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broadinstitute/picard : latest

A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.

Ubuntu 20.04.3 LTS

Latest release: 4 months ago - 1,241,685 downloads - 640 dependencies

JSON

Dependencies

ubuntu/adduser 3.118ubuntu2
ubuntu/ant 1.10.7-1
ubuntu/apt 2.0.6
ubuntu/base-files 11ubuntu5.4
ubuntu/base-passwd 3.5.47
ubuntu/bash 5.0-6ubuntu1.1
ubuntu/bsdutils 1:2.34-0.1ubuntu9.1
ubuntu/bzip2 1.0.8-2
ubuntu/ca-certificates-java 20190405ubuntu1
ubuntu/ca-certificates 20210119~20.04.2
ubuntu/coreutils 8.30-3ubuntu2
ubuntu/curl 7.68.0-1ubuntu2.7
ubuntu/dash 0.5.10.2-6
ubuntu/debconf 1.5.73
ubuntu/debianutils 4.9.1
ubuntu/default-jre-headless 2:1.11-72
ubuntu/diffutils 1:3.7-3
ubuntu/dpkg 1.19.7ubuntu3
ubuntu/e2fsprogs 1.45.5-2ubuntu1
ubuntu/fdisk 2.34-0.1ubuntu9.1
ubuntu/findutils 4.7.0-1ubuntu1
ubuntu/fontconfig-config 2.13.1-2ubuntu3
ubuntu/fontconfig 2.13.1-2ubuntu3
ubuntu/fonts-dejavu-core 2.37-1
ubuntu/gcc-10-base 10.3.0-1ubuntu1~20.04
ubuntu/git-man 1:2.25.1-1ubuntu3.6
ubuntu/git 1:2.25.1-1ubuntu3.6
ubuntu/gpgv 2.2.19-3ubuntu2.1
ubuntu/grep 3.4-1
ubuntu/gzip 1.10-0ubuntu4
ubuntu/hostname 3.23
ubuntu/init-system-helpers 1.57
ubuntu/java-common 0.72
ubuntu/libacl1 2.2.53-6
ubuntu/libapt-pkg6.0 2.0.6
ubuntu/libasn1-8-heimdal 7.7.0 dfsg-1ubuntu1
ubuntu/libasound2-data 1.2.2-2.1ubuntu2.5
ubuntu/libasound2 1.2.2-2.1ubuntu2.5
ubuntu/libattr1 1:2.4.48-5
ubuntu/libaudit-common 1:2.8.5-2ubuntu6
ubuntu/libaudit1 1:2.8.5-2ubuntu6
ubuntu/libavahi-client3 0.7-4ubuntu7.1
ubuntu/libavahi-common-data 0.7-4ubuntu7.1
ubuntu/libavahi-common3 0.7-4ubuntu7.1
ubuntu/libblas3 3.9.0-1build1
ubuntu/libblkid1 2.34-0.1ubuntu9.1
ubuntu/libbrotli1 1.0.7-6ubuntu0.1
ubuntu/libbsd0 0.10.0-1
ubuntu/libbz2-1.0 1.0.8-2
ubuntu/libc-bin 2.31-0ubuntu9.2
ubuntu/libc6 2.31-0ubuntu9.2
ubuntu/libcairo2 1.16.0-4ubuntu1
ubuntu/libcap-ng0 0.7.9-2.1build1
ubuntu/libcom-err2 1.45.5-2ubuntu1
ubuntu/libcrypt1 1:4.4.10-10ubuntu4
ubuntu/libcups2 2.3.1-9ubuntu1.2
ubuntu/libcurl3-gnutls 7.68.0-1ubuntu2.15
ubuntu/libcurl4 7.68.0-1ubuntu2.7
ubuntu/libdatrie1 0.2.12-3
ubuntu/libdb5.3 5.3.28 dfsg1-0.6ubuntu2
ubuntu/libdbus-1-3 1.12.16-2ubuntu2.3
ubuntu/libdebconfclient0 0.251ubuntu1
ubuntu/liberror-perl 0.17029-1
ubuntu/libexpat1 2.2.9-1build1
ubuntu/libext2fs2 1.45.5-2ubuntu1
ubuntu/libfdisk1 2.34-0.1ubuntu9.1
ubuntu/libffi7 3.3-4
ubuntu/libfontconfig1 2.13.1-2ubuntu3
ubuntu/libfreetype6 2.10.1-2ubuntu0.1
ubuntu/libfribidi0 1.0.8-2ubuntu0.1
ubuntu/libgcc-s1 10.3.0-1ubuntu1~20.04
ubuntu/libgcrypt20 1.8.5-5ubuntu1.1
ubuntu/libgdbm-compat4 1.18.1-5
ubuntu/libgdbm6 1.18.1-5
ubuntu/libgfortran5 10.3.0-1ubuntu1~20.04
ubuntu/libglib2.0-0 2.64.6-1~ubuntu20.04.4
ubuntu/libgmp10 2:6.2.0 dfsg-4
ubuntu/libgnutls30 3.6.13-2ubuntu1.6
ubuntu/libgomp1 10.3.0-1ubuntu1~20.04
ubuntu/libgpg-error0 1.37-1
ubuntu/libgraphite2-3 1.3.13-11build1
ubuntu/libgssapi-krb5-2 1.17-6ubuntu4.1
ubuntu/libgssapi3-heimdal 7.7.0 dfsg-1ubuntu1
ubuntu/libharfbuzz0b 2.6.4-1ubuntu4.2
ubuntu/libhcrypto4-heimdal 7.7.0 dfsg-1ubuntu1
ubuntu/libheimbase1-heimdal 7.7.0 dfsg-1ubuntu1
ubuntu/libheimntlm0-heimdal 7.7.0 dfsg-1ubuntu1
ubuntu/libhogweed5 3.5.1 really3.5.1-2ubuntu0.2
ubuntu/libhx509-5-heimdal 7.7.0 dfsg-1ubuntu1
ubuntu/libice6 2:1.0.10-0ubuntu1
ubuntu/libicu66 66.1-2ubuntu2.1
ubuntu/libidn2-0 2.2.0-2
ubuntu/libjbig0 2.1-3.1ubuntu0.20.04.1
ubuntu/libjpeg-turbo8 2.0.3-0ubuntu1.20.04.3
ubuntu/libjpeg8 8c-2ubuntu8
ubuntu/libk5crypto3 1.17-6ubuntu4.1
ubuntu/libkeyutils1 1.6-6ubuntu1
ubuntu/libkrb5-26-heimdal 7.7.0 dfsg-1ubuntu1
ubuntu/libkrb5-3 1.17-6ubuntu4.1
ubuntu/libkrb5support0 1.17-6ubuntu4.1
ubuntu/liblapack3 3.9.0-1build1
ubuntu/liblcms2-2 2.9-4
ubuntu/libldap-2.4-2 2.4.49 dfsg-2ubuntu1.8
ubuntu/libldap-common 2.4.49 dfsg-2ubuntu1.8
ubuntu/liblz4-1 1.9.2-2ubuntu0.20.04.1
ubuntu/liblzma5 5.2.4-1ubuntu1
ubuntu/libmount1 2.34-0.1ubuntu9.1
ubuntu/libncurses6 6.2-0ubuntu2
ubuntu/libncursesw6 6.2-0ubuntu2
ubuntu/libnettle7 3.5.1 really3.5.1-2ubuntu0.2
ubuntu/libnghttp2-14 1.40.0-1build1
ubuntu/libnspr4 2:4.25-1
ubuntu/libnss3 2:3.49.1-1ubuntu1.8
ubuntu/libp11-kit0 0.23.20-1ubuntu0.1
ubuntu/libpam-modules-bin 1.3.1-5ubuntu4.2
ubuntu/libpam-modules 1.3.1-5ubuntu4.2
ubuntu/libpam-runtime 1.3.1-5ubuntu4.2
ubuntu/libpam0g 1.3.1-5ubuntu4.2
ubuntu/libpango-1.0-0 1.44.7-2ubuntu4
ubuntu/libpangocairo-1.0-0 1.44.7-2ubuntu4
ubuntu/libpangoft2-1.0-0 1.44.7-2ubuntu4
ubuntu/libpaper-utils 1.1.28
ubuntu/libpaper1 1.1.28
ubuntu/libpcre2-8-0 10.34-7
ubuntu/libpcre3 2:8.39-12build1
ubuntu/libpcsclite1 1.8.26-3
ubuntu/libperl5.30 5.30.0-9ubuntu0.3
ubuntu/libpixman-1-0 0.38.4-0ubuntu2.1
ubuntu/libpng16-16 1.6.37-2
ubuntu/libprocps8 2:3.3.16-1ubuntu2.3
ubuntu/libpsl5 0.21.0-1ubuntu1
ubuntu/libquadmath0 10.3.0-1ubuntu1~20.04
ubuntu/libreadline8 8.0-4
ubuntu/libroken18-heimdal 7.7.0 dfsg-1ubuntu1
ubuntu/librtmp1 2.4 20151223.gitfa8646d.1-2build1
ubuntu/libsasl2-2 2.1.27 dfsg-2
ubuntu/libsasl2-modules-db 2.1.27 dfsg-2
ubuntu/libseccomp2 2.5.1-1ubuntu1~20.04.1
ubuntu/libselinux1 3.0-1build2
ubuntu/libsemanage-common 3.0-1build2
ubuntu/libsemanage1 3.0-1build2
ubuntu/libsepol1 3.0-1
ubuntu/libsm6 2:1.2.3-1
ubuntu/libsmartcols1 2.34-0.1ubuntu9.1
ubuntu/libsqlite3-0 3.31.1-4ubuntu0.2
ubuntu/libss2 1.45.5-2ubuntu1
ubuntu/libssh-4 0.9.3-2ubuntu2.2
ubuntu/libssl1.1 1.1.1f-1ubuntu2.8
ubuntu/libstdc 6 10.3.0-1ubuntu1~20.04
ubuntu/libsystemd0 245.4-4ubuntu3.13
ubuntu/libtasn1-6 4.16.0-2
ubuntu/libtcl8.6 8.6.10 dfsg-1
ubuntu/libthai-data 0.1.28-3
ubuntu/libthai0 0.1.28-3
ubuntu/libtiff5 4.1.0 git191117-2ubuntu0.20.04.7
ubuntu/libtinfo6 6.2-0ubuntu2
ubuntu/libtk8.6 8.6.10-1
ubuntu/libudev1 245.4-4ubuntu3.13
ubuntu/libunistring2 0.9.10-2
ubuntu/libuuid1 2.34-0.1ubuntu9.1
ubuntu/libwebp6 0.6.1-2ubuntu0.20.04.1
ubuntu/libwind0-heimdal 7.7.0 dfsg-1ubuntu1
ubuntu/libx11-6 2:1.6.9-2ubuntu1.2
ubuntu/libx11-data 2:1.6.9-2ubuntu1.2
ubuntu/libxau6 1:1.0.9-0ubuntu1
ubuntu/libxcb-render0 1.14-2
ubuntu/libxcb-shm0 1.14-2
ubuntu/libxcb1 1.14-2
ubuntu/libxdmcp6 1:1.1.3-0ubuntu1
ubuntu/libxext6 2:1.3.4-0ubuntu1
ubuntu/libxft2 2.3.3-0ubuntu1
ubuntu/libxrender1 1:0.9.10-1
ubuntu/libxss1 1:1.2.3-1
ubuntu/libxt6 1:1.1.5-1
ubuntu/libzstd1 1.4.4 dfsg-3ubuntu0.1
ubuntu/locales 2.31-0ubuntu9.2
ubuntu/login 1:4.8.1-1ubuntu5.20.04.1
ubuntu/logsave 1.45.5-2ubuntu1
ubuntu/lsb-base 11.1.0ubuntu2
ubuntu/mawk 1.3.4.20200120-2
ubuntu/mount 2.34-0.1ubuntu9.1
ubuntu/ncurses-base 6.2-0ubuntu2
ubuntu/ncurses-bin 6.2-0ubuntu2
ubuntu/openjdk-11-jre-headless 11.0.17 8-1ubuntu2~20.04
ubuntu/openssl 1.1.1f-1ubuntu2.8
ubuntu/passwd 1:4.8.1-1ubuntu5.20.04.1
ubuntu/perl-base 5.30.0-9ubuntu0.3
ubuntu/perl-modules-5.30 5.30.0-9ubuntu0.3
ubuntu/perl 5.30.0-9ubuntu0.3
ubuntu/procps 2:3.3.16-1ubuntu2.3
ubuntu/r-base-core 3.6.3-2
ubuntu/r-base 3.6.3-2
ubuntu/r-cran-boot 1.3-24-2
ubuntu/r-cran-class 7.3-15-1
ubuntu/r-cran-cluster 2.1.0-2
ubuntu/r-cran-codetools 0.2-16-1
ubuntu/r-cran-foreign 0.8.75-1
ubuntu/r-cran-kernsmooth 2.23-16-1 1
ubuntu/r-cran-lattice 0.20-40-1
ubuntu/r-cran-mass 7.3-51.5-2
ubuntu/r-cran-matrix 1.2-18-1
ubuntu/r-cran-mgcv 1.8-31-1
ubuntu/r-cran-nlme 3.1.144-1
ubuntu/r-cran-nnet 7.3-13-1
ubuntu/r-cran-rpart 4.1-15-2
ubuntu/r-cran-spatial 7.3-11-2build2
ubuntu/r-cran-survival 3.1-8-1
ubuntu/r-recommended 3.6.3-2
ubuntu/readline-common 8.0-4
ubuntu/sed 4.7-1
ubuntu/sensible-utils 0.0.12 nmu1
ubuntu/sysvinit-utils 2.96-2.1ubuntu1
ubuntu/tar 1.30 dfsg-7ubuntu0.20.04.1
ubuntu/tzdata 2021a-0ubuntu0.20.04
ubuntu/ubuntu-keyring 2020.02.11.4
ubuntu/ucf 3.0038 nmu1
ubuntu/unzip 6.0-25ubuntu1.1
ubuntu/util-linux 2.34-0.1ubuntu9.1
ubuntu/x11-common 1:7.7 19ubuntu14
ubuntu/xdg-utils 1.1.3-2ubuntu1.20.04.2
ubuntu/zip 3.0-11build1
ubuntu/zlib1g 1:1.2.11.dfsg-2ubuntu1.2

tools:tools *
US_export_policy:US_export_policy *
barclay:barclay 4.0.2
biz.aQute.bndlib:biz.aQute.bndlib 4.0.0
bsh:bsh 2.0b6
charsets:charsets *
cldrdata:cldrdata *
com.amazonaws:aws-java-sdk-core 1.11.407
com.amazonaws:aws-java-sdk-kms 1.11.407
com.amazonaws:aws-java-sdk-s3 1.11.407
com.amazonaws:jmespath-java 1.11.407
com.esotericsoftware.kryo:kryo 2.24.0
com.esotericsoftware.minlog:minlog 1.2
com.esotericsoftware.reflectasm:reflectasm 1.09
com.fasterxml.jackson.core:jackson-annotations 2.9.8
com.fasterxml.jackson.core:jackson-core 2.13.1
com.fasterxml.jackson.core:jackson-core 2.9.8
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com.google.api-client:google-api-client 1.33.2
commons-lang:commons-lang 2.4
com.google.api.apicommon:api-common 2.1.4
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com.google.api.grpc:proto-google-common-protos 2.7.4
com.google.api.grpc:proto-google-iam-v1 1.2.6
com.google.api.services.storage:google-api-services-storage-v1-rev20220210 1.32.1
com.google.apis:google-api-services-storage v1-rev136-1.25.0
com.google.apis:google-api-services-storage v1-rev20220210-1.32.1
com.google.auth:google-auth-library-credentials 1.5.3
com.google.auth:google-auth-library-oauth2-http 1.5.3
com.google.auto.value:auto-value-annotations 1.9
com.google.cloud:google-cloud-core-http 2.5.6
com.google.cloud:google-cloud-core 2.5.6
com.google.cloud:google-cloud-nio 0.123.25
com.google.cloud:google-cloud-storage 2.4.5
com.google.code.findbugs:jsr305 3.0.2
com.google.code.gson:gson 2.8.5
com.google.code.gson:gson 2.9.0
com.google.errorprone:error_prone_annotations 2.7.1
com.google.gson:gson 2.2.2
com.google.guava:failureaccess 1.0.1
com.google.guava:guava 15.0
com.google.guava:guava 19.0
com.google.guava:guava 27.1-android
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com.google.guava:listenablefuture 9999.0-empty-to-avoid-conflict-with-guava
com.google.http-client.google-http-client:google-http-client 1.25.0
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com.google.http-client:google-http-client-appengine 1.41.4
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com.googlecode.jatl:jatl 0.2.3
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com.googlecode.plist:dd-plist 1.21
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com.jcraft:jzlib 1.1.1
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com.sun:jce 1.8.0_292
com.sun:sunec 1.8.0_292
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dt:dt *
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opencensus-api:opencensus-api 0.31.0
opencensus-contrib-http-util:opencensus-contrib-http-util 0.31.0
org.ajoberstar.grgit.gradle:grgit-gradle 4.0.0-rc.1
org.ajoberstar.grgit:grgit-core 4.0.0-rc.1
org.apache.commons:commons-collections4 4.3
org.apache.commons:commons-compress 1.18
org.apache.commons:commons-compress 1.19
org.apache.commons:commons-jexl 2.1.1
org.apache.commons:commons-lang3 3.4
org.apache.commons:commons-math3 3.5
org.apache.httpcomponents:httpclient 4.3.6
org.apache.httpcomponents:httpclient 4.5.13
org.apache.httpcomponents:httpclient 4.5.6
org.apache.httpcomponents:httpcore 4.3.3
org.apache.httpcomponents:httpcore 4.4.10
org.apache.httpcomponents:httpcore 4.4.15
org.apache.httpcomponents:httpmime 4.3
org.apache.ivy:ivy 2.3.0
org.apache.logging.log4j:log4j-api 2.11.0
org.apache.logging.log4j:log4j-api 2.17.1
org.apache.logging.log4j:log4j-core 2.11.0
org.apache.logging.log4j:log4j-core 2.17.1
org.apache.maven.wagon:wagon-file 3.0.0
org.apache.maven.wagon:wagon-http-shared 3.0.0
org.apache.maven.wagon:wagon-http 3.0.0
org.apache.maven.wagon:wagon-provider-api 3.0.0
org.apache.maven:maven-aether-provider 3.0.4
org.apache.maven:maven-artifact 3.0.4
org.apache.maven:maven-compat 3.0.4
org.apache.maven:maven-core 3.0.4
org.apache.maven:maven-model-builder 3.0.4
org.apache.maven:maven-model 3.0.4
org.apache.maven:maven-plugin-api 3.0.4
org.apache.maven:maven-repository-metadata 3.0.4
org.apache.maven:maven-settings-builder 3.0.4
org.apache.maven:maven-settings 3.0.4
org.apache.tools.ant.Main:ant-bootstrap *
org.apache.tools.ant.launch.Launcher:ant-launcher 1.10.7
org.apache.tools.ant.launch.Launcher:ant-launcher 1.9.14
org.apache.tools.ant.launch.Launcher:ant-launcher 1.9.7
org.apache.tools.ant:ant 1.10.7
org.apache.tools.ant:ant 1.9.14
org.apache.tools.ant:ant 1.9.7
org.apache.xbean:xbean-reflect 3.7
org.apache.xerces.impl.Version:xercesImpl 2.12.0
org.apache.xml.resolver.Catalog:xml-resolver 1.2
org.apache.xmlcommons.Version:xml-apis 1.3.04
org.apiguardian.api:apiguardian-api 1.0.0
org.bouncycastle.bcpg:bcpg-jdk15on 1.61
org.bouncycastle.bcpkix:bcpkix-jdk15on 1.61
org.bouncycastle.bcprovider:bcprov-jdk15on 1.61
org.checkerframework.checker.qual:checker-qual 3.21.3
org.codehaus.groovy.modules.http-builder:http-builder 0.7.1
org.codehaus.plexus:plexus-classworlds 2.5.1
org.codehaus.plexus:plexus-component-annotations 1.5.5
org.codehaus.plexus:plexus-container-default 1.7.1
org.codehaus.plexus:plexus-interpolation 1.14
org.codehaus.plexus:plexus-utils 3.0.24
org.codehaus.plexus:plexus-utils 3.1.0
org.debian.security.UpdateCertificates:ca-certificates-java *
org.eclipse.jgit:org.eclipse.jgit 5.0.3.201809091024-r
org.eclipse.jgit:org.eclipse.jgit 5.5.0.201909110433-r
org.freemarker.freemarker:freemarker 2.3.30
org.fusesource.hawtjni:hawtjni-runtime 1.16
org.fusesource.jansi:jansi-freebsd32 1.8
org.fusesource.jansi:jansi-freebsd64 1.8
org.fusesource.jansi:jansi-linux32 1.8
org.fusesource.jansi:jansi-linux64 1.8
org.fusesource.jansi:jansi-native 1.8
org.fusesource.jansi:jansi-osx 1.8
org.fusesource.jansi:jansi-windows32 1.8
org.fusesource.jansi:jansi-windows64 1.8
org.fusesource.jansi:jansi 1.17.1
org.glassfish.jaxb:jaxb-runtime 2.3.1
org.glassfish:javax.annotation-api 1.3.2
org.gradle.launcher.GradleMain:gradle-launcher 5.6
org.jdom2.transform:jdom2 2.0.6
org.jetbrains:annotations 13.0
org.joda:joda-time 2.10
org.junit.platform.commons:junit-platform-commons 1.3.1
org.junit.platform.engine:junit-platform-engine 1.3.1
org.junit.platform.launcher:junit-platform-launcher 1.3.1
org.mozilla.javascript.tools.shell.Main:rhino 1.7.10
org.objectweb.asm.commons:asm-commons 7.0-beta
org.objectweb.asm.commons:asm-commons 7.1
org.objectweb.asm.tree.analysis:asm-analysis 7.0-beta
org.objectweb.asm.tree.analysis:asm-analysis 7.1
org.objectweb.asm.tree:asm-tree 7.0-beta
org.objectweb.asm.tree:asm-tree 7.1
org.objectweb.asm.util:asm-util 7.1
org.objectweb.asm:asm 7.0-beta
org.objectweb.asm:asm 7.1
org.objenesis:objenesis 2.6
org.opentest4j:opentest4j 1.1.1
org.sharegov:mjson 1.4.1
org.simpleframework:simple 4.1.21
org.slf4j:jcl-over-slf4j 1.7.25
org.slf4j:jul-to-slf4j 1.7.25
org.slf4j:log4j-over-slf4j 1.7.25
org.slf4j:slf4j-api 1.7.2
org.slf4j:slf4j-api 1.7.25
org.sonatype.aether:aether-api 1.13.1
org.sonatype.aether:aether-connector-wagon 1.13.1
org.sonatype.aether:aether-impl 1.13.1
org.sonatype.aether:aether-spi 1.13.1
org.sonatype.aether:aether-util 1.13.1
org.sonatype.plexus:plexus-cipher 1.7
org.sonatype.plexus:plexus-sec-dispatcher 1.3
org.sonatype.pmaven:pmaven-common 0.8-SNAPSHOT
org.sonatype.pmaven:pmaven-groovy 0.8-SNAPSHOT
org.testng:testng 6.3.1
org.threeten:threetenbp 1.5.2
org.tukaani.xz:xz 1.8
org.vafer:jdependency 2.1.1
org.w3c.dom.ls:xercesImpl 2.12.0
org.w3c.dom.ls:xml-apis 1.4.01
org.w3c.dom:xercesImpl 2.9.1
org.w3c.dom:xml-apis 1.4.01
org.xerial.snappy.snappy-java:snappy-java 1.1.8.4
org.yaml:snakeyaml 1.17
picard:picard 2.27.5-5-gbdfea14-SNAPSHOT
resources:resources 1.8.0_292
rt:rt 1.8.0_292
sa-jdi:sa-jdi *
shadow:shadow 5.1.0
trove4j:trove4j 1.0.20181211
zipfs:zipfs 1.8.0_292

java 1.8.0_292-b10