Re: Help to detect java classes in drop-seq (covid-19 relevant) needed

2020-05-21 Thread Felix Natter
Andreas Tille writes: > Hi, hello Andreas, > On Wed, May 20, 2020 at 10:07:48PM +0200, Andreas Tille wrote: >> >> Thanks. This was pretty helpful. Now I need to package the >> remaining JAR which is not yet packaged from >> >>http://la4j.org/ > > I made some progress and also uploaded lib

Re: Help to detect java classes in drop-seq (covid-19 relevant) needed

2020-05-21 Thread Andreas Tille
Hi, On Wed, May 20, 2020 at 10:07:48PM +0200, Andreas Tille wrote: > > Thanks. This was pretty helpful. Now I need to package the > remaining JAR which is not yet packaged from > >http://la4j.org/ I made some progress and also uploaded libla4j-java[1] to new. With this I tried to build d

Re: Help to detect java classes in drop-seq (covid-19 relevant) needed

2020-05-20 Thread Andreas Tille
HI Felix, On Wed, May 20, 2020 at 06:12:54PM +0200, Felix Natter wrote: > > 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

Re: Help to detect java classes in drop-seq (covid-19 relevant) needed

2020-05-20 Thread Felix Natter
Andreas Tille 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 bu

Re: Help to detect java classes in drop-seq (covid-19 relevant) needed

2020-05-20 Thread Andrius Merkys
Hi Andreas, On 2020-05-20 14:20, Andreas Tille wrote: > Any hint how to take this hurdle would be welcome. Try setting the CLASSPATH in your d/rules like this: export CLASSPATH := $(DEBJAR)/htsjdk.jar:$(DEBJAR)/picard.jar:$(DEBJAR)/commons-collections4.jar I did this in one of packages and it s

Help to detect java classes in drop-seq (covid-19 relevant) needed

2020-05-20 Thread Andreas Tille
Hi, 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 s