Groups > linux.debian.maint.java > #8603

How to obtain sources for org.bioinfo? (Was: Hopefully final problems with maven rules)

From	Andreas Tille <andreas@an3as.eu>
Newsgroups	linux.debian.maint.java
Subject	How to obtain sources for org.bioinfo? (Was: Hopefully final problems with maven rules)
Date	2015-11-26 19:30 +0100
Message-ID	<qz9sS-nO-17@gated-at.bofh.it> (permalink)
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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

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Thread

Continuing work on qualimap (Was: Any help?) Andreas Tille <andreas@an3as.eu> - 2015-11-24 14:20 +0100
  Re: Continuing work on qualimap (Was: Any help?) Emmanuel Bourg <ebourg@apache.org> - 2015-11-24 14:30 +0100
    Re: Continuing work on qualimap (Was: Any help?) Andreas Tille <andreas@an3as.eu> - 2015-11-24 15:50 +0100
      Re: Continuing work on qualimap Bas Couwenberg <sebastic@xs4all.nl> - 2015-11-24 16:00 +0100
        Re: Continuing work on qualimap Emmanuel Bourg <ebourg@apache.org> - 2015-11-24 16:10 +0100
    Hopefully final problems with maven rules (Re: Continuing work on  qualimap) Andreas Tille <andreas@an3as.eu> - 2015-11-26 09:00 +0100
      Re: Hopefully final problems with maven rules (Re: Continuing work on  qualimap) Sebastiaan Couwenberg <sebastic@xs4all.nl> - 2015-11-26 09:10 +0100
      Re: Hopefully final problems with maven rules (Re: Continuing work on  qualimap) Emmanuel Bourg <ebourg@apache.org> - 2015-11-26 09:20 +0100
        Providing Maven input files for picard-tools (Was: Hopefully final  problems with maven rules) Andreas Tille <andreas@an3as.eu> - 2015-11-26 12:00 +0100
          Re: Providing Maven input files for picard-tools (Was: Hopefully  final problems with maven rules) Vincent Danjean <vdanjean@debian.org> - 2015-11-26 12:50 +0100
        How to obtain sources for org.bioinfo? (Was: Hopefully final  problems with maven rules) Andreas Tille <andreas@an3as.eu> - 2015-11-26 19:30 +0100

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