[med-svn] [libalter-java] 02/02: Add initial debian/ dir
Andreas Tille
tille at debian.org
Sat Sep 5 06:20:28 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libalter-java.
commit 518c50a3976e022ed548d288f329665cbdebd48d
Author: Andreas Tille <tille at debian.org>
Date: Sat Sep 5 08:18:51 2015 +0200
Add initial debian/ dir
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 25 ++++++
debian/copyright | 23 +++++
debian/doc-base | 20 +++++
debian/patches/fix_unmappable_characters.patch | 105 ++++++++++++++++++++++
debian/patches/series | 3 +
debian/patches/suppress_build_web_interface.patch | 27 ++++++
debian/patches/use_debian_packaged_jar.patch | 22 +++++
debian/rules | 9 ++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++
debian/watch | 4 +
13 files changed, 257 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a6b7622
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+libalter-java (1.3.3+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Sat, 05 Sep 2015 07:13:34 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..9faa2d3
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,25 @@
+Source: libalter-java
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ javahelper,
+ default-jdk,
+ ant,
+ ant-contrib,
+ javacc
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libalter-java.git
+Vcs-Git: git://anonscm.debian.org/debian-med/libalter-java.git
+Homepage: http://sing.ei.uvigo.es/ALTER/
+
+Package: libalter-java
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: genomic sequences ALignment Transformation EnviRonment
+ ALTER (ALignment Transformation EnviRonment) is a web-based tool to
+ transform between multiple sequence alignment formats. ALTER focuses on
+ the specifications of mainstream alignment and analysis programs rather
+ than on the conversion among more or less specific formats.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..9743d4c
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,23 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ALTER
+Upstream-Contact: alter at sing.ei.uvigo.es
+Source: http://sourceforge.net/projects/alterconverter/files/
+Files-Excluded: ant-contrib
+ javacc-*
+ javadoc
+ web
+ CVS
+ */CVS
+ .cvsignore
+ */*/.cvsignore
+ */*/.DS_Store
+ */alter.bat
+
+Files: *
+Copyright: 2009-2014 David Posada <dposada at uvigo.es>,
+ Florentino Fdez-Riverola <riverola at uvigo.es>
+License: <license>
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: <license>
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..5e7e1d4
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,20 @@
+Document: <pkg>
+Title: <title for this doc>
+Author: <author of this doc>
+Abstract: <if you have no better clue the short and
+ long description from debian/control might fit here as well>
+Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
+
+# pick one of the below options
+Format: Text
+Files: /usr/share/doc/<pkg>/<pkg>.txt.gz
+
+Format: html
+Index: /usr/share/doc/<pkg>/html/index.html
+Files: /usr/share/doc/<pkg>/html/*
+
+Format: pdf
+Files: /usr/share/doc/<pkg>/<pkg>.pdf.gz
+
+Format: postscript
+Files: /usr/share/doc/<pkg>/<pkg>.ps.gz
diff --git a/debian/patches/fix_unmappable_characters.patch b/debian/patches/fix_unmappable_characters.patch
new file mode 100644
index 0000000..0f3cfdd
--- /dev/null
+++ b/debian/patches/fix_unmappable_characters.patch
@@ -0,0 +1,105 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
+Description: Build has problems with non-ASCII characters in comments
+
+--- a/alter-lib/src/converter/ProgramOptions.java
++++ b/alter-lib/src/converter/ProgramOptions.java
+@@ -22,7 +22,7 @@ import java.util.*;
+ /**
+ * Provides methods to check the supported programs and formats, as well as
+ * the possible options for each one of them.
+- * @author Daniel Gonzalez Peña
++ * @author Daniel Gonzalez Pena
+ */
+ public class ProgramOptions{
+
+--- a/alter-lib/src/reader/ReaderUtils.java
++++ b/alter-lib/src/reader/ReaderUtils.java
+@@ -38,7 +38,7 @@ public class ReaderUtils
+ public static void replaceMatch(Sequence seq, Sequence first) throws ParseException
+ {
+ if (seq.getData().contains("."))
+- //Lanzar excepción si el caracter está en la primera secuencia
++ //Lanzar excepcion si el caracter esta en la primera secuencia
+ if (seq == first)
+ throw new ParseException("Match character \".\" in first sequence of MSA.");
+ else
+--- a/alter-lib/src/writer/Writer.java
++++ b/alter-lib/src/writer/Writer.java
+@@ -20,7 +20,7 @@ package writer;
+ import types.MSA;
+
+ /**
+- * Define los métodos que deben implementar todos los escritores.
++ * Define los metodos que deben implementar todos los escritores.
+ * @author Daniel Gomez Blanco
+ * @version 1.1
+ */
+--- a/alter-lib/src/writer/FastaWriter.java
++++ b/alter-lib/src/writer/FastaWriter.java
+@@ -145,7 +145,7 @@ public class FastaWriter implements Writ
+ //Mientras queden caracteres por escribir
+ while(!data.isEmpty())
+ {
+- //Si hay caracteres para hacer una línea
++ //Si hay caracteres para hacer una linea
+ if (data.length() > 60)
+ {
+ outb.append(data.substring(0, 60));
+--- a/alter-lib/src/writer/NexusWriter.java
++++ b/alter-lib/src/writer/NexusWriter.java
+@@ -343,7 +343,7 @@ public class NexusWriter implements Writ
+ outb.append(id + WriterUtils.align(id.length(),longestId)
+ + WriterUtils.align(longestId, 10) + " ");
+
+- //Escribir una línea si es posible
++ //Escribir una linea si es posible
+ if (data[index].length() > 50)
+ {
+ outb.append(data[index].substring(0, 50));
+--- a/alter-lib/src/writer/PhylipCodABCWriter.java
++++ b/alter-lib/src/writer/PhylipCodABCWriter.java
+@@ -25,7 +25,7 @@ import types.Typeable;
+
+ /**
+ * Extends class PhylipWriter to adapt the output to CodABC.
+- * @author Daniel Glez-Peña
++ * @author Daniel Glez-Pena
+ * @version 1.0
+ */
+
+--- a/alter-lib/src/writer/PirDnaSPWriter.java
++++ b/alter-lib/src/writer/PirDnaSPWriter.java
+@@ -34,7 +34,7 @@ public class PirDnaSPWriter extends PirW
+ /**
+ * Constructor de la clase. Llama al constructor de la superclase.
+ * @param os Sistema operativo de salida.
+- * @param lowerCase Salida en letras minúsculas.
++ * @param lowerCase Salida en letras minusculas.
+ * @param match Salida codificada con caracteres match.
+ * @param logger Nombre del logger a instanciar.
+ */
+@@ -45,7 +45,7 @@ public class PirDnaSPWriter extends PirW
+
+ /**
+ * Escribe un MSA en formato PIR adaptado a dnaSP. Para ello
+- * comprueba que el MSA no sea de proteínas. Luego llama al método de la superclase.
++ * comprueba que el MSA no sea de proteinas. Luego llama al metodo de la superclase.
+ * @param msa MSA de entrada.
+ * @return Cadena con la el MSA en formato PIR.
+ */
+--- a/alter-lib/src/writer/PirWriter.java
++++ b/alter-lib/src/writer/PirWriter.java
+@@ -114,10 +114,10 @@ public class PirWriter implements Writer
+
+ /**
+ * Devuelve una cadena con el identificador de la secuencia. En caso de
+- * que el identificador de secuencia esté repetido se renombra.
++ * que el identificador de secuencia este repetido se renombra.
+ * @param seq Secuencia de la cual se desea obtener el identificador.
+ * @param ids Secuencias copiadas hasta el momento.
+- * @return Identificador de secuencia único.
++ * @return Identificador de secuencia unico.
+ */
+ protected String getId(Sequence seq, LinkedHashSet<String> ids)
+ {
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..3624acc
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+suppress_build_web_interface.patch
+use_debian_packaged_jar.patch
+fix_unmappable_characters.patch
diff --git a/debian/patches/suppress_build_web_interface.patch b/debian/patches/suppress_build_web_interface.patch
new file mode 100644
index 0000000..735fcef
--- /dev/null
+++ b/debian/patches/suppress_build_web_interface.patch
@@ -0,0 +1,27 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
+Description: Currently only the library is packaged while the web interface is ignored
+ The rationale is that libalter-java is packaged as a dependency for
+ other packages. There was no explicite request to package the
+ web interface which involves a lot of third party JARs and thus
+ makes it complex to package.
+
+--- a/build.xml
++++ b/build.xml
+@@ -3,7 +3,6 @@
+
+ <target name="buildlib">
+ <ant antfile="build.xml" dir="./alter-lib" inheritAll="false"/>
+- <copy file="./alter-lib/dist/ALTER.jar" tofile="./web/ALTER.jar"/>
+ </target>
+
+ <target name="buildall" depends="clean, buildlib">
+@@ -11,8 +10,6 @@
+ </target>
+ <target name="clean">
+ <ant antfile="build.xml" dir="./alter-lib" target="clean" inheritAll="false"/>
+- <ant antfile="build.xml" dir="./web" target="clean" inheritAll="false"/>
+- <delete file="./web/ALTER.jar"/>
+ </target>
+
+ </project>
diff --git a/debian/patches/use_debian_packaged_jar.patch b/debian/patches/use_debian_packaged_jar.patch
new file mode 100644
index 0000000..3bf960d
--- /dev/null
+++ b/debian/patches/use_debian_packaged_jar.patch
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
+Description: Use Debian packaged JARs
+
+--- a/alter-lib/build.xml
++++ b/alter-lib/build.xml
+@@ -5,13 +5,13 @@
+ <property name="build" location="${ALTERLIB.basedir}/build"/>
+ <property name="src" location="${ALTERLIB.basedir}/src"/>
+ <property name="dist" location="${ALTERLIB.basedir}/dist"/>
+- <property name="javacchome" location="${ALTERLIB.basedir}/javacc-5.0"/>
++ <property name="javacchome" location="/usr/share/java/"/>
+ <property name="grammars" location="${src}/parser"/>
+ <property name="javaversion" value="1.6" />
+
+ <taskdef resource="net/sf/antcontrib/antcontrib.properties">
+ <classpath>
+- <pathelement location="${ALTERLIB.basedir}/ant-contrib/ant-contrib-1.0b3.jar"/>
++ <pathelement location="/usr/share/ant/lib/ant-contrib.jar"/>
+ </classpath>
+ </taskdef>
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..3cabee1
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+ dh $@ --with javahelper
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..dd11b70
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Daniel Glez-Peña and Daniel Gómez-Blanco and Miguel Reboiro-Jato and Florentino Fdez-Riverola and David Posada
+ Title: "ALTER: program-oriented conversion of DNA and protein alignments"
+ Journal: Nucl. Acids Res.
+ Year: 2010
+ Volume: 38
+ Number: suppl 2
+ Pages: W14-W18
+ DOI: 10.1093/nar/gkq321
+ PMID: 20439312
+ URL: http://nar.oxfordjournals.org/content/38/suppl_2/W14
+ eprint: http://nar.oxfordjournals.org/content/38/suppl_2/W14.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..6b04ee2
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ http://sf.net/alterconverter/alter-source-(\d[\d\.]+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libalter-java.git
More information about the debian-med-commit
mailing list