George He

Visualization Issues in Mango Notebook

1

Ran a visualization issue today [the widget did not load after data was computed and sent over] - not sure if this was a one-off but posting here to track....

Errors Building Mango Viz

4

When running make develop for mango-viz, I run into the following error: https://gist.github.com/Georgehe4/91bd849caac046b65a81b10b5cef9d90 I suspect this is due to an out-of-date node installation.

Startup Issues in Mango Notebook on GCE

1

When creating the SparkContext in mango notebook, the following error occurs: ``` Exception in thread "Thread-5" java.lang.NoClassDefFoundError: org/apache/hadoop/mapreduce/TaskAttemptContext at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:264) at org.apache.hadoop.hive.shims.ShimLoader.createShim(ShimLoader.java:146) at org.apache.hadoop.hive.shims.ShimLoader.loadShims(ShimLoader.java:141) at org.apache.hadoop.hive.shims.ShimLoader.getHadoopShims(ShimLoader.java:100) at...

https://github.com/bigdatagenomics/mango/blob/3d75a198b153a4ff824cea10cee96f54ad6999d8/bin/emr/run-browser.sh#L57 As far as I understand, SPARK_LIBRARY_PATH has been deprecated as of version 0.9.0. http://apache-spark-user-list.1001560.n3.nabble.com/replacement-for-SPARK-LIBRARY-PATH-td10078.html

Fasta files do not work with HDFS

1

Currently Mango only looks at the local repository for fasta files.

Coverage data loss in frontend [Pileup issue]

1

Coverage is currently missing the bottom half. https://github.com/hammerlab/pileup.js/issues/439

Currently, submodules can only be updated by running scripts stored in [scripts/](https://github.com/bigdatagenomics/mango/tree/master/scripts). It would streamline the build process to incorporate these into our maven build.

Reproduce by loading several regions and then going to /quit Oct 4, 2016 10:27:49 PM INFO: org.apache.parquet.hadoopException in thread "main" java.lang.IllegalStateException: Could not find monitor with tag [statistic=DriverTotalTime] at org.bdgenomics.utils.instrumentation.Metrics$.org$bdgenomics$utils$instrumentation$Metrics$$findMonitor(Metrics.scala:209)...

#195

Variants do not support ends

3

The variant type structure in main/vcf.js supports only a starting position without an ending position.