Andreas Tille <andr...@an3as.eu> writes:
> Hi,
hello Andreas,
> I've started packaging of drop-seq[1] and replaced those JARs that are
> replacable by Debian packaged versions. I also have set CLASS_PATH in
> d/rules, but it seems to be ignored. I have dealt with similar cases by
> patching it into build.xml but here I have not found the relevant place
> to do so. I'm aware that I did not yet added all needed classes to
> CLASS_PATH, but currently I get
>
>
> dh_auto_build
> ant -Duser.name debian
> Buildfile: /build/drop-seq-2.3.0+dfsg/build.xml
> [taskdef] Could not load definitions from resource testngtasks. It could
> not be found.
>
> compile-src:
> [mkdir] Created dir: /build/drop-seq-2.3.0+dfsg/classes
> [javac] Compiling 201 source files to /build/drop-seq-2.3.0+dfsg/classes
> [javac]
> /build/drop-seq-2.3.0+dfsg/src/java/org/broadinstitute/dropseqrna/TranscriptomeException.java:28:
> error: package htsjdk.samtools does not exist
> [javac] import htsjdk.samtools.SAMException;
> [javac] ^
> [javac]
> /build/drop-seq-2.3.0+dfsg/src/java/org/broadinstitute/dropseqrna/TranscriptomeException.java:34:
> error: cannot find symbol
> [javac] public class TranscriptomeException extends SAMException
> [javac] ^
> [javac] symbol: class SAMException
> ...
Since the upstream jars were in ${lib}, you need to point ${lib} to
/usr/share/java/:
diff --git a/debian/patches/debian_packaged_libs.patch
b/debian/patches/debian_packaged_libs.patch
index 1d3790c..4fc1ed9 100644
--- a/debian/patches/debian_packaged_libs.patch
+++ b/debian/patches/debian_packaged_libs.patch
@@ -1,6 +1,6 @@
--- a/build.xml
+++ b/build.xml
-@@ -35,7 +35,7 @@
+@@ -35,13 +35,15 @@
<property name="classes.test" location="testclasses"/>
<property name="test.output" location="dist/test"/>
<property name="javadoc" location="javadoc"/>
@@ -9,3 +9,13 @@
<property name="public.dir" location="."/>
<!-- INIT -->
+ <path id="classpath">
+- <fileset dir="${lib}">
+- <include name="*.jar"/>
++ <fileset dir="/usr/share/java">
++ <include name="htsjdk.jar"/>
++ <include name="picard.jar"/>
++ <include name="commons-collections4.jar"/>
+ </fileset>
+ </path>
+ <path id="test.classpath">
You have to add more libraries like these.
Cheers and Best Regards,
--
Felix Natter
debian/rules!
