Commit 2da2948b authored by Andreas Tille's avatar Andreas Tille
Browse files

After running dh-maven helper

parent 5acd02d3

debian/README.source

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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.

debian/control

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@@ -6,10 +6,11 @@ Priority: optional 
Build-Depends: debhelper (>= 11~),

               javahelper,

               default-jdk,

               default-jdk-doc,

               maven-debian-helper,

               libmaven-assembly-plugin-java,

               libtrove-java,

               liblog4j2-java,

               liblog4j1.2-java,

               libhtsjdk-java,

               libbiojava4-java,

               junit4,
@@ -18,14 +19,22 @@ Build-Depends: debhelper (>= 11~), 
               libcommons-cli-java,

               libcommons-math3-java,

               libcommons-cli-java-doc,

               libfreemarker-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,

               libtrove-java-doc

Standards-Version: 4.1.4

Vcs-Browser: https://salsa.debian.org/med-team/snpeff

Vcs-Git: https://salsa.debian.org/med-team/snpeff.git

Homepage: http://snpeff.sourceforge.net/



Package: snpeff

Architecture: any

Architecture: all

Depends: ${shlibs:Depends},

         ${misc:Depends}

Description: genetic variant annotation and effect prediction toolbox
@@ -41,3 +50,21 @@ Description: genetic variant annotation and effect prediction toolbox 
 calculates the effects they produce on known genes (e.g. amino acid

 changes). A list of effects and annotations that SnpEff can calculate

 can be found here. 



Package: libsnpeff-java

Architecture: all

Depends: ${misc:Depends}, ${maven:Depends}

Suggests: ${maven:OptionalDepends}, libsnpeff-java-doc

Description: Snp Effect

 Variant annotation and effect prediction package.



Package: libsnpeff-java-doc

Architecture: all

Section: doc

Depends: ${misc:Depends}

Recommends: ${maven:DocDepends}, ${maven:DocOptionalDepends}

Suggests: libsnpeff-java

Description: Documentation for Snp Effect

 Variant annotation and effect prediction package.

 .

 This package contains the API documentation of libsnpeff-java.

debian/copyright

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@@ -9,16 +9,16 @@ Files-Excluded: */config/OLD 


Files: *

Copyright: © 2008-2016, Pablo Cingolani <pcingola@users.sourceforge.net>

License: LGPL-3+

License: Apache-2.0 or BSD or LGPL-2 or LGPL-2.1



Files: debian/*

Copyright: © 2012 Andreas Tille <tille@debian.org>

License: LGPL-3+

License: Apache-2.0



License: LGPL-3+

License: LGPL-2.1

 This program is free software: you can redistribute it and/or modify

 it under the terms of the GNU Lesser General Public License as published by

 the Free Software Foundation, either version 3 of the License, or

 the Free Software Foundation, either version 2.1 of the License, or

 (at your option) any later version.

 .

 This program is distributed in the hope that it will be useful,
@@ -26,8 +26,16 @@ License: LGPL-3+ 
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 GNU General Public License for more details.

 .

 You should have received a copy of the GNU Lesser General Public License

 along with this program.  If not, see <http://www.gnu.org/licenses/>.

 .

 On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included

 in the file ‘/usr/share/common-licenses/LGPL-3’.
 
 in the file ‘/usr/share/common-licenses/LGPL-2.1’.



License: Apache-2.0

 On Debian systems, the full text of the Apache-2.0 license

 can be found in the file '/usr/share/common-licenses/Apache-2.0'



License: BSD

  FIXME: include the full text of the license here



License: LGPL-2

 On Debian systems, the full text of the LGPL-2 license

 can be found in the file '/usr/share/common-licenses/LGPL-2'

debian/libsnpeff-java-doc.doc-base.api

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Document: libsnpeff-java

Title: API Javadoc for Snp Effect

Author: Snp Effect developers

Abstract: This is the API Javadoc provided for the

 libsnpeff-java library.

Section: Programming



Format: HTML

Index: /usr/share/doc/libsnpeff-java/api/index.html

Files: /usr/share/doc/libsnpeff-java/api/*

debian/libsnpeff-java-doc.install

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target/apidocs/* usr/share/doc/libsnpeff-java/api