[DOCKTESTERS] Core workflow icgc reference data location and gosu

[Miguel Vazquez]

Denis,

I've tried updating to the latest dockstore and ran into a bug.

ubuntu at ip-10-253-35-14:~$ dockstore
Error: A JNI error has occurred, please check your installation and try
again
Exception in thread "main" java.lang.NoClassDefFoundError:
io/cwl/avro/CWL$GsonBuildException
        at java.lang.Class.getDeclaredMethods0(Native Method)
        at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
        at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
        at java.lang.Class.getMethod0(Class.java:3018)
        at java.lang.Class.getMethod(Class.java:1784)
        at
sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
        at
sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
Caused by: java.lang.ClassNotFoundException:
io.cwl.avro.CWL$GsonBuildException
        at java.net.URLClassLoader$1.run(URLClassLoader.java:370)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 7 more
Caused by: java.util.zip.ZipException: invalid LOC header (bad signature)
        at java.util.zip.ZipFile.read(Native Method)
        at java.util.zip.ZipFile.access$1400(ZipFile.java:60)
        at java.util.zip.ZipFile$ZipFileInputStream.read(ZipFile.java:717)
        at
java.util.zip.ZipFile$ZipFileInflaterInputStream.fill(ZipFile.java:419)
        at
java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
        at sun.misc.Resource.getBytes(Resource.java:124)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:462)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
        ... 13 more

What I did is that I moved the old version of dockstore from
~/bin/dockstore to ~/bin/dockstore.old and downloaded the new version from

https://github.com/ga4gh/dockstore/releases/download/1.1/dockstore

I ran the new dockstore, it downloaded

https://seqwaremaven.oicr.on.ca/artifactory/collab-release/io/dockstore/dockstore-client/1.1/dockstore-client-1.1.jar

and then when I tried running dockstore --version I got the error above.
Anything I can do?

Best regards

Miguel


On Fri, Dec 2, 2016 at 6:15 PM, Denis Yuen <Denis.Yuen at oicr.on.ca> wrote:

> Hi,
>
> I've gone through and created a new release for each of the core tools
> (bwa-mem, delly, dkfz, sanger) with two (non-scientific) changes.
>
> 1) Each of these tools has been redirected to use reference data hosted on
> the icgc portal ( https://dcc.icgc.org/releases/PCAWG ) rather than aws
> in order to conserve our use of S3. This means that sample json parameter
> files have been updated and any references inside the Docker images that
> we're aware of also have been updated. As usual, if re-running workflows
> frequently, you'll want to host these files locally.
>
> If you are using the Dockstore command-line interface, you'll need to
> upgrade to the latest release of dockstore (1.2) to use this new file
> location.
>
> 2) A number of users have run into problems running the workflow when
> running in a multi-user environment (i.e. not running Docker containers
> with the first user on a host). This release replaces most usage of sudo
> inside the tools with gosu to deal with this issue.
>
> The new release numbers are documented at https://wiki.oicr.on.ca/
> display/PANCANCER/Workflow+Testing+Data
> In particular:
>
>    - bwa-mem 2.6.8_1.2
>    - dkfz 2.0.1_cwl1.0
>    - sanger 2.0.3
>    - embl 2.0.1-cwl1.0
>
>
>
> *Denis Yuen*
> Bioinformatics Software Developer
>
>
> *Ontario* *Institute* *for* *Cancer* *Research*
> MaRS Centre
> 661 University Avenue
> Suite 510
> Toronto, Ontario, Canada M5G 0A3
>
> Toll-free: 1-866-678-6427
> Twitter: @OICR_news
> *www.oicr.on.ca <http://www.oicr.on.ca/>*
>
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