[med-svn] [Git][med-team/snpeff][master] After running dh-maven helper
Andreas Tille
gitlab at salsa.debian.org
Sat Oct 27 11:19:36 BST 2018
Andreas Tille pushed to branch master at Debian Med / snpeff
Commits:
2da2948b by Andreas Tille at 2018-10-27T10:19:05Z
After running dh-maven helper
- - - - -
12 changed files:
- + debian/README.source
- debian/control
- debian/copyright
- + debian/libsnpeff-java-doc.doc-base.api
- + debian/libsnpeff-java-doc.install
- + debian/libsnpeff-java.poms
- + debian/maven.cleanIgnoreRules
- + debian/maven.ignoreRules
- + debian/maven.properties
- + debian/maven.publishedRules
- + debian/maven.rules
- + debian/snpeff.poms
Changes:
=====================================
debian/README.source
=====================================
@@ -0,0 +1,9 @@
+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
=====================================
@@ -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
=====================================
@@ -9,16 +9,16 @@ Files-Excluded: */config/OLD
Files: *
Copyright: © 2008-2016, Pablo Cingolani <pcingola at 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 at 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
=====================================
@@ -0,0 +1,10 @@
+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
=====================================
@@ -0,0 +1,2 @@
+target/apidocs/* usr/share/doc/libsnpeff-java/api
+
=====================================
debian/libsnpeff-java.poms
=====================================
@@ -0,0 +1,28 @@
+# List of POM files for the package
+# Format of this file is:
+# <path to pom file> [option]*
+# where option can be:
+# --ignore: ignore this POM and its artifact if any
+# --ignore-pom: don't install the POM. To use on POM files that are created
+# temporarily for certain artifacts such as Javadoc jars. [mh_install, mh_installpoms]
+# --no-parent: remove the <parent> tag from the POM
+# --package=<package>: an alternative package to use when installing this POM
+# and its artifact
+# --has-package-version: to indicate that the original version of the POM is the same as the upstream part
+# of the version for the package.
+# --keep-elements=<elem1,elem2>: a list of XML elements to keep in the POM
+# during a clean operation with mh_cleanpom or mh_installpom
+# --artifact=<path>: path to the build artifact associated with this POM,
+# it will be installed when using the command mh_install. [mh_install]
+# --java-lib: install the jar into /usr/share/java to comply with Debian
+# packaging guidelines
+# --usj-name=<name>: name to use when installing the library in /usr/share/java
+# --usj-version=<version>: version to use when installing the library in /usr/share/java
+# --no-usj-versionless: don't install the versionless link in /usr/share/java
+# --dest-jar=<path>: the destination for the real jar.
+# It will be installed with mh_install. [mh_install]
+# --classifier=<classifier>: Optional, the classifier for the jar. Empty by default.
+# --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.
+# Empty by default. [mh_install]
+#
+pom.xml --has-package-version
=====================================
debian/maven.cleanIgnoreRules
=====================================
@@ -0,0 +1 @@
+
=====================================
debian/maven.ignoreRules
=====================================
@@ -0,0 +1,10 @@
+
+com.googlecode.charts4j charts4j * * * *
+com.typesafe.akka akka-actor * * * *
+distlib distlib * * * *
+org.apache.maven.plugins maven-assembly-plugin * * * *
+org.apache.maven.plugins maven-javadoc-plugin * * * *
+org.apfloat apfloat * * * *
+org.biojava biojava3-core * * * *
+org.biojava biojava3-structure * * * *
+samtools samtools * * * *
=====================================
debian/maven.properties
=====================================
@@ -0,0 +1,5 @@
+# Include here properties to pass to Maven during the build.
+# For example:
+# maven.test.skip=true
+# project.build.sourceEncoding=UTF-8
+
=====================================
debian/maven.publishedRules
=====================================
@@ -0,0 +1,2 @@
+
+org.snpeff SnpEff jar s/.*/debian/ * *
=====================================
debian/maven.rules
=====================================
@@ -0,0 +1,6 @@
+
+junit junit jar s/4\..*/4.x/ * *
+org.snpeff SnpEff jar * * *
+org.snpeff SnpEff jar s/.*/debian/ * *
+log4j log4j * s/1\.2\..*/1.2.x/ * *
+net.sf.trove4j trove4j * s/.*/2.x/ * *
=====================================
debian/snpeff.poms
=====================================
@@ -0,0 +1,28 @@
+# List of POM files for the package
+# Format of this file is:
+# <path to pom file> [option]*
+# where option can be:
+# --ignore: ignore this POM and its artifact if any
+# --ignore-pom: don't install the POM. To use on POM files that are created
+# temporarily for certain artifacts such as Javadoc jars. [mh_install, mh_installpoms]
+# --no-parent: remove the <parent> tag from the POM
+# --package=<package>: an alternative package to use when installing this POM
+# and its artifact
+# --has-package-version: to indicate that the original version of the POM is the same as the upstream part
+# of the version for the package.
+# --keep-elements=<elem1,elem2>: a list of XML elements to keep in the POM
+# during a clean operation with mh_cleanpom or mh_installpom
+# --artifact=<path>: path to the build artifact associated with this POM,
+# it will be installed when using the command mh_install. [mh_install]
+# --java-lib: install the jar into /usr/share/java to comply with Debian
+# packaging guidelines
+# --usj-name=<name>: name to use when installing the library in /usr/share/java
+# --usj-version=<version>: version to use when installing the library in /usr/share/java
+# --no-usj-versionless: don't install the versionless link in /usr/share/java
+# --dest-jar=<path>: the destination for the real jar.
+# It will be installed with mh_install. [mh_install]
+# --classifier=<classifier>: Optional, the classifier for the jar. Empty by default.
+# --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.
+# Empty by default. [mh_install]
+#
+pom.xml
View it on GitLab: https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3
--
View it on GitLab: https://salsa.debian.org/med-team/snpeff/commit/2da2948bfbdc6849e8412423a1ad0db4916faad3
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