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packing.gradle
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packing.gradle
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configurations {
capsule
defaultCfg.extendsFrom api
//provided
console.extendsFrom defaultCfg
ga4gh.extendsFrom defaultCfg
google.extendsFrom defaultCfg
amazon.extendsFrom defaultCfg
azure.extendsFrom defaultCfg
legacy.extendsFrom defaultCfg
tower.extendsFrom defaultCfg
wave.extendsFrom defaultCfg
}
dependencies {
api project(':nextflow')
// include Ivy at runtime in order to have Grape @Grab work correctly
defaultCfg "org.apache.ivy:ivy:2.5.2"
// default cfg = runtime + httpfs + amazon + tower client + wave client
defaultCfg project(':nf-httpfs')
// Capsule manages the fat jar building process
capsule 'io.nextflow:capsule:1.1.1'
capsule 'io.nextflow:capsule-maven:1.0.3.2'
console project(':plugins:nf-console')
ga4gh project(':plugins:nf-ga4gh')
google project(':plugins:nf-google')
amazon project(':plugins:nf-amazon')
tower project(':plugins:nf-tower')
wave project(':plugins:nf-wave')
}
ext.mainClassName = 'nextflow.cli.Launcher'
ext.homeDir = System.properties['user.home']
ext.nextflowDir = "$homeDir/.nextflow/framework/$version"
ext.releaseDir = "$buildDir/releases"
ext.s3CmdOpts="--acl public-read --storage-class STANDARD --region eu-west-1"
protected error(String message) {
logger.error message
throw new StopExecutionException(message)
}
protected checkVersionExits(String version) {
if(version.endsWith('-SNAPSHOT'))
return
def cmd = "AWS_ACCESS_KEY_ID=${System.env.NXF_AWS_ACCESS} AWS_SECRET_ACCESS_KEY=${System.env.NXF_AWS_SECRET} aws s3 ls s3://www2.nextflow.io/releases/v$version/nextflow"
def status=['bash','-c', cmd].execute().waitFor()
if( status == 0 )
error("STOP!! Version $version already deployed!")
}
protected resolveDeps( String configName, String... x ) {
final deps = [] as Set
final config = configurations.getByName(configName)
//final root = config.getIncoming().getResolutionResult().root.moduleVersion.toString()
config.getResolvedConfiguration().getResolvedArtifacts().each{ deps << coordinates(it) }
if( x )
deps.addAll(x as List)
logger.info ">> Dependencies for configuration: $configName"
deps.sort().each { logger.info " - $it" }
// make sure there aren't any version conflict
def conflicts = deps.countBy { it.tokenize(":")[0..1].join(':') }.findAll { k,v -> v>1 }
if( conflicts ) {
def err = "There are multiple versions for the following lib(s):"
conflicts.each { name, count -> err += "\n- $name: " + deps.findAll{ it.startsWith(name) }.collect{ it.tokenize(':')[2] } }
throw new IllegalStateException(err)
}
//println "** $configName\n${deps.sort().collect{"- $it"}.join('\n')}\n"
//println ">> Config: $configName \n${deps.sort().join('\n')}\n\n"
return deps.collect{ "$it(*:*)" }.join(' ')
}
protected coordinates( it ) {
if( it instanceof Dependency )
return "${it.group}:${it.name}:${it.version}".toString()
if( it instanceof ResolvedArtifact ) {
def result = it.moduleVersion.id.toString()
if( it.classifier ) result += ":${it.classifier}"
return result
}
throw new IllegalArgumentException("Not a valid dependency object [${it?.class?.name}]: $it")
}
/*
* Default nextflow package. It contains the capsule loader
*/
task packOne(type: Jar) {
dependsOn configurations.capsule, configurations.defaultCfg
archiveFileName = "nextflow-${version}-one.jar"
from (configurations.capsule.collect { zipTree(it) })
// main manifest attributes
def deps = resolveDeps('defaultCfg')
manifest.attributes(
'Main-Class' : 'NextflowLoader',
'Application-Name' : 'nextflow',
'Application-Class' : mainClassName,
'Application-Version': version,
'Min-Java-Version' : '1.8.0',
'Caplets' : 'MavenCapsule',
'Dependencies' : deps
)
// enable snapshot dependencies lookup
if( version.endsWith('-SNAPSHOT') ) {
manifest.attributes 'Allow-Snapshots': true
manifest.attributes 'Repositories': 'local https://oss.sonatype.org/content/repositories/snapshots central seqera'
}
else {
manifest.attributes 'Repositories': 'central seqera'
}
doLast {
ant.copy(file: "$buildDir/libs/nextflow-${version}-one.jar", todir: releaseDir, overwrite: true)
ant.copy(file: "$buildDir/libs/nextflow-${version}-one.jar", todir: nextflowDir, overwrite: true)
println "\n+ Nextflow package `ONE` copied to: $releaseDir"
}
}
task packAll(type: Jar) {
dependsOn configurations.capsule, configurations.defaultCfg
archiveFileName = "nextflow-${version}-all.jar"
from jar // embed our application jar
from (configurations.amazon + configurations.google + configurations.tower + configurations.wave)
from (configurations.capsule.collect { zipTree(it) })
duplicatesStrategy = DuplicatesStrategy.EXCLUDE
manifest.attributes( 'Main-Class' : 'NextflowLoader',
'Application-Name' : 'nextflow-all',
'Application-Class' : mainClassName,
'Application-Version': version,
'Min-Java-Version' : '1.8.0'
)
manifest.attributes('Main-Class': 'NextflowLoader', 'amazon')
manifest.attributes('Main-Class': 'NextflowLoader', 'google')
if( project.hasProperty('GA4GH') ) {
println "The build will include GA4GH dependencies."
from(configurations.ga4gh)
manifest.attributes('Main-Class': 'CapsuleLoader', 'ga4gh')
}
doLast {
file(releaseDir).mkdir()
// cleanup
def source = file("$buildDir/libs/nextflow-${version}-all.jar")
def target = file("$releaseDir/nextflow-${version}-all"); target.delete()
// append the big jar
target.withOutputStream {
it << file('nextflow').text.replaceAll(/NXF_PACK\=.*/, 'NXF_PACK=all')
it << new FileInputStream(source)
}
// execute permission
"chmod +x $target".execute()
// done
println "+ Nextflow package `ALL` copied to: $releaseDir\n"
}
}
task packCore(type: Jar) {
dependsOn configurations.capsule, configurations.defaultCfg
archiveFileName = "nextflow-${version}-core.jar"
from jar // embed our application jar
from (configurations.defaultCfg)
from (configurations.capsule.collect { zipTree(it) })
duplicatesStrategy = DuplicatesStrategy.EXCLUDE
manifest.attributes( 'Main-Class' : 'NextflowLoader',
'Application-Name' : 'nextflow-core',
'Application-Class' : mainClassName,
'Application-Version': version,
'Min-Java-Version' : '1.8.0'
)
doLast {
file(releaseDir).mkdir()
// cleanup
def source = file("$buildDir/libs/nextflow-${version}-core.jar")
def target = file("$releaseDir/nextflow-${version}-core"); target.delete()
// append the big jar
target.withOutputStream {
it << file('nextflow').text.replaceAll(/NXF_PACK\=.*/, 'NXF_PACK=all')
it << new FileInputStream(source)
}
// execute permission
"chmod +x $target".execute()
// done
println "+ Nextflow package `CORE` copied to: $releaseDir\n"
}
}
/*
* Compile and pack all packages
*/
task pack( dependsOn: [packOne, packAll]) {
}
task deploy( type: Exec, dependsOn: [clean, compile, pack]) {
def temp = File.createTempFile('upload',null)
temp.deleteOnExit()
def files = []
doFirst {
checkVersionExits(version)
def path = new File(releaseDir)
if( !path.exists() ) error("Releases path does not exist: $path")
path.eachFile {
if( it.name.startsWith("nextflow-$version"))
files << it
}
if( !files ) error("Can't find any file to upload -- Check path: $path")
files << file('nextflow').absoluteFile
files << file('nextflow.sha1').absoluteFile
files << file('nextflow.sha256').absoluteFile
files << file('nextflow.md5').absoluteFile
println "Uploading artifacts: "
files.each { println "- $it"}
def script = []
script << "export AWS_ACCESS_KEY_ID=${System.env.NXF_AWS_ACCESS}"
script << "export AWS_SECRET_ACCESS_KEY=${System.env.NXF_AWS_SECRET}"
script.addAll( files.collect { "aws s3 cp ${it} s3://www2.nextflow.io/releases/v${version}/${it.name} ${s3CmdOpts}"})
temp.text = script.join('\n')
}
commandLine 'bash', '-e', temp.absolutePath
}
task installLauncher(type: Copy, dependsOn: ['pack']) {
from "$releaseDir/nextflow-$version-one.jar"
into "$homeDir/.nextflow/framework/$version/"
}
/*
* build, tag and publish a and new docker packaged nextflow release
*/
task dockerImage(type: Exec) {
def temp = File.createTempFile('upload',null)
temp.deleteOnExit()
temp.text = """\
grep $version nextflow
cp nextflow docker/nextflow
cd docker
make release version=$version
""".stripIndent()
commandLine 'bash', '-e', temp.absolutePath
}
/*
* Build a docker container image with the current snapshot
* DO NOT CALL IT DIRECTLY! Use the `make dockerPack` command instead
*/
task dockerPack(type: Exec, dependsOn: ['packOne']) {
def source = new File("$releaseDir/nextflow-$version-one.jar")
def target = new File("$buildDir/docker/.nextflow/framework/$version/")
def dockerBase = new File("$buildDir/docker")
if( dockerBase.exists() ) dockerBase.deleteDir()
dockerBase.mkdirs()
def dockerFile = new File("$buildDir/docker/Dockerfile")
dockerFile.text = """
FROM amazoncorretto:17-alpine-jdk
RUN apk update && apk add bash && apk add coreutils && apk add curl
COPY .nextflow /.nextflow
COPY nextflow /usr/local/bin/nextflow
COPY entry.sh /usr/local/bin/entry.sh
COPY dist/docker /usr/local/bin/docker
ENV NXF_HOME=/.nextflow
RUN chmod +x /usr/local/bin/nextflow /usr/local/bin/entry.sh
RUN nextflow info
ENTRYPOINT ["/usr/local/bin/entry.sh"]
"""
def temp = File.createTempFile('upload',null)
temp.deleteOnExit()
temp.text = """\
mkdir -p $target
cp $source $target
cp nextflow $buildDir/docker
cp docker/entry.sh $buildDir/docker
cd $buildDir/docker
mkdir -p dist
curl -fsSLO https://get.docker.com/builds/Linux/x86_64/docker-17.03.1-ce.tgz && tar --strip-components=1 -xvzf docker-17.03.1-ce.tgz -C dist
NXF_HOME=\$PWD/.nextflow ./nextflow info
docker build -t nextflow/nextflow:$version .
""".stripIndent()
commandLine 'bash', '-e', temp.absolutePath
}
/*
* Tag and upload the release
*
* https://github.com/aktau/github-release/
*/
task release(type: Exec, dependsOn: [pack, dockerImage]) {
def launcherFile = file('nextflow').absoluteFile
def launcherSha1 = file('nextflow.sha1').absoluteFile
def launcherSha256 = file('nextflow.sha256').absoluteFile
def nextflowAllFile = file("$releaseDir/nextflow-${version}-all")
def versionFile = file('VERSION').absoluteFile
def snapshot = version ==~ /^.+(-RC\d+|-SNAPSHOT)$/
def edge = version ==~ /^.+(-edge|-EDGE)$/
def isLatest = !snapshot && !edge
def cmd = """\
# tag the release
git push || exit \$?
(git tag -a v$version -m 'Tagging version $version [release]' -f && git push origin v$version -f) || exit \$?
sleep 1
gh release create --repo nextflow-io/nextflow --prerelease --title "Version $version" v$version
sleep 1
gh release upload --repo nextflow-io/nextflow v$version ${launcherFile} ${nextflowAllFile}
""".stripIndent()
if( edge )
cmd += """
# publish the script as the latest
export AWS_ACCESS_KEY_ID=${System.env.NXF_AWS_ACCESS}
export AWS_SECRET_ACCESS_KEY=${System.env.NXF_AWS_SECRET}
aws s3 cp $launcherFile s3://www2.nextflow.io/releases/edge/nextflow $s3CmdOpts
aws s3 cp $launcherSha1 s3://www2.nextflow.io/releases/edge/nextflow.sha1 $s3CmdOpts
aws s3 cp $launcherSha256 s3://www2.nextflow.io/releases/edge/nextflow.sha256 $s3CmdOpts
aws s3 cp $launcherSha256 s3://www2.nextflow.io/releases/edge/nextflow.md5 $s3CmdOpts
aws s3 cp $versionFile s3://www2.nextflow.io/releases/edge/version $s3CmdOpts
""".stripIndent()
else if( isLatest )
cmd += """
# publish the script as the latest
export AWS_ACCESS_KEY_ID=${System.env.NXF_AWS_ACCESS}
export AWS_SECRET_ACCESS_KEY=${System.env.NXF_AWS_SECRET}
aws s3 cp $launcherFile s3://www2.nextflow.io/releases/latest/nextflow $s3CmdOpts
aws s3 cp $launcherSha1 s3://www2.nextflow.io/releases/latest/nextflow.sha1 $s3CmdOpts
aws s3 cp $launcherSha256 s3://www2.nextflow.io/releases/latest/nextflow.sha256 $s3CmdOpts
aws s3 cp $launcherSha256 s3://www2.nextflow.io/releases/latest/nextflow.md5 $s3CmdOpts
aws s3 cp $versionFile s3://www2.nextflow.io/releases/latest/version $s3CmdOpts
""".stripIndent()
def temp = File.createTempFile('upload',null)
temp.deleteOnExit()
temp.text = cmd
commandLine 'bash', '-e', temp.absolutePath
}