Ecosyste.ms: Docker

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mugicrow/pfal_variant_call : latest

bcftools-based variant calling pipeline

Ubuntu 22.04.1 LTS

Latest release: almost 2 years ago - 32 downloads - 243 dependencies

JSON

Dependencies

base 4.2.2
compiler 4.2.2
datasets 4.2.2
grDevices 4.2.2
graphics 4.2.2
grid 4.2.2
methods 4.2.2
parallel 4.2.2
splines 4.2.2
stats4 4.2.2
stats 4.2.2
tcltk 4.2.2
tools 4.2.2
translations 4.2.2
utils 4.2.2

ubuntu/adduser 3.118ubuntu5
ubuntu/apt 2.4.8
ubuntu/base-files 12ubuntu4.2
ubuntu/base-passwd 3.5.52build1
ubuntu/bash 5.1-6ubuntu1
ubuntu/bsdutils 1:2.37.2-4ubuntu3
ubuntu/ca-certificates 20211016
ubuntu/coreutils 8.32-4.1ubuntu1
ubuntu/cuda-compat-11-8 520.61.05-1
ubuntu/cuda-cudart-11-8 11.8.89-1
ubuntu/cuda-keyring 1.0-1
ubuntu/cuda-toolkit-11-8-config-common 11.8.89-1
ubuntu/cuda-toolkit-11-config-common 11.8.89-1
ubuntu/cuda-toolkit-config-common 11.8.89-1
ubuntu/dash 0.5.11 git20210903 057cd650a4ed-3build1
ubuntu/debconf 1.5.79ubuntu1
ubuntu/debianutils 5.5-1ubuntu2
ubuntu/diffutils 1:3.8-0ubuntu2
ubuntu/dirmngr 2.2.27-3ubuntu2.1
ubuntu/dpkg 1.21.1ubuntu2.1
ubuntu/e2fsprogs 1.46.5-2ubuntu1.1
ubuntu/findutils 4.8.0-1ubuntu3
ubuntu/gcc-12-base 12.1.0-2ubuntu1~22.04
ubuntu/gnupg-l10n 2.2.27-3ubuntu2.1
ubuntu/gnupg-utils 2.2.27-3ubuntu2.1
ubuntu/gnupg2 2.2.27-3ubuntu2.1
ubuntu/gnupg 2.2.27-3ubuntu2.1
ubuntu/gpg-agent 2.2.27-3ubuntu2.1
ubuntu/gpg-wks-client 2.2.27-3ubuntu2.1
ubuntu/gpg-wks-server 2.2.27-3ubuntu2.1
ubuntu/gpg 2.2.27-3ubuntu2.1
ubuntu/gpgconf 2.2.27-3ubuntu2.1
ubuntu/gpgsm 2.2.27-3ubuntu2.1
ubuntu/gpgv 2.2.27-3ubuntu2.1
ubuntu/grep 3.7-1build1
ubuntu/gzip 1.10-4ubuntu4.1
ubuntu/hostname 3.23ubuntu2
ubuntu/init-system-helpers 1.62
ubuntu/libacl1 2.3.1-1
ubuntu/libapt-pkg6.0 2.4.8
ubuntu/libassuan0 2.5.5-1build1
ubuntu/libattr1 1:2.5.1-1build1
ubuntu/libaudit-common 1:3.0.7-1build1
ubuntu/libaudit1 1:3.0.7-1build1
ubuntu/libblkid1 2.37.2-4ubuntu3
ubuntu/libbz2-1.0 1.0.8-5build1
ubuntu/libc-bin 2.35-0ubuntu3.1
ubuntu/libc6 2.35-0ubuntu3.1
ubuntu/libcap-ng0 0.7.9-2.2build3
ubuntu/libcap2 1:2.44-1build3
ubuntu/libcom-err2 1.46.5-2ubuntu1.1
ubuntu/libcrypt1 1:4.4.27-1
ubuntu/libdb5.3 5.3.28 dfsg1-0.8ubuntu3
ubuntu/libdebconfclient0 0.261ubuntu1
ubuntu/libext2fs2 1.46.5-2ubuntu1.1
ubuntu/libffi8 3.4.2-4
ubuntu/libgcc-s1 12.1.0-2ubuntu1~22.04
ubuntu/libgcrypt20 1.9.4-3ubuntu3
ubuntu/libgmp10 2:6.2.1 dfsg-3ubuntu1
ubuntu/libgnutls30 3.7.3-4ubuntu1.1
ubuntu/libgpg-error0 1.43-3
ubuntu/libgssapi-krb5-2 1.19.2-2
ubuntu/libhogweed6 3.7.3-1build2
ubuntu/libidn2-0 2.3.2-2build1
ubuntu/libk5crypto3 1.19.2-2
ubuntu/libkeyutils1 1.6.1-2ubuntu3
ubuntu/libkrb5-3 1.19.2-2
ubuntu/libkrb5support0 1.19.2-2
ubuntu/libksba8 1.6.0-2ubuntu0.1
ubuntu/libldap-2.5-0 2.5.13 dfsg-0ubuntu0.22.04.1
ubuntu/liblz4-1 1.9.3-2build2
ubuntu/liblzma5 5.2.5-2ubuntu1
ubuntu/libmount1 2.37.2-4ubuntu3
ubuntu/libncurses6 6.3-2
ubuntu/libncursesw6 6.3-2
ubuntu/libnettle8 3.7.3-1build2
ubuntu/libnpth0 1.6-3build2
ubuntu/libnsl2 1.3.0-2build2
ubuntu/libp11-kit0 0.24.0-6build1
ubuntu/libpam-modules-bin 1.4.0-11ubuntu2
ubuntu/libpam-modules 1.4.0-11ubuntu2
ubuntu/libpam-runtime 1.4.0-11ubuntu2
ubuntu/libpam0g 1.4.0-11ubuntu2
ubuntu/libpcre2-8-0 10.39-3ubuntu0.1
ubuntu/libpcre3 2:8.39-13ubuntu0.22.04.1
ubuntu/libprocps8 2:3.3.17-6ubuntu2
ubuntu/libreadline8 8.1.2-1
ubuntu/libsasl2-2 2.1.27 dfsg2-3ubuntu1
ubuntu/libsasl2-modules-db 2.1.27 dfsg2-3ubuntu1
ubuntu/libseccomp2 2.5.3-2ubuntu2
ubuntu/libselinux1 3.3-1build2
ubuntu/libsemanage-common 3.3-1build2
ubuntu/libsemanage2 3.3-1build2
ubuntu/libsepol2 3.3-1build1
ubuntu/libsmartcols1 2.37.2-4ubuntu3
ubuntu/libsqlite3-0 3.37.2-2
ubuntu/libss2 1.46.5-2ubuntu1.1
ubuntu/libssl3 3.0.2-0ubuntu1.6
ubuntu/libstdc 6 12.1.0-2ubuntu1~22.04
ubuntu/libsystemd0 249.11-0ubuntu3.6
ubuntu/libtasn1-6 4.18.0-4build1
ubuntu/libtinfo6 6.3-2
ubuntu/libtirpc-common 1.3.2-2ubuntu0.1
ubuntu/libtirpc3 1.3.2-2ubuntu0.1
ubuntu/libudev1 249.11-0ubuntu3.6
ubuntu/libunistring2 1.0-1
ubuntu/libuuid1 2.37.2-4ubuntu3
ubuntu/libxxhash0 0.8.1-1
ubuntu/libzstd1 1.4.8 dfsg-3build1
ubuntu/login 1:4.8.1-2ubuntu2
ubuntu/logsave 1.46.5-2ubuntu1.1
ubuntu/lsb-base 11.1.0ubuntu4
ubuntu/mawk 1.3.4.20200120-3
ubuntu/mount 2.37.2-4ubuntu3
ubuntu/ncurses-base 6.3-2
ubuntu/ncurses-bin 6.3-2
ubuntu/openssl 3.0.2-0ubuntu1.6
ubuntu/passwd 1:4.8.1-2ubuntu2
ubuntu/perl-base 5.34.0-3ubuntu1.1
ubuntu/pinentry-curses 1.1.1-1build2
ubuntu/procps 2:3.3.17-6ubuntu2
ubuntu/readline-common 8.1.2-1
ubuntu/sed 4.8-1ubuntu2
ubuntu/sensible-utils 0.0.17
ubuntu/sysvinit-utils 3.01-1ubuntu1
ubuntu/tar 1.34 dfsg-1build3
ubuntu/ubuntu-keyring 2021.03.26
ubuntu/usrmerge 25ubuntu2
ubuntu/util-linux 2.37.2-4ubuntu3
ubuntu/zlib1g 1:1.2.11.dfsg-2ubuntu9.2

bash 5.1.16
java 17.0.3-internal 0-adhoc..src
python 3.9.15

ch.qos.logback:logback-classic 1.2.11
ch.qos.logback:logback-core 1.2.11
com.beust:jcommander 1.35
com.esotericsoftware.kryo:kryo 2.24.0
com.esotericsoftware.reflectasm:reflectasm 1.09
com.fasterxml.jackson.core:jackson-annotations 2.10.5
com.fasterxml.jackson.core:jackson-core 2.10.5
com.fasterxml.jackson.core:jackson-databind 2.10.5
com.github.zafarkhaja:java-semver 0.9.0
com.google.code.findbugs:jsr305 3.0.2
com.google.code.gson:gson 2.8.7
com.google.errorprone:error_prone_annotations 2.11.0
com.google.gson:gson 2.2.4
com.google.guava:failureaccess 1.0.1
com.google.guava:guava 15.0
com.google.guava:guava 31.1-jre
com.google.guava:listenablefuture 9999.0-empty-to-avoid-conflict-with-guava
com.google.j2objc:j2objc-annotations 1.3
com.googlecode.charts4j:charts4j 1.3
com.googlecode.javaewah:JavaEWAH 1.1.13
com.sun.activation:jakarta.activation 1.2.2
com.sun.istack:istack-commons-runtime 3.0.12
com.sun:activation 1.1.1
commons-cli:commons-cli 1.5.0
commons-codec:commons-codec 1.15
commons-io:commons-io 2.11.0
commons-io:commons-io 2.4
commons-lang:commons-lang 2.4
commons-lang:commons-lang 2.6
commons-logging:commons-logging 1.1.1
dev.failsafe:failsafe 3.1.0
gpars:gpars 1.2.1
grengine:grengine 1.3.0
jakarta.xml.bind:jakarta.xml.bind-api 2.3.3
javax.activation:javax.activation-api 1.2.0
javax.annotation:javax.annotation-api 1.3.2
javax.mail:mail 1.4.7
javax.xml.bind:jaxb-api 2.3.1
jline:jline 2.9
jrt-fs:jrt-fs 17.0.3-internal
jsr166y:jsr166y 1.7.0
net.sf.jopt-simple:jopt-simple 5.0.3
nextflow:nextflow 22.10.1
nextflow:nextflow 22.10.1-one
nf-commons:nf-commons 22.10.1
nf-httpfs:nf-httpfs 22.10.1
org.apache.commons:commons-collections4 4.3
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.commons:commons-math3 3.6.1
org.apache.logging.log4j:log4j-api 2.17.1
org.apache.logging.log4j:log4j-core 2.17.1
org.apache.logging.log4j:log4j-slf4j-impl 2.17.1
org.apache:ivy 2.3.0
org.apfloat:apfloat 1.10.1
org.biojava.thirdparty:forester 1.039
org.checkerframework.checker.qual:checker-qual 3.12.0
org.codehaus.groovy.json:groovy-json 3.0.13
org.codehaus.groovy.nio:groovy-nio 3.0.13
org.codehaus.groovy.templates:groovy-templates 3.0.13
org.codehaus.groovy.xml:groovy-xml 3.0.13
org.codehaus.groovy:groovy 3.0.13
org.eclipse.jgit:org.eclipse.jgit 6.2.0.202206071550-r
org.glassfish.jaxb:jaxb-runtime 2.3.5
org.glassfish.jaxb:txw2 2.3.5
org.iq80.leveldb:leveldb-api 0.12
org.iq80.leveldb:leveldb 0.12
org.jgrapht:jgrapht-core 1.4.0
org.jsoup:jsoup 1.14.3
org.multiverse:multiverse-core 0.7.0
org.objenesis:objenesis 2.1
org.pf4j:pf4j-update 2.3.0
org.pf4j:pf4j 3.4.1
org.rcsb:ciftools-java-jdk8 3.0.0
org.sharegov:mjson 1.4.1
org.slf4j:jcl-over-slf4j 1.7.36
org.slf4j:jul-to-slf4j 1.7.36
org.slf4j:log4j-over-slf4j 1.7.36
org.slf4j:slf4j-api 1.7.30
org.slf4j:slf4j-api 1.7.36
org.snpeff.SnpEff:snpEff *
org.yaml:snakeyaml 1.30
picard:picard 2.27.4-SNAPSHOT

numpy 1.23.5
pandas 1.5.2
pip 22.3.1
pysam 0.19.1
python-dateutil 2.8.2
pytz 2022.6
setuptools 65.5.1
six 1.16.0
vcfpy 0.13.6
wheel 0.38.4