Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Example script #314

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Example script #314

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
fe18549
updated example to run locally with hdfs
akmorrow13 Sep 19, 2017
832416d
added hdfs example
akmorrow13 Sep 19, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 8 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,9 @@ $ 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.
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`
````
Expand Down Expand Up @@ -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.
11 changes: 11 additions & 0 deletions example-files/run-hdfs.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
# get current local directory
DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )
hdfs dfs -put ${DIR}

bin/mango-submit ${DIR}/hg19.17.2bit \
-genes http://www.biodalliance.org/datasets/ensGene.bb \
-reads example-files/chr17.7500000-7515000.bam.adam \
-variants example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf \
-show_genotypes \
-discover \
-port 8080
9 changes: 7 additions & 2 deletions example-files/run-example.sh → example-files/run-local.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,12 @@
bin/mango-submit ./example-files/hg19.17.2bit \
# get current local directory
DIR=$( 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