[med-svn] [Git][med-team/libgoby-java][master] 12 commits: Setting myself as uploader

Pierre Gruet (@pgt) gitlab at salsa.debian.org
Sun Aug 1 21:21:46 BST 2021 


Pierre Gruet pushed to branch master at Debian Med / libgoby-java


Commits:
e264fe84 by Pierre Gruet at 2021-07-30T11:26:03+02:00
Setting myself as uploader

- - - - -
a5b194ce by Pierre Gruet at 2021-07-30T11:27:09+02:00
Indicating the Salsa paths in d/control

- - - - -
c6e7c71f by Pierre Gruet at 2021-07-30T11:28:21+02:00
Rephrasing the long description to remove first-person pronouns

- - - - -
c33a3932 by Pierre Gruet at 2021-07-30T11:29:57+02:00
Using my debian.org email address

- - - - -
7518194c by Pierre Gruet at 2021-07-30T11:30:23+02:00
Setting Standards version to 4.5.1

- - - - -
92e19d92 by Pierre Gruet at 2021-08-01T22:17:32+02:00
Adding the needed dependencies in d/control

- - - - -
61f7556c by Pierre Gruet at 2021-08-01T22:18:33+02:00
Adding R_HOME and the JRI location into the path to run tests

- - - - -
72fde330 by Pierre Gruet at 2021-08-01T22:19:20+02:00
Skipping the -spi artifact, which is a manifest-only jar

- - - - -
6a71cd0a by Pierre Gruet at 2021-08-01T22:19:48+02:00
Excluding more tests needing the network or non-existing files

- - - - -
e20aa312 by Pierre Gruet at 2021-08-01T22:20:23+02:00
Correcting my patch about reading CLI-like arguments

- - - - -
fa035ec7 by Pierre Gruet at 2021-08-01T22:20:54+02:00
Having the right classpath in the generated jars

- - - - -
5e7b16b8 by Pierre Gruet at 2021-08-01T22:21:17+02:00
Adding a symlink named goby.jar, as needed by the wrapper script

- - - - -


14 changed files:

- debian/changelog
- debian/control
- + debian/libgoby-java.links
- + debian/libgoby-java.manifest
- debian/libgoby-java.poms
- debian/patches/adding_dependencies.patch
- debian/patches/catch_IOException_LineIterator.patch
- debian/patches/computing_Fisher_test_pvalue.patch
- debian/patches/exclude_not_runnable_tests.patch
- debian/patches/inclusions_in_SplitTranscriptsMode.patch
- debian/patches/protoc.patch
- debian/patches/using_commons-cli.patch
- debian/patches/using_correct_SamReader_api.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -10,4 +10,4 @@ libgoby-java (3.3.1+dfsg-1) UNRELEASED; urgency=medium
     - See also https://lists.debian.org/debian-med/2013/02/msg00152.html,
       although written for a previous upstream version of goby.
 
- -- Pierre Gruet <pgtdebian at free.fr>  Tue, 10 Nov 2020 17:50:48 +0100
+ -- Pierre Gruet <pgt at debian.org>  Fri, 30 Jul 2021 11:48:56 +0200


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: libgoby-java
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Pierre Gruet <pgt at debian.org>,
+           Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
@@ -43,9 +44,9 @@ Build-Depends: debhelper-compat (= 13),
                junit4 <!nocheck>,
                testng <!nocheck>,
                libpicard-java <!nocheck>
-Standards-Version: 4.5.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libgoby-java.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libgoby-java.git
+Standards-Version: 4.5.1
+Vcs-Browser: https://salsa.debian.org/med-team/libgoby-java/
+Vcs-Git: https://salsa.debian.org/med-team/libgoby-java.git
 Homepage: http://campagnelab.org/software/goby/
 Rules-Requires-Root: no
 
@@ -53,19 +54,22 @@ Package: libgoby-java
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${java:Depends}
-Recommends: ${java:Recommends}
+         ${maven:Depends},
+         libcommons-collections3-java,
+         libjbzip2-java,
+         libpj-java,
+         r-cran-rjava
+Recommends: ${java:Recommends},
+            ${maven:OptionalDepends}
 Description: store next-generation sequencing data and intermediary analysis results
  Goby is a next-gen data management framework designed to facilitate the
  implementation of efficient data analysis pipelines.
  .
- Goby provides very efficient file formats to store next-generation
- sequencing data and intermediary analysis results. Goby 1.x files were
- compressed with GZip. In Goby 2.0, we introduced novel compression
- approaches that result in state of the art compression of alignment
- data. Goby 2.0 files can compress to a few percent of a BAM file and are
- often smaller than CRAM files.  
+ Goby provides very efficient file formats to store next-generation sequencing
+ data and intermediary analysis results. Goby 1.x files were compressed with
+ GZip. Goby 2.0 introduced novel compression approaches that result in state
+ of the art compression of alignment data. Goby 2.0 files can compress to a few
+ percent of a BAM file and are often smaller than CRAM files.
  .
- Goby also provides utilities that implement common next-gen data
- computations. We design these utilities to make them relatively easy to
- use, yet very efficient.
+ Goby also provides utilities that implement common next-gen data computations.
+ These utilities are designed to be relatively easy to use, yet very efficient.


=====================================
debian/libgoby-java.links
=====================================
@@ -0,0 +1 @@
+usr/share/java/goby-distribution.jar usr/share/java/goby.jar


=====================================
debian/libgoby-java.manifest
=====================================
@@ -0,0 +1,6 @@
+usr/share/java/goby-io.jar:
+ Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar /usr/share/java/jbzip2.jar /usr/lib/R/site-library/rJava/jri/JRI.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar
+
+usr/share/java/goby-distribution.jar:
+ Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/goby-io.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar /usr/share/java/jbzip2.jar /usr/lib/R/site-library/rJava/jri/JRI.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar
+ Main-Class: org.campagnelab.goby.modes.GobyDriver


=====================================
debian/libgoby-java.poms
=====================================
@@ -28,4 +28,4 @@
 pom.xml --has-package-version
 goby-distribution/pom.xml
 goby-io/pom.xml
-goby-spi/pom.xml
+goby-spi/pom.xml --ignore


=====================================
debian/patches/adding_dependencies.patch
=====================================
@@ -1,5 +1,5 @@
 Description: Adding missing dependencies to goby-io/pom.xml
-Author: Pierre Gruet <pgtdebian at free.fr>
+Author: Pierre Gruet <pgt at debian.org>
 Last-Update: 2020-10-31
 
 --- a/goby-io/pom.xml


=====================================
debian/patches/catch_IOException_LineIterator.patch
=====================================
@@ -1,5 +1,5 @@
 Description: Catch the IOException launched by close() method of LineIterator
-Author: Pierre Gruet <pgtdebian at free.fr>
+Author: Pierre Gruet <pgt at debian.org>
 Forwarded: no
 Last-Update: 2020-11-03
 


=====================================
debian/patches/computing_Fisher_test_pvalue.patch
=====================================
@@ -1,5 +1,5 @@
 Description: Computing the Fisher p-value with a Debian-packaged tool
-Author: Pierre Gruet <pgtdebian at free.fr>
+Author: Pierre Gruet <pgt at debian.org>
 Forwarded: not-needed
 Last-Update: 2020-11-01
 


=====================================
debian/patches/exclude_not_runnable_tests.patch
=====================================
@@ -6,9 +6,12 @@ Description: modify a few tests when requiring unpackaged tools
  uses are not provided in the source.
  Two tests in TestSamRecordParser are skipped for the same reason.
  gominer is not packaged, the tests using it are slightly modified.
-Author: Pierre Gruet <pgtdebian at free.fr>
+ One test in TestConcatAlignmentReader needs a file that does not exist.
+ The tests in TestIterateSortedAlignment all use a file that does not exist.
+ One test in TestSkipTo needs to use the network.
+Author: Pierre Gruet <pgt at debian.org>
 Forwarded: no
-Last-Update: 2020-11-08
+Last-Update: 2021-07-31
 
 --- a/goby-distribution/pom.xml
 +++ b/goby-distribution/pom.xml
@@ -23,7 +26,7 @@ Last-Update: 2020-11-08
                  </configuration>
              </plugin>
              <plugin>
-@@ -73,6 +77,16 @@
+@@ -73,6 +77,17 @@
                  </executions>
              </plugin>
              <plugin>
@@ -33,6 +36,7 @@ Last-Update: 2020-11-08
 +                <configuration>
 +                    <excludes>
 +                        <exclude>**/TestGobyPaperTop5000s.java</exclude>
++                        <exclude>**/TestIterateSortedAlignment.java</exclude>
 +                    </excludes>
 +                </configuration>
 +            </plugin>
@@ -121,3 +125,39 @@ Last-Update: 2020-11-08
      @Test
      public void testTestTargetIndexCreation() throws IOException {
          final RoundTripAlignment rtc = new RoundTripAlignment();
+--- a/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestConcatAlignmentReader.java
++++ b/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestConcatAlignmentReader.java
+@@ -26,6 +26,7 @@
+ import org.junit.AfterClass;
+ import org.junit.Before;
+ import org.junit.BeforeClass;
++import org.junit.Ignore;
+ import org.junit.Test;
+ 
+ import java.io.File;
+@@ -338,6 +339,7 @@
+     }
+ 
+ 
++    @Ignore
+     @Test
+     public void testLoadTwoFromFileURLs() throws IOException {
+         final int count;
+--- a/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestSkipTo.java
++++ b/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestSkipTo.java
+@@ -24,6 +24,7 @@
+ import org.apache.commons.logging.LogFactory;
+ import org.junit.AfterClass;
+ import org.junit.BeforeClass;
++import org.junit.Ignore;
+ import org.junit.Test;
+ 
+ import java.io.DataInputStream;
+@@ -439,6 +440,7 @@
+ 
+     }
+ 
++    @Ignore
+     @Test
+     public void testUrlRange() throws IOException {
+ 


=====================================
debian/patches/inclusions_in_SplitTranscriptsMode.patch
=====================================
@@ -1,6 +1,6 @@
 Description: reading class GeneTranscriptRelationships from Goby archive
  The above-named class is in the archive of Goby and thus does not need to be read elsewhere.
-Author: Pierre Gruet <pgtdebian at free.fr>
+Author: Pierre Gruet <pgt at debian.org>
 Forwarded: no
 Last-Update: 2020-11-02
 


=====================================
debian/patches/protoc.patch
=====================================
@@ -1,5 +1,5 @@
 Description: Using Debian-packaged protoc compiler
-Author: Pierre Gruet <pgtdebian at free.fr>
+Author: Pierre Gruet <pgt at debian.org>
 Last-Update: 2020-08-24
 
 --- a/goby-io/pom.xml


=====================================
debian/patches/using_commons-cli.patch
=====================================
@@ -1,7 +1,7 @@
 Description: using classes of commons-cli instead of unpackaged ones
-Author: Pierre Gruet <pgtdebian at free.fr>
+Author: Pierre Gruet <pgt at debian.org>
 Forwarded: not-needed
-Last-Update: 2020-11-02
+Last-Update: 2021-07-31
 
 --- a/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java
 +++ b/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java
@@ -816,12 +816,15 @@ Last-Update: 2020-11-02
  import org.apache.commons.lang.StringUtils;
  import org.campagnelab.goby.alignments.Alignments;
  import org.campagnelab.goby.alignments.filters.AlignmentQualityFilter;
-@@ -62,8 +62,28 @@
+@@ -61,9 +61,30 @@
+     }
  
      public void setParameters(final String parameters) {
-         final String[] args = StringUtils.defaultString(parameters).split("[',=]");
+-        final String[] args = StringUtils.defaultString(parameters).split("[',=]");
 -        qualityThresholdPercent = CLI.getDoubleOption(args, "threshold", 0.05d);
 -        System.err.println("Setting quality threshold to " + qualityThresholdPercent);
++        final String parametersWithHyphens = StringUtils.replace(parameters, "threshold", "-threshold");
++        final String[] args = StringUtils.defaultString(parametersWithHyphens).split("[',=]");
 +        Options options = new Options();
 +
 +        Option threshold = new Option("threshold", "threshold", true, "threshold");


=====================================
debian/patches/using_correct_SamReader_api.patch
=====================================
@@ -1,5 +1,5 @@
 Description: using the correct SamReader api
-Author: Pierre Gruet <pgtdebian at free.fr>
+Author: Pierre Gruet <pgt at debian.org>
 Origin: https://sources.debian.org/src/fastqc/0.11.9+dfsg-4/debian/patches/htsjdk-api.patch
 Forwarded: no
 Last-Update: 2020-11-06


=====================================
debian/rules
=====================================
@@ -3,7 +3,7 @@
 # DH_VERBOSE := 1
 
 %:
-	dh $@
+	dh $@ --with javahelper
 #
 #override_dh_auto_clean:
 #	rm -rf buildsupport/*
@@ -26,5 +26,9 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	# Create a symlink to the directory with test data for tests run from the
 	# goby-distribution directory.
 	ln -s ../test-data goby-distribution/test-data
-	dh_auto_test
+	# Putting the JRI location in the path, as indicated in GobyRengine.java.
+	# Also indicating R_HOME, as found in http://rforge.net/JRI/.
+	export LD_LIBRARY_PATH="$$LD_LIBRARY_PATH:/usr/lib/R/site-library/rJava/jri" && \
+	        export R_HOME="/usr/lib/R" && \
+	        dh_auto_test
 endif



View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/1e72a3f187f726b1f77b1b27323c42aa69ca70cb...5e7b16b802d334b2b3178ae968c4573c4d8a4078

-- 
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/1e72a3f187f726b1f77b1b27323c42aa69ca70cb...5e7b16b802d334b2b3178ae968c4573c4d8a4078
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