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Release 0.10.0 #31

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4 changes: 0 additions & 4 deletions build.sbt
Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,6 @@ libraryDependencies ++= Seq(
"ohnosequences-bundles" %% "jellyfish" % "0.2.0"
)

/*dependencyOverrides ++= Set(
"ohnosequences" %% "aws-scala-tools" % "0.15.0"
)*/


// Showing time spent on each test
testOptions in Test += Tests.Argument("-oD")
Expand Down
2 changes: 1 addition & 1 deletion docs/src/main/scala/era7.bundles/awsCompats.scala.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
```scala
package era7.bundles

import ohnosequences.statika._, bundles._, aws._
import ohnosequences.statika._, aws._
import ohnosequences.awstools.ec2._
import ohnosequences.awstools.regions._

Expand Down
36 changes: 18 additions & 18 deletions docs/src/test/scala/era7.bundles/Tests.scala.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
```scala
package era7.bundles.tests

import ohnosequences.statika._, bundles._, aws._
import ohnosequences.statika._, aws._
import era7.bundles._, std._, awsCompats._

import java.io._
Expand All @@ -13,7 +13,7 @@ import ohnosequences.awstools.regions.Region._
import ohnosequences.awstools.ec2._, InstanceType._


class ApplicationTest extends FunSuite with ParallelTestExecution {
class StdBundlesInstall extends FunSuite with ParallelTestExecution {

val ec2 = EC2.create(new ProfileCredentialsProvider("default"))
// val testKeyPair = "aalekhin"
Expand Down Expand Up @@ -63,32 +63,32 @@ class ApplicationTest extends FunSuite with ParallelTestExecution {
)

def testCompat(name: String, specs: AnyLaunchSpecs) = {
test(s"testing ${name}") {
ignore(s"testing ${name}") {
// println(specs.userData)
val instances = launchAndWait(ec2, name, specs)
// if it was successful, we kill the instance immediately
//instances.foreach{ _.terminate }
instances.foreach{ _.terminate }
assert{ instances.length == 1 }
}
}

val compats = Map(
// "velvet" -> specs(awsCompats.velvet),
// "samtools" -> specs(awsCompats.samtools),
// "bowtie2" -> specs(awsCompats.bowtie2),
// "tophat" -> specs(awsCompats.tophat),
// "cufflinks" -> specs(awsCompats.cufflinks)
// "blast" -> specs(awsCompats.blast),
//"flash" -> specs(awsCompats.flash),
// "spades" -> specs(awsCompats.spades),
//"fastqc" -> specs(awsCompats.fastqc),
// "metaVelvet" -> specs(awsCompats.metaVelvet)
//"cutadapt" -> specs(awsCompats.cutadapt),
//"trimgalore" -> specs(awsCompats.trimgalore),
"jellyfish" -> specs(awsCompats.jellyfish)
"velvet" -> specs(awsCompats.velvet),
"metaVelvet" -> specs(awsCompats.metaVelvet),
"samtools" -> specs(awsCompats.samtools),
"bowtie2" -> specs(awsCompats.bowtie2),
"tophat" -> specs(awsCompats.tophat),
"cufflinks" -> specs(awsCompats.cufflinks),
"blast" -> specs(awsCompats.blast),
"flash" -> specs(awsCompats.flash),
"spades" -> specs(awsCompats.spades),
"fastqc" -> specs(awsCompats.fastqc),
"cutadapt" -> specs(awsCompats.cutadapt),
"trimgalore" -> specs(awsCompats.trimgalore),
"jellyfish" -> specs(awsCompats.jellyfish)
)

compats.foreach{ case (name, specs) => testCompat(name, specs) }
compats.foreach{ case (name, specs) => testCompat(name, specs) }
```


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4 changes: 4 additions & 0 deletions notes/0.10.0.markdown
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
- update build plugin
- update all bundle version to compatibles with statika 2.0.0-M5
- update code to statika 2.0.0-M5, enable all bundles in tests
- test all bundles, successful
3 changes: 1 addition & 2 deletions project/plugins.sbt
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
resolvers += "Era7 maven releases" at "https://s3-eu-west-1.amazonaws.com/releases.era7.com"
resolvers += "Era7 maven snapshots" at "https://s3-eu-west-1.amazonaws.com/snapshots.era7.com"

addSbtPlugin("ohnosequences" % "nice-sbt-settings" % "0.7.0-SNAPSHOT")
addSbtPlugin("ohnosequences" % "nice-sbt-settings" % "0.7.0")
addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.5.0")
2 changes: 1 addition & 1 deletion src/test/scala/era7.bundles/Tests.scala
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ import ohnosequences.awstools.regions.Region._
import ohnosequences.awstools.ec2._, InstanceType._


class ApplicationTest extends FunSuite with ParallelTestExecution {
class StdBundlesInstall extends FunSuite with ParallelTestExecution {

val ec2 = EC2.create(new ProfileCredentialsProvider("default"))
// val testKeyPair = "aalekhin"
Expand Down
2 changes: 1 addition & 1 deletion version.sbt
Original file line number Diff line number Diff line change
@@ -1 +1 @@
version in ThisBuild := "0.10.0-SNAPSHOT"
version in ThisBuild := "0.11.0-SNAPSHOT"