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adam-commands_2.10

External commands for ADAM: Genomic Data System.

License

License
GroupId

GroupId

com.github.heuermh.adamcommands
ArtifactId

ArtifactId

adam-commands_2.10
Last Version

Last Version

0.22.0
Release Date

Release Date
Type

Type

jar
Description

Description

adam-commands_2.10
External commands for ADAM: Genomic Data System.
Project URL

Project URL

http://github.com/heuermh/adam-commands
Source Code Management

Source Code Management

https://github.com/heuermh/adam-commands.git

Download adam-commands_2.10

Filename Size
adam-commands_2.10-0.22.0.pom
adam-commands_2.10-0.22.0.jar 30 KB
adam-commands_2.10-0.22.0-sources.jar 2 KB
adam-commands_2.10-0.22.0-javadoc.jar 372 KB
Browse

How to add to project

<!-- https://jarcasting.com/artifacts/com.github.heuermh.adamcommands/adam-commands_2.10/ -->
<dependency>
    <groupId>com.github.heuermh.adamcommands</groupId>
    <artifactId>adam-commands_2.10</artifactId>
    <version>0.22.0</version>
</dependency>
// https://jarcasting.com/artifacts/com.github.heuermh.adamcommands/adam-commands_2.10/
implementation 'com.github.heuermh.adamcommands:adam-commands_2.10:0.22.0'
// https://jarcasting.com/artifacts/com.github.heuermh.adamcommands/adam-commands_2.10/
implementation ("com.github.heuermh.adamcommands:adam-commands_2.10:0.22.0")
'com.github.heuermh.adamcommands:adam-commands_2.10:jar:0.22.0'
<dependency org="com.github.heuermh.adamcommands" name="adam-commands_2.10" rev="0.22.0">
  <artifact name="adam-commands_2.10" type="jar" />
</dependency>
@Grapes(
@Grab(group='com.github.heuermh.adamcommands', module='adam-commands_2.10', version='0.22.0')
)
libraryDependencies += "com.github.heuermh.adamcommands" % "adam-commands_2.10" % "0.22.0"
[com.github.heuermh.adamcommands/adam-commands_2.10 "0.22.0"]

Dependencies

compile (4)

Group / Artifact Type Version
net.codingwell : scala-guice_2.10 jar 4.1.0
org.bdgenomics.adam : adam-apis-spark2_2.10 jar 0.22.0
org.bdgenomics.adam : adam-cli-spark2_2.10 jar 0.22.0
org.bdgenomics.adam : adam-core-spark2_2.10 jar 0.22.0

provided (1)

Group / Artifact Type Version
org.apache.spark : spark-core_2.10 jar 2.1.0

test (2)

Group / Artifact Type Version
org.bdgenomics.adam : adam-core-spark2_2.10 test-jar 0.22.0
org.scalatest : scalatest_2.10 jar 2.2.6

Project Modules

There are no modules declared in this project.

adam-commands

Build Status Maven Central

External commands in Java and Scala for ADAM: Genomic Data System. Apache 2 licensed.

Hacking adam-commands

Install

To build

$ mvn install

Running adam-commands using adam-submit

$ cp target/adam-commands_2.12-${ADAM_VERSION}.jar $ADAM_DIR
$ cd $ADAM_DIR

To run the external commands in this repository via the ADAM command line, specify ADAM_MAIN and add the adam-commands jar to the classpath with the Spark --jars argument.

Note the -- argument separator between Spark arguments and ADAM arguments.

External commands are now listed in the usage text.

$ ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain \
  ./bin/adam-submit \
  --jars adam-commands_2.12-${ADAM_VERSION}.jar \
  --

Using ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
INFO ADAMMain: ADAM invoked with args:

       e        888~-_         e            e    e
      d8b       888   \       d8b          d8b  d8b
     /Y88b      888    |     /Y88b        d888bdY88b
    /  Y88b     888    |    /  Y88b      / Y88Y Y888b
   /____Y88b    888   /    /____Y88b    /   YY   Y888b
  /      Y88b   888_-~    /      Y88b  /          Y888b

Usage: adam-submit [<spark-args> --] <adam-args>

Choose one of the following commands:

ADAM ACTIONS
...

EXTERNAL COMMANDS
         count_alignments : Counts the alignments in a read dataset.
count_alignments_per_read : Counts the alignments per read in a read dataset.

Run external commands

$ ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain \
  ./bin/adam-submit \
  --jars adam-commands_2.12-${ADAM_VERSION}.jar \
  -- \
  count_alignments adam-core/src/test/resources/small.sam

Using ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
INFO ADAMMain: ADAM invoked with args: "count_alignments" "adam-core/src/test/resources/small.sam"
...
(1,20)


$ ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain \
  ./bin/adam-submit \
  --jars adam-commands_2.12-${ADAM_VERSION}.jar \
  -- \
  count_alignments_per_read adam-core/src/test/resources/small.sam

Using ADAM_MAIN=com.github.heuermh.adam.commands.ADAMCommandsMain
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
INFO ADAMMain: ADAM invoked with args: "count_alignments_per_read" "adam-core/src/test/resources/small.sam"
...
(simread:1:237728409:true,1)
(simread:1:195211965:false,1)
(simread:1:163841413:false,1)
(simread:1:231911906:false,1)
(simread:1:26472783:false,1)
(simread:1:165341382:true,1)
(simread:1:240344442:true,1)
(simread:1:50683371:false,1)
(simread:1:240997787:true,1)
(simread:1:14397233:false,1)
(simread:1:207027738:true,1)
(simread:1:20101800:true,1)
(simread:1:5469106:true,1)
(simread:1:186794283:true,1)
(simread:1:189606653:true,1)
(simread:1:101556378:false,1)
(simread:1:37577445:false,1)
(simread:1:89554252:false,1)
(simread:1:153978724:false,1)
(simread:1:169801933:true,1)

Versions

Version
0.22.0
0.19.0
0.18.2
0.18.1
0.18.0