Hi Emmanuel and Bas, thanks to Bas's tip about the typo in d/rules and Emmanuel's suggested patch
On Thu, Nov 26, 2015 at 09:18:40AM +0100, Emmanuel Bourg wrote: > The groupId for samtools is net.sf.picard and not net/sf, you can see it > in the pom.xml file. Also you can consider patching pom.xml instead of > running "mvn install:install-file" in debian/rules. You want something > like this: > > <dependency> > <groupId>net.sf.samtools</groupId> > <artifactId>samtools</artifactId> > <version>1.70</version> > <scope>compile</scope> > <systemPath>/usr/share/java/sam.jar</systemPath> > </dependency> I made some progress which I commited to Git[1]. Unfortunately it seems I'm not ready yet since in contrast to my assumption that BioJava would be needed I seem to need some other classes that are described here: http://www.massapi.com/package/org/bioinfo/index.html At least I guess so when reading in pom.xml: <dependency> <groupId>org.bioinfo</groupId> <artifactId>bioinfo-formats</artifactId> <version>0.2.0</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.bioinfo</groupId> <artifactId>bioinfo-ngs</artifactId> <version>0.1.0</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.bioinfo</groupId> <artifactId>bioinfo-commons</artifactId> <version>0.10.1</version> <type>jar</type> <scope>compile</scope> </dependency> <dependency> <groupId>org.bioinfo</groupId> <artifactId>bioinfo-math</artifactId> <version>0.3.0</version> </dependency> <dependency> <groupId>org.bioinfo</groupId> <artifactId>bioinfo-graphics</artifactId> <version>0.4.0</version> <scope>compile</scope> </dependency> (-math and -graphics are not at the said URL) Unfortunately I have no idea how to find these? Any hint? Kind regards Andreas. [1] git://anonscm.debian.org/debian-med/qualimap.git -- http://fam-tille.de
