gkno troubleshooting in Mac OS 10.8.5

Question

[Kizuna]

Hi Guys,

I just started to build gkno on my personal MacBook, the building process seemed ok, however some tools were not built:

verifyBamID, musket, rufus, jellyfish, mutatrix..

Do you have any idea why ? Has anyone encountered these issue before ?

P.S:

$java -version
java version "1.7.0_55"
Java(TM) SE Runtime Environment (build 1.7.0_55-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.55-b03, mixed mode)

Best !
Kizuna

[Alex Reynolds]

Try running gkno update and perhaps examining or posting the logs for problem tools.

[Kizuna]

Hi Alex,

once doing gkno update:

bamtools...done.
blast...done.
freebayes...done.
gatk...done.
glia...done.
libStatGen...done.
bamUtil...done.
fastQValidator...ERROR: See logs/update_fastQValidator.* files for more details.

Logs:

/opt/local/bin/ranlib: archive member: ../libStatGen.a(FortranFormat.o) size too large (archive member extends past the end of the file)
ar: internal ranlib command failed
make[3]: *** [../libStatGen.a] Error 1
make[2]: *** [bam] Error 2
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [../../libStatGen/libStatGen.a] Error 2
make: *** [src] Error 2

[Alex Reynolds]

If you're running into a compilation issue, you might also post an issue on the gkno Github site for the developers to look at, including a description of your build toolkit (versions of gcc/llvm, ant, cmake, etc.), a transcript of your build, test and update logs, as well as the text of all error logs.

[Kizuna]

I have re-installed newer versions of apache-ant and python and gkno was re-built again. Although missing verifyBamID, musket, rufus, jellyfish, mutatrix, as these are not the principal pipes everything is ok :))

thanks again Al Ward

Answer 1

[alistairnward]

Hi Kizuna,

We're looking into these problems at BC. Unfortunately, we haven't been able to test all of the tools on all possible operating systems, so we sometimes run into some problems. In the meantime, gkno is completely operational using all of the other tools. If you type ./gkno, you should see a list of available tools and pipelines (those beginning with '!') are unavailable due to the failed compilations. But everything else is there are ready to use.

We'll try and get a fix for the other tools asap.

Answer 2

[Kizuna]

Important updates regarding this conversation can be found at https://github.com/gkno/gkno_launcher/issues/10