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.

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

Add docs for transform pipeline, ADAM-on-Toil #1262

Merged
merged 4 commits into from Nov 16, 2016

Conversation

Projects
None yet
3 participants
@fnothaft
Member

fnothaft commented Nov 11, 2016

Resolves #1084, #1085.

@hannes-ucsc @benedictpaten @almussel would be great to get your eyes on a3b1611. Some of that documentation might be useful mirrored over to toil-lib as well.

@@ -0,0 +1,244 @@
# Core Algorithms

This comment has been minimized.

@heuermh

heuermh Nov 12, 2016

Member

This is very nice! :)

@heuermh

heuermh Nov 12, 2016

Member

This is very nice! :)

but any more recent Spark distribution should also work.
[Spark website](http://spark.apache.org/downloads.html). Our [continuous integration setup](
https://amplab.cs.berkeley.edu/jenkins/job/ADAM/) builds ADAM against Spark 1.4.1, 1.5.2, 1.6.2,
and 2.0.0, as well as Hadoop 2.3.0 and 2.6.0.
Once this alias is in place, you can run ADAM by simply typing `adam-submit` at the commandline, e.g.
```bash
$ adam-submit
```

This comment has been minimized.

@heuermh

heuermh Nov 12, 2016

Member

Would it be appropriate to add a section about installation and running via Homebrew and Linuxbrew here?

@heuermh

heuermh Nov 12, 2016

Member

Would it be appropriate to add a section about installation and running via Homebrew and Linuxbrew here?

This comment has been minimized.

@fnothaft

fnothaft Nov 12, 2016

Member

Yeah, that'd be great!

@fnothaft

fnothaft Nov 12, 2016

Member

Yeah, that'd be great!

@@ -1,32 +1,3 @@
# Building Downstream Applications
ADAM is packaged so that it can be used via the base CLI, to run plugins via the CLI, or as a library which can be used when building downstream applications. This document covers some of the important things to note when building applications downstream of ADAM.

This comment has been minimized.

@heuermh

heuermh Nov 12, 2016

Member

Yep, I'll fill in here

@heuermh

heuermh Nov 12, 2016

Member

Yep, I'll fill in here

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Nov 12, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1592/
Test PASSed.

AmplabJenkins commented Nov 12, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1592/
Test PASSed.

it will give you the location of your spark master web UI and ganglia UI. You
may want to open both URLs in tabs and 'pin' them to return to later.
Once you have the cluster running, you will need to scp `adam-x.y.jar` to the

This comment has been minimized.

@heuermh

heuermh Nov 14, 2016

Member

If you mean the assembly uberjar, then it would be adam[-spark2]_${scala.version.prefix}-${project.version}.jar

@heuermh

heuermh Nov 14, 2016

Member

If you mean the assembly uberjar, then it would be adam[-spark2]_${scala.version.prefix}-${project.version}.jar

This comment has been minimized.

@fnothaft

fnothaft Nov 16, 2016

Member

Sorry, these are old docs that need to be removed. @jpdna will fix this section in #493, so I've left as is. Can you accept the changes and merge? We'll need this to merge for #1274.

@fnothaft

fnothaft Nov 16, 2016

Member

Sorry, these are old docs that need to be removed. @jpdna will fix this section in #493, so I've left as is. Can you accept the changes and merge? We'll need this to merge for #1274.

This comment has been minimized.

@heuermh

heuermh Nov 16, 2016

Member

SGTM

@heuermh
@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Nov 15, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1606/
Test PASSed.

AmplabJenkins commented Nov 15, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1606/
Test PASSed.

@heuermh heuermh merged commit df5762d into bigdatagenomics:master Nov 16, 2016

1 check passed

default Merged build finished.
Details
@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Nov 16, 2016

Member

Merged from BART. Thank you, @fnothaft!

Member

heuermh commented Nov 16, 2016

Merged from BART. Thank you, @fnothaft!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment