luisas/gatk : latest

Latest release: about 8 years ago - 110 downloads - 374 dependencies

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Dependencies

KernSmooth 2.23-13
MASS 7.3-34
Matrix 1.1-4
RColorBrewer 1.0-5
Rcpp 0.11.3
Rcpp 0.12.9
RcppTestA 1.0
abind 1.4-0
base 3.1.1
boot 1.3-13
class 7.3-11
cluster 1.15.3
codetools 0.2-9
colorspace 1.2-4
compiler 3.1.1
datasets 3.1.1
dichromat 2.0-0
digest 0.6.4
doMC 1.3.3
foreach 1.4.2
foreign 0.8-61
getopt 1.20.0
ggplot2 1.0.0
grDevices 3.1.1
graphics 3.1.1
grid 3.1.1
gtable 0.1.2
iterators 1.0.7
labeling 0.3
lattice 0.20-29
magrittr 1.5
mapproj 1.2-2
maps 2.3-7
methods 3.1.1
mgcv 1.8-3
multicore 0.2
munsell 0.4.2
nlme 3.1-117
nnet 7.3-8
nstest 0.1
optparse 1.3.2
parallel 3.1.1
pkgKitten 0.1.2
plyr 1.8.1
plyr 1.8.4
proto 0.3-10
reshape2 1.4
reshape2 1.4.2
rpart 4.1-8
scales 0.2.4
sp 1.0-15
spatial 7.3-8
splines 3.1.1
stats4 3.1.1
stats 3.1.1
stringi 1.1.2
stringr 0.6.2
stringr 1.2.0
survival 2.37-7
tcltk 3.1.1
testRcppClass 0.1
testRcppModule 0.1
testRcppPackage 0.1.0
tools 3.1.1
translations 3.1.1
utils 3.1.1

bash 4.3.30

US_export_policy:US_export_policy *
args4j:args4j 2.0.23
ch.qos.logback:logback-classic 1.1.10
ch.qos.logback:logback-core 1.1.10
charsets:charsets *
cldrdata:cldrdata *
com.amazonaws:aws-java-sdk-batch 1.11.324
com.amazonaws:aws-java-sdk-core 1.11.324
com.amazonaws:aws-java-sdk-ec2 1.11.324
com.amazonaws:aws-java-sdk-kms 1.11.324
com.amazonaws:aws-java-sdk-s3 1.11.324
com.amazonaws:jmespath-java 1.11.324
com.beust:jcommander 1.35
com.cedarsoftware:java-util 1.9.0
com.cedarsoftware:json-io 2.5.1
com.clearspring.analytics:stream 2.7.0
com.esotericsoftware.kryo:kryo 2.24.0
com.esotericsoftware.reflectasm:reflectasm 1.09
com.esotericsoftware:kryo-shaded 3.0.3
com.esotericsoftware:kryo 3.0.3
com.esotericsoftware:minlog 1.3.0
com.esotericsoftware:reflectasm 1.10.0
com.fasterxml.jackson.core:jackson-annotations 2.4.0
com.fasterxml.jackson.core:jackson-annotations 2.6.0
com.fasterxml.jackson.core:jackson-core 2.1.3
com.fasterxml.jackson.core:jackson-core 2.6.7
com.fasterxml.jackson.core:jackson-databind 2.6.5
com.fasterxml.jackson.core:jackson-databind 2.6.7.1
com.fasterxml.jackson.dataformat:jackson-dataformat-cbor 2.6.7
com.fasterxml.jackson.module:jackson-module-paranamer 2.6.5
com.github.fommil.netlib:core 1.1
com.github.fommil.netlib:core 1.1.2
com.github.fommil.netlib:native_ref-java 1.1
com.github.fommil.netlib:native_system-java 1.1
com.github.fommil.netlib:netlib-native_ref-linux-x86_64 1.1
com.github.fommil.netlib:netlib-native_ref-osx-x86_64 1.1
com.github.fommil.netlib:netlib-native_system-linux-x86_64 1.1
com.github.fommil.netlib:netlib-native_system-osx-x86_64 1.1
com.github.fommil:jniloader 1.1
com.github.jsr203hadoop:jsr203hadoop 1.0.3
com.github.rwl:jtransforms 2.4.0
com.github.wendykierp:JTransforms 3.1
com.google.apis:google-api-services-storage v1-rev108-1.22.0
com.google.auth:google-auth-library-credentials 0.7.0
com.google.auth:google-auth-library-oauth2-http 0.7.0
com.google.auto.service:auto-service 1.0-rc2
com.google.auto.value:auto-value 1.2
com.google.auto:auto-common 1.0-SNAPSHOT
com.google.cloud.bigdataoss:gcs-connector 1.6.3-hadoop2
com.google.cloud.bigdataoss:gcsio 1.6.3
com.google.cloud.bigdataoss:util-hadoop 1.6.3-hadoop2
com.google.cloud.bigdataoss:util 1.6.3
com.google.cloud:google-cloud-core-http 1.2.3
com.google.cloud:google-cloud-core 1.2.3
com.google.cloud:google-cloud-storage 1.2.3
com.google.code.gson:gson 2.7
com.google.guava:guava 15.0
com.google.guava:guava 16.0.1
com.google.guava:guava 18.0
com.google.protobuf:protobuf-java-util 3.3.0
com.google.protobuf:protobuf-java 3.3.0
com.googlecode.javaewah:JavaEWAH 1.1.6
com.googlecode.json-simple:json-simple 1.1.1
com.googlecode.protobuf-java-format:protobuf-java-format 1.2
com.intel:genomicsdb 0.9.2-proto-3.0.0-beta-1 uuid-static
com.jamesmurty.utils:java-xmlbuilder 1.0
com.jcraft:jsch 0.1.54
com.nimbusds:nimbus-jose-jwt 3.9
com.ning:compress-lzf 1.0.3
com.opencsv:opencsv 3.4
com.squareup.okhttp:okhttp 2.4.0
com.squareup.okio:okio 1.4.0
com.sun.activation:javax.activation 1.2.0
com.sun.jersey.contribs:jersey-guice 1.9
com.sun.jersey:jersey-client 1.9
com.sun.jersey:jersey-core 1.9
com.sun.jersey:jersey-json 1.9
com.sun.jersey:jersey-server 1.9
com.sun:activation 1.1
com.sun:jce 1.8.0_121
com.sun:sunec 1.8.0_131
com.sun:sunjce_provider 1.8.0_112
com.sun:sunpkcs11 1.8.0_131
com.thoughtworks.paranamer:paranamer 2.7
com.univocity:univocity-parsers 2.2.1
commons-cli:commons-cli 1.2
commons-codec:commons-codec 1.10
commons-codec:commons-codec 1.9
commons-collections:commons-collections 3.2.2
commons-configuration:commons-configuration 1.6
commons-daemon:commons-daemon 1.0.13
commons-io:commons-io 2.5
commons-lang:commons-lang 2.6
commons-logging:commons-logging 1.1.1
commons-net:commons-net 3.1
de.javakaffee:kryo-serializers 0.41
de.ruedigermoeller:fst 2.50
deploy:deploy *
dnsns:dnsns *
gov.nist.math.jama:gov.nist.math.jama 1.1.1
gpars:gpars 1.2.1
grengine:grengine 1.2.1
groovy-json:groovy-json 2.4.15
groovy-nio:groovy-nio 2.4.15
groovy-templates:groovy-templates 2.4.15
groovy-xml:groovy-xml 2.4.15
groovy:groovy 2.4.15
io.dropwizard.metrics:metrics-core 3.1.2
io.dropwizard.metrics:metrics-graphite 3.1.2
io.dropwizard.metrics:metrics-json 3.1.2
io.dropwizard.metrics:metrics-jvm 3.1.2
io.netty:netty-all 4.0.43.Final
io.netty:netty 3.9.9.Final
jaccess:jaccess *
jarhdf5:jarhdf5 2.11.0
javaws:javaws *
javax.annotation:javax.annotation-api 1.2
javax.mail:mail 1.4.7
javax.servlet:javax.servlet-api 3.1.0
javax.validation:validation-api 1.1.0.Final
javax.ws.rs:javax.ws.rs-api 2.0.1
jfr:jfr 1.8.0_121
jfxrt:jfxrt *
jfxswt:jfxswt *
jline:jline 0.9.94
joda-time:joda-time 2.8.1
joda-time:joda-time 2.9.2
jsr166y:jsr166y 1.7.0
jsse:jsse 1.8.0_121
local_policy:local_policy *
localedata:localedata *
log4j:log4j 1.2.17
management-agent:management-agent *
nashorn:nashorn 1.8.0_121-b13
net.iharder:base64 2.3.8
net.java.dev.jets3t:jets3t 0.9.3
net.minidev:json-smart 1.1.1
net.razorvine:pyrolite 4.13
net.sf.jopt-simple:jopt-simple 5.0.3
net.sf.opencsv:opencsv 2.3
net.sf.py4j:py4j 0.10.4
nextflow:nextflow 0.30.1
nextflow:nextflow 0.30.1-one
nxf-commons:nxf-commons 0.30.1
nxf-httpfs:nxf-httpfs 0.30.1
nxf-s3fs:nxf-s3fs 1.0.3
org.aeonbits.owner:owner 1.0.9
org.antlr:antlr4-runtime 4.5.3
org.apache.avro:avro-guava-dependencies 1.8.0
org.apache.avro:avro-ipc 1.7.7
org.apache.avro:avro-mapred 1.7.7
org.apache.avro:avro 1.8.0
org.apache.commons:commons-collections4 4.1
org.apache.commons:commons-compress 1.4.1
org.apache.commons:commons-compress 1.8.1
org.apache.commons:commons-crypto 1.0.0
org.apache.commons:commons-jexl 2.1.1
org.apache.commons:commons-lang3 3.5
org.apache.commons:commons-math3 3.5
org.apache.commons:commons-math 2.2
org.apache.commons:commons-vfs2 2.0
org.apache.curator:curator-client 2.7.1
org.apache.curator:curator-framework 2.7.1
org.apache.curator:curator-recipes 2.7.1
org.apache.curator:curator-test 2.7.1
org.apache.directory.api:api-util 1.0.0-M20
org.apache.hadoop:hadoop-annotations 2.8.2
org.apache.hadoop:hadoop-auth 2.8.2
org.apache.hadoop:hadoop-client 2.8.2
org.apache.hadoop:hadoop-common 2.8.2
org.apache.hadoop:hadoop-hdfs-client 2.8.2
org.apache.hadoop:hadoop-hdfs 2.8.2
org.apache.hadoop:hadoop-mapreduce-client-app 2.8.2
org.apache.hadoop:hadoop-mapreduce-client-common 2.8.2
org.apache.hadoop:hadoop-mapreduce-client-core 2.8.2
org.apache.hadoop:hadoop-mapreduce-client-hs 2.8.2
org.apache.hadoop:hadoop-mapreduce-client-jobclient 2.8.2
org.apache.hadoop:hadoop-mapreduce-client-shuffle 2.8.2
org.apache.hadoop:hadoop-minicluster 2.8.2
org.apache.hadoop:hadoop-yarn-api 2.8.2
org.apache.hadoop:hadoop-yarn-client 2.8.2
org.apache.hadoop:hadoop-yarn-common 2.8.2
org.apache.hadoop:hadoop-yarn-server-applicationhistoryservice 2.8.2
org.apache.hadoop:hadoop-yarn-server-common 2.8.2
org.apache.hadoop:hadoop-yarn-server-nodemanager 2.8.2
org.apache.hadoop:hadoop-yarn-server-resourcemanager 2.8.2
org.apache.hadoop:hadoop-yarn-server-tests 2.8.2
org.apache.hadoop:hadoop-yarn-server-web-proxy 2.8.2
org.apache.htrace:htrace-core4 4.0.1-incubating
org.apache.httpcomponents:httpclient 4.0.1
org.apache.httpcomponents:httpclient 4.5.5
org.apache.httpcomponents:httpcore 4.0.1
org.apache.httpcomponents:httpcore 4.4.9
org.apache.logging.log4j:log4j-api 2.5
org.apache.logging.log4j:log4j-core 2.5
org.apache.maven.scm:maven-scm-api 1.4
org.apache.maven.scm:maven-scm-provider-svn-commons 1.4
org.apache.maven.scm:maven-scm-provider-svnexe 1.4
org.apache.parquet:parquet-avro 1.8.1
org.apache.parquet:parquet-column 1.8.1
org.apache.parquet:parquet-column 1.8.2
org.apache.parquet:parquet-common 1.8.1
org.apache.parquet:parquet-common 1.8.2
org.apache.parquet:parquet-encoding 1.8.1
org.apache.parquet:parquet-encoding 1.8.2
org.apache.parquet:parquet-format 2.3.0-incubating
org.apache.parquet:parquet-format 2.3.1
org.apache.parquet:parquet-hadoop 1.8.1
org.apache.parquet:parquet-hadoop 1.8.2
org.apache.parquet:parquet-jackson 1.8.1
org.apache.parquet:parquet-jackson 1.8.2
org.apache.parquet:parquet-scala_2.10 1.8.1
org.apache.spark:spark-catalyst_2.11 2.2.0
org.apache.spark:spark-core_2.11 2.2.0
org.apache.spark:spark-graphx_2.11 2.2.0
org.apache.spark:spark-launcher_2.11 2.2.0
org.apache.spark:spark-mllib-local_2.11 2.2.0
org.apache.spark:spark-mllib_2.11 2.2.0
org.apache.spark:spark-network-common_2.11 2.2.0
org.apache.spark:spark-network-shuffle_2.11 2.2.0
org.apache.spark:spark-sketch_2.11 2.2.0
org.apache.spark:spark-sql_2.11 2.2.0
org.apache.spark:spark-streaming_2.11 2.2.0
org.apache.spark:spark-tags_2.11 2.2.0
org.apache.spark:spark-unsafe_2.11 2.2.0
org.apache.xbean:xbean-asm-util 4.4
org.apache.xbean:xbean-asm5-shaded 4.4
org.apache:ivy 2.3.0
org.bdgenomics.adam:adam-core-spark2_2.11 0.20.0
org.bdgenomics.bdg-formats:bdg-formats 0.9.0
org.bdgenomics.utils:utils-cli-spark2_2.11 0.2.8
org.bdgenomics.utils:utils-intervalrdd-spark2_2.11 0.2.8
org.bdgenomics.utils:utils-io-spark2_2.11 0.2.8
org.bdgenomics.utils:utils-metrics-spark2_2.11 0.2.8
org.bdgenomics.utils:utils-misc-spark2_2.11 0.2.8
org.broadinstitute.hellbender.Main:gatk-package 4.0.4.0-local
org.broadinstitute.hellbender.Main:gatk-package 4.0.4.0-spark
org.broadinstitute:google-cloud-nio-GATK4-custom-patch 0.20.4-alpha-GCS-RETRY-FIX
org.codehaus.jettison:jettison 1.1
org.codehaus.plexus:plexus-interpolation 1.0
org.codehaus.plexus:plexus-utils 1.5.6
org.eclipse.jetty:jetty-client 9.3.11.v20160721
org.eclipse.jetty:jetty-continuation 9.3.11.v20160721
org.eclipse.jetty:jetty-http 9.3.11.v20160721
org.eclipse.jetty:jetty-io 9.3.11.v20160721
org.eclipse.jetty:jetty-plus 9.3.11.v20160721
org.eclipse.jetty:jetty-proxy 9.3.11.v20160721
org.eclipse.jetty:jetty-security 9.3.11.v20160721
org.eclipse.jetty:jetty-server 9.3.11.v20160721
org.eclipse.jetty:jetty-servlet 9.3.11.v20160721
org.eclipse.jetty:jetty-servlets 9.3.11.v20160721
org.eclipse.jetty:jetty-util 9.3.11.v20160721
org.eclipse.jgit:org.eclipse.jgit 4.8.0.201706111038-r
org.fusesource.leveldbjni:leveldbjni-all 1.8
org.glassfish.hk2.external:aopalliance-repackaged 2.4.0-b34
org.glassfish.hk2.external:javax.inject 2.4.0-b34
org.glassfish.hk2:hk2-api 2.4.0-b34
org.glassfish.hk2:hk2-locator 2.4.0-b34
org.glassfish.hk2:hk2-utils 2.4.0-b34
org.glassfish.hk2:osgi-resource-locator 1.0.1
org.glassfish.jersey.bundles.repackaged:jersey-guava 2.22.2
org.glassfish.jersey.containers:jersey-container-servlet-core 2.22.2
org.glassfish.jersey.containers:jersey-container-servlet 2.22.2
org.glassfish.jersey.core:jersey-client 2.22.2
org.glassfish.jersey.core:jersey-common 2.22.2
org.glassfish.jersey.core:jersey-server 2.22.2
org.glassfish.jersey.media:jersey-media-jaxb 2.22.2
org.iq80.leveldb:leveldb-api 0.7
org.iq80.leveldb:leveldb 0.7
org.javassist:javassist 3.18.2-GA
org.jgrapht:jgrapht-core 0.9.1
org.jpmml:pmml-model 1.2.15
org.jpmml:pmml-schema 1.2.15
org.json:json 20160810
org.jsoup:jsoup 1.11.2
org.jvnet:tiger-types 1.4
org.mortbay.jetty:jetty-sslengine 6.1.26
org.mortbay.jetty:jetty-util 6.1.26
org.mortbay.jetty:jetty 6.1.26
org.multiverse:multiverse-core 0.7.0
org.objenesis:objenesis 2.1
org.ojalgo:ojalgo-commons-math3 1.0.0
org.ojalgo:ojalgo 44.0.0
org.reflections:reflections 0.9.10
org.roaringbitmap:RoaringBitmap 0.5.11
org.seqdoop:hadoop-bam 7.9.1
org.slf4j:jcl-over-slf4j 1.7.16
org.slf4j:jcl-over-slf4j 1.7.21
org.slf4j:jul-to-slf4j 1.7.21
org.slf4j:log4j-over-slf4j 1.7.21
org.slf4j:slf4j-api 1.7.2
org.slf4j:slf4j-api 1.7.22
org.slf4j:slf4j-api 1.7.25
org.slf4j:slf4j-log4j12 1.7.21
org.spark-project.spark:unused 1.0.0
org.threeten:threetenbp 1.3.3
org.xerial.snappy:snappy-java 1.0.3-rc3
org.xerial:sqlite-jdbc 3.20.1
org.yaml:snakeyaml 1.17
org.yaml:snakeyaml 1.18
picard:picard 2.9.0-1-gf5b9f50-SNAPSHOT
pl.edu.icm:JLargeArrays 1.5
plugin:plugin *
resources:resources 1.8.0_121
rt:rt 1.8.0_121
software.amazon.ion:ion-java 1.0.2
zipfs:zipfs 1.8.0_121

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