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) | |
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| 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 |
| README.source for snpeff_4.3t+dfsg1-1.dsc (click to toggle) | |
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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) | |
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| 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. |
| contents of libsnpeff-java_4.3t+dfsg1-1_all.deb (click to toggle) | |
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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 | |
| copyright of libsnpeff-java_4.3t+dfsg1-1_all.deb (click to toggle) | |
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Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: snpEff
Upstream-Contact: Pablo Cingolani <pcingola@users.sourceforge.net>
Source: https://github.com/pcingola/SnpEff/releases
Files-Excluded: */config/OLD
*.jar
*/papers/*.pdf
*/scripts_build/OLD
examples
git
html/css
html/js
html/*.pdf
html/commonPrint.css
src/main/java/org/snpeff/fastq/Fastq.java
src/main/java/org/snpeff/fastq/FastqBuilder.java
src/main/java/org/snpeff/fastq/FastqVariant.java
Comment: The three last files are provided by biojava4-live. Other files are
useless or have unclear copyright.
Files: *
Copyright: 2008-2021 Pablo Cingolani <pcingola@users.sourceforge.net>
License: LGPL-3
Comment: The source files are not properly copyrighted but the license is
clearly stated in html/SnpEff.html as well as on the website, see
https://pcingola.github.io/SnpEff/download/
Files: src/main/java/net/sf/samtools/tabix/TabixReader.java
Copyright: 2010 Broad Institute
License: Expat
Files: src/main/java/org/broad/*
Copyright: 2007-2011 The Broad Institute of MIT and Harvard
License: LGPL-2.1
Files: src/main/java/org/broad/tribble/*
Copyright: 2007-2009 The Broad Institute, Inc. and the Massachusetts Institute of Technology
License: LGPL-2.1
Files: debian/*
Copyright: 2012 Andreas Tille <tille@debian.org>
2020-2021 Pierre Gruet <pgt@debian.org>
License: LGPL-3
License: LGPL-3
On Debian systems the full text of the LGPL-3 can be found in
/usr/share/common-licenses/LGPL-3
License: Expat
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
.
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
License: LGPL-2.1
On Debian systems the full text of the LGPL-3 can be found in
/usr/share/common-licenses/LGPL-2.1
| |
| control file for libsnpeff-java-doc_4.3t+dfsg1-1_all.deb (click to toggle) | |
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| 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. |
| contents of libsnpeff-java-doc_4.3t+dfsg1-1_all.deb (click to toggle) | |
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| copyright of libsnpeff-java-doc_4.3t+dfsg1-1_all.deb (click to toggle) | |
|---|---|
NOTE: Copyright is the same as libsnpeff-java (libsnpeff-java_4.3t+dfsg1-1_all.deb). Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: snpEff
Upstream-Contact: Pablo Cingolani <pcingola@users.sourceforge.net>
Source: https://github.com/pcingola/SnpEff/releases
Files-Excluded: */config/OLD
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*/papers/*.pdf
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examples
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html/js
html/*.pdf
html/commonPrint.css
src/main/java/org/snpeff/fastq/Fastq.java
src/main/java/org/snpeff/fastq/FastqBuilder.java
src/main/java/org/snpeff/fastq/FastqVariant.java
Comment: The three last files are provided by biojava4-live. Other files are
useless or have unclear copyright.
Files: *
Copyright: 2008-2021 Pablo Cingolani <pcingola@users.sourceforge.net>
License: LGPL-3
Comment: The source files are not properly copyrighted but the license is
clearly stated in html/SnpEff.html as well as on the website, see
https://pcingola.github.io/SnpEff/download/
Files: src/main/java/net/sf/samtools/tabix/TabixReader.java
Copyright: 2010 Broad Institute
License: Expat
Files: src/main/java/org/broad/*
Copyright: 2007-2011 The Broad Institute of MIT and Harvard
License: LGPL-2.1
Files: src/main/java/org/broad/tribble/*
Copyright: 2007-2009 The Broad Institute, Inc. and the Massachusetts Institute of Technology
License: LGPL-2.1
Files: debian/*
Copyright: 2012 Andreas Tille <tille@debian.org>
2020-2021 Pierre Gruet <pgt@debian.org>
License: LGPL-3
License: LGPL-3
On Debian systems the full text of the LGPL-3 can be found in
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License: Expat
Permission is hereby granted, free of charge, to any person obtaining
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.
The above copyright notice and this permission notice shall be
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On Debian systems the full text of the LGPL-3 can be found in
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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. |
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drwxr-xr-x root/root 0 2021-03-31 13:59 ./ drwxr-xr-x root/root 0 2021-03-31 13:59 ./etc/ -rw-r--r-- root/root 8196216 2021-03-31 13:59 ./etc/snpEff.config drwxr-xr-x root/root 0 2021-03-31 13:59 ./usr/ drwxr-xr-x root/root 0 2021-03-31 13:59 ./usr/bin/ -rwxr-xr-x root/root 1376 2021-03-31 13:59 ./usr/bin/snpEff 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/snpeff/ -rw-r--r-- root/root 161 2021-03-31 13:59 ./usr/share/doc/snpeff/changelog.Debian.gz -rw-r--r-- root/root 2885 2021-03-17 17:20 ./usr/share/doc/snpeff/copyright drwxr-xr-x root/root 0 2021-03-31 13:59 ./usr/share/man/ drwxr-xr-x root/root 0 2021-03-31 13:59 ./usr/share/man/man1/ -rw-r--r-- root/root 1857 2021-03-31 13:59 ./usr/share/man/man1/snpEff.1.gz | |
| copyright of snpeff_4.3t+dfsg1-1_all.deb (click to toggle) | |
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NOTE: Copyright is the same as libsnpeff-java (libsnpeff-java_4.3t+dfsg1-1_all.deb). Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: snpEff
Upstream-Contact: Pablo Cingolani <pcingola@users.sourceforge.net>
Source: https://github.com/pcingola/SnpEff/releases
Files-Excluded: */config/OLD
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html/js
html/*.pdf
html/commonPrint.css
src/main/java/org/snpeff/fastq/Fastq.java
src/main/java/org/snpeff/fastq/FastqBuilder.java
src/main/java/org/snpeff/fastq/FastqVariant.java
Comment: The three last files are provided by biojava4-live. Other files are
useless or have unclear copyright.
Files: *
Copyright: 2008-2021 Pablo Cingolani <pcingola@users.sourceforge.net>
License: LGPL-3
Comment: The source files are not properly copyrighted but the license is
clearly stated in html/SnpEff.html as well as on the website, see
https://pcingola.github.io/SnpEff/download/
Files: src/main/java/net/sf/samtools/tabix/TabixReader.java
Copyright: 2010 Broad Institute
License: Expat
Files: src/main/java/org/broad/*
Copyright: 2007-2011 The Broad Institute of MIT and Harvard
License: LGPL-2.1
Files: src/main/java/org/broad/tribble/*
Copyright: 2007-2009 The Broad Institute, Inc. and the Massachusetts Institute of Technology
License: LGPL-2.1
Files: debian/*
Copyright: 2012 Andreas Tille <tille@debian.org>
2020-2021 Pierre Gruet <pgt@debian.org>
License: LGPL-3
License: LGPL-3
On Debian systems the full text of the LGPL-3 can be found in
/usr/share/common-licenses/LGPL-3
License: Expat
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
.
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
License: LGPL-2.1
On Debian systems the full text of the LGPL-3 can be found in
/usr/share/common-licenses/LGPL-2.1
| |
Timestamp: 31.03.2021 / 16:00:57 (UTC)