Debian NEW package overview for snpeff
snpeff_4.3t+dfsg1-1_amd64.changes (click to toggle)
Format:1.8
Date:Wed, 31 Mar 2021 15:59:41 +0200
Source:snpeff
Binary:libsnpeff-java libsnpeff-java-doc snpeff
Architecture:source all
Version:4.3t+dfsg1-1
Distribution:experimental
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Pierre Gruet <pgt@debian.org>
Description:
libsnpeff-java - genetic variant annotation and effect prediction toolbox - lib
libsnpeff-java-doc - Documentation for Snp Effect
snpeff     - genetic variant annotation and effect prediction toolbox - tool
Closes:986141
Changes:
snpeff (4.3t+dfsg1-1) experimental; urgency=medium

  * Initial release (Closes: #986141)
Files:
1cf504d4a210a662e8fc017e6ecabe2d 2661 java optional snpeff_4.3t+dfsg1-1.dsc
b836426733b3b4d1504199d82f10b3c7 101389664 java optional snpeff_4.3t+dfsg1.orig.tar.xz
152d8eb3a9c64c81cc76122835d6d7cc 16208 java optional snpeff_4.3t+dfsg1-1.debian.tar.xz
c7d49a23bf55b574440811f71de9c480 1046252 doc optional libsnpeff-java-doc_4.3t+dfsg1-1_all.deb
1cc842bf1131d2ed2a312acb19dfbf9b 1524556 java optional libsnpeff-java_4.3t+dfsg1-1_all.deb
b3be0b553f7ea073089df259548244b1 408896 java optional snpeff_4.3t+dfsg1-1_all.deb
73a7e62c15b33ae6ba6f4757e74b4006 17859 java optional snpeff_4.3t+dfsg1-1_amd64.buildinfo
snpeff_4.3t+dfsg1-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:snpeff
Binary:libsnpeff-java, snpeff, libsnpeff-java-doc
Architecture:all
Version:4.3t+dfsg1-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Andreas Tille <tille@debian.org>, Pierre Gruet <pgt@debian.org>
Homepage:https://pcingola.github.io/SnpEff/
Standards-Version:4.5.1
Vcs-Browser:https://salsa.debian.org/med-team/snpeff
Vcs-Git:https://salsa.debian.org/med-team/snpeff.git
Build-Depends:debhelper-compat (=13), javahelper, default-jdk, default-jdk-doc, maven-debian-helper, libmaven-assembly-plugin-java, libtrove3-java, liblog4j1.2-java, libhtsjdk-java, libbiojava4-java, junit4, libcommons-codec-java, libcommons-io-java, libcommons-cli-java, libcommons-math3-java, libfreemarker-java, libmaven-javadoc-plugin-java, junit4-doc, libcommons-codec-java-doc, libcommons-io-java-doc, libcommons-math3-java-doc, libfreemarker-java-doc, liblog4j1.2-java-doc, libhtsjdk-java-doc, libbiojava4-java-doc, libtrove3-java-doc, libcharts4j-java, libapfloat-java, libdistlib-java, scala-library
Package-List:libsnpeff-java deb java optional arch=all libsnpeff-java-doc deb doc optional arch=all snpeff deb java optional arch=all
Files:
b836426733b3b4d1504199d82f10b3c7 101389664 snpeff_4.3t+dfsg1.orig.tar.xz
152d8eb3a9c64c81cc76122835d6d7cc 16208 snpeff_4.3t+dfsg1-1.debian.tar.xz
lintian 2.94.0~bpo10+1 check for snpeff_4.3t+dfsg1-1.dsc (click to toggle)
README.source for snpeff_4.3t+dfsg1-1.dsc (click to toggle)
Information about snpeff
------------------------

This package was debianized using the mh_make command
from the maven-debian-helper package.

The build system uses Maven but prevents it from downloading
anything from the Internet, making the build compliant with
the Debian policy.
control file for libsnpeff-java_4.3t+dfsg1-1_all.deb (click to toggle)
Package:libsnpeff-java
Source:snpeff
Version:4.3t+dfsg1-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:1603
Depends:junit4 (>=4.13.1), libapfloat-java (>=1.9.1), libcharts4j-java (>=1.3), libcommons-cli-java (>=1.4), libcommons-codec-java (>=1.15), libcommons-io-java (>=2.8.0), libcommons-math3-java (>=3.6.1), libdistlib-java (>=1.0), libfreemarker-java, libhtsjdk-java (>=2.14.3), liblog4j1.2-java (>=1.2.17), libtrove3-java
Suggests:libsnpeff-java-doc
Section:java
Priority:optional
Homepage:https://pcingola.github.io/SnpEff/
Description:
genetic variant annotation and effect prediction toolbox - lib
 SnpEff is a variant annotation and effect prediction tool. It annotates
 and predicts the effects of variants on genes (such as amino acid
 changes).
 .
 The inputs are predicted variants (SNPs, insertions, deletions and
 MNPs). The input file is usually obtained as a result of a sequencing
 experiment, and it is usually in variant call format (VCF).
 .
 SnpEff analyzes the input variants. It annotates the variants and
 calculates the effects they produce on known genes (e.g. amino acid
 changes).
 .
 This package contains the library.
lintian 2.94.0~bpo10+1 check for libsnpeff-java_4.3t+dfsg1-1_all.deb (click to toggle)
contents of libsnpeff-java_4.3t+dfsg1-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2021-03-31 13:59 ./
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/doc/libsnpeff-java/
-rw-r--r-- root/root       743 2021-03-17 17:14 ./usr/share/doc/libsnpeff-java/README.Debian
-rw-r--r-- root/root       161 2021-03-31 13:59 ./usr/share/doc/libsnpeff-java/changelog.Debian.gz
-rw-r--r-- root/root      2885 2021-03-17 17:20 ./usr/share/doc/libsnpeff-java/copyright
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/java/
-rw-r--r-- root/root   1606877 2021-03-31 13:59 ./usr/share/java/snpeff.jar
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/maven-repo/
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/maven-repo/org/
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/maven-repo/org/snpeff/
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/maven-repo/org/snpeff/snpeff/
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/maven-repo/org/snpeff/snpeff/4.3t/
-rw-r--r-- root/root      5410 2021-03-31 13:59 ./usr/share/maven-repo/org/snpeff/snpeff/4.3t/snpeff-4.3t.pom
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/maven-repo/org/snpeff/snpeff/debian/
-rw-r--r-- root/root      5412 2021-03-31 13:59 ./usr/share/maven-repo/org/snpeff/snpeff/debian/snpeff-debian.pom
lrwxrwxrwx root/root         0 2021-03-31 13:59 ./usr/share/java/snpeff-4.3t.jar -> snpeff.jar
lrwxrwxrwx root/root         0 2021-03-31 13:59 ./usr/share/maven-repo/org/snpeff/snpeff/4.3t/snpeff-4.3t.jar -> ../../../../../java/snpeff.jar
lrwxrwxrwx root/root         0 2021-03-31 13:59 ./usr/share/maven-repo/org/snpeff/snpeff/debian/snpeff-debian.jar -> ../../../../../java/snpeff.jar
control file for libsnpeff-java-doc_4.3t+dfsg1-1_all.deb (click to toggle)
Package:libsnpeff-java-doc
Source:snpeff
Version:4.3t+dfsg1-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:23033
Recommends:default-jdk-doc, junit4-doc, libcommons-codec-java-doc, libcommons-io-java-doc, libcommons-math3-java-doc, libfreemarker-java-doc, libhtsjdk-java-doc, liblog4j1.2-java-doc, libtrove3-java-doc
Suggests:libsnpeff-java
Section:doc
Priority:optional
Homepage:https://pcingola.github.io/SnpEff/
Description:
Documentation for Snp Effect
 Variant annotation and effect prediction package.
 .
 This package contains the API documentation of libsnpeff-java.
lintian 2.94.0~bpo10+1 check for libsnpeff-java-doc_4.3t+dfsg1-1_all.deb (click to toggle)
contents of libsnpeff-java-doc_4.3t+dfsg1-1_all.deb (click to toggle)
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drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-03-31 13:59 ./usr/share/doc/libsnpeff-java/
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control file for snpeff_4.3t+dfsg1-1_all.deb (click to toggle)
Package:snpeff
Version:4.3t+dfsg1-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:8024
Depends:libsnpeff-java (=4.3t+dfsg1-1)
Suggests:vcfanno
Section:java
Priority:optional
Homepage:https://pcingola.github.io/SnpEff/
Description:
genetic variant annotation and effect prediction toolbox - tool
 "We are all different!" Geneticists agree to this.
 Even twins, who are said to be identical are on a molecular
 level only "mostly" identical. And even within the exact same individual,
 healthy cells acquire mutations such that we are all genetic mosaics.
 Changes to individual cells may be induced by environmental factors,
 e.g. like UV light, or happen sporadically as mishaps during cellular
 divisions.
 .
 Because there are so many genetic differences, and most have just no
 particular meaning for the development of a phenotype, i.e. most have no
 effect, it would be nice to have heuristics implemented that direct the
 researcher towards single-nucleotide polymorphisms (SNPs) that are most
 likely to be relevant. This identifies the gene that causes or contributes
 to, e.g, an illness, and possibly also genes that are affected by that
 change. Such mechanistic understanding of a disease, particularly when
 multiple genes and multiple genetic variants are contributing to the
 then "polygenic" phenotype, is at the onset of drug development and
 increasingly also for selecting individualized therapies in the clinic.
 .
 SnpEff is a variant annotation and effect prediction tool. It annotates
 and predicts the effects of variants on genes (such as amino acid
 changes).
 The inputs are predicted variants (SNPs, insertions, deletions and
 MNPs). The input file is usually obtained as a result of a sequencing
 experiment, and it is usually in variant call format (VCF).
 .
 SnpEff analyzes the input variants. It annotates the variants and
 calculates the effects they produce on known genes (e.g. amino acid
 changes).
 .
 This package contains the command line tool.
lintian 2.94.0~bpo10+1 check for snpeff_4.3t+dfsg1-1_all.deb (click to toggle)
contents of snpeff_4.3t+dfsg1-1_all.deb (click to toggle)
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-rw-r--r-- root/root   8196216 2021-03-31 13:59 ./etc/snpEff.config
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-rwxr-xr-x root/root      1376 2021-03-31 13:59 ./usr/bin/snpEff
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Timestamp: 31.03.2021 / 16:00:57 (UTC)