[Debian-med-packaging] How to obtain sources for org.bioinfo? (Was: Hopefully final problems with maven rules)

[Andreas Tille]

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 

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