ggittu

EC2 instance to EMR connection

4

We want to experiment the possibility of using the enterprise_gateway for our current setup. We have setup JupyterHub (TLJH) within an EC2 instance. From this TLJH we would like to...

Connecting EC2 instance to EMR Livy enabled spark cluster

1

@devstein We are experimenting the connection from EC2 instance (where Jupiter is setup with sparkmagic) to EMR spark cluster(Livy enabled). I am following this blog post https://towardsdatascience.com/every-data-scientist-can-need-some-spark-magic-853da0b81006. But unfortunately its...

Dealing with loci with no SNP

4

Hi Huwenbo- @shihuwenbo @huwenboshi I am trying to work this out for the step2, but I am getting error , [INFO] Loaded results for 1703 loci from step 1 [INFO]...

I am trying to use jointer for the Adam files generated from biallelicGenotyper, ./avocado-submit jointer hdfs:///GATKexp/\*.adam hdfs:///GATKexp/combineavocadofrombillalic.vcf but it complaint saying unable to locate the file Command body threw exception:...

Error while compiling

8

Finished running all the prerequisites cd ~ && wget https://dl.bintray.com/boostorg/release/1.69.0/source/boost_1_69_0.tar.gz tar -xzvf boost_1_69_0.tar.gz && cd boost_1_69_0 ./bootstrap.sh --with-libraries=program_options,filesystem,system,date_time ./b2 --clean && ./b2 --j12 -a cd ~ && git clone --recursive...