-variants example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf \
+-show_genotypes \
+-discover \
+-port 8080
diff --git a/example-files/run-example.sh b/example-files/run-local.sh
similarity index 100%
rename from example-files/run-example.sh
rename to example-files/run-local.sh