Comments (4)
I was gonna ask about this when I see you. The main things I want are code reusability and a make-like ability to figure out what's complete. Luigi has been less good than expected in the reusability.
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I was mostly trolling (hence the gif). OCaml's a pretty big hill to climb and Ketrew is still stabilizing. That said we're using it to run pipelines these days and a few of our lab members have gotten familiar enough with it to write their own extensions.
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@hammer Thanks for mentioning Ketrew. I agree it would be good to choose a single pipeline execution framework. I think Luigi is a reasonable choice at this point, but we could replace it in the future if the replacement has the properties Uri mentions (plus ability to easily run on a Hadoop cluster).
Luigi is an implementation detail for eggo, so it would be possible to change it without users noticing, since the important thing is having a well-defined way to turn input sources into output datasets.
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Closing cuz..... :)
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Related Issues (20)
- 1000 Genomes Phase 3 VCF data set to be hosted in S3 in parquet format HOT 4
- ENCODE data set to be hosted in S3 in parquet format
- Reduce number of CM/CDH restarts during cluster config
- Platinum Genomes data set
- dnload_raw operation requires the ability to `sudo -u hdfs` HOT 2
- `dnload_raw` shouldn't hardcode `ec2-user` when it `chown`s data
- Extract Hive queries into separate reusable files
- asking for password HOT 4
- AMI in eu-west-1 ? HOT 6
- tried to substitute ami-00a11e68 w/o success HOT 9
- Default parallelism set to 2 on cluster with 4 executor nodes? HOT 2
- Verify that requested AMIs are consistent with the requested region/AZ HOT 1
- us-east-1b is hardcoded into cloudformation.template HOT 2
- eggo-cluster provision - fails with return code 12 while executing HOT 1
- Remove minCount line from aws.conf
- how to set the instance type for master, manager and workers separately ? HOT 1
- No handlers could be found for logger "cm_api.resource" HOT 2
- results of "genotype count" are different - depending on used programs HOT 2
- sql query on Adam's flattened file -> Non-local session path expected to be non-null; HOT 4
- Upgrade Spark from 1.3 to 1.5 to make use of project Tungsten performance improvements. HOT 6
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