akmorrow13

API doc links in readthedocs are broken

3

It looks like all the API links on [readthedocs are broken ](https://adam.readthedocs.io/en/latest/api/overview/python.html). They are incorrectly linking to a folder (overview/) when they should link to api/python.html. I have not been...

Timeout waiting for connection from pool for 1000 genomes vcf on AWS

9

val x = sc.loadGenotypes("s3a://1000genomes/phase1/analysis_results/integrated_call_sets/ALL.chr17.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz") generates error Unable to execute HTTP request: Timeout waiting for connection from pool with net.fnothaft:jsr203-s3a:0.0.2. This error was tested with Hadoop-BAM 7.9.2 and 7.9.1

``` >> pip install-r requirements.txt file not found #include ^~~~~~~~ 1 error generated. error: command 'clang' failed with exit status 1 ``` Fix is to set: `export MACOSX_DEPLOYMENT_TARGET=10.14`

Local docs do not match production docs

2

If you pull this repo and run the local docs with `while true; do IGNORE_DASH_BIO=true python index.py; sleep 2; done`, they do not match [the production docs](https://dash.plotly.com/dash-bio/igv). For example, the...

not being used: `from bdgenomics.adam.rdd import AlignmentDataset, CoverageDataset` https://github.com/bigdatagenomics/mango/blob/master/example-files/notebooks/aws-1000genomes.ipynb

Need to run the following after setup: `$jupyter nbextension enable --py widgetsnbextension $jupyter nbextension install --overwrite --py --symlink --user bdgenomics.mango.pileup $jupyter nbextension enable bdgenomics.mango.pileup --user --py `

https://github.com/bigdatagenomics/mango/blob/master/mango-viz/bdgenomics/mango/pileup/sources.py#L83 should not default to None