[DOCKTESTERS] Core workflow icgc reference data location and gosu

Mon Dec 5 09:18:58 EST 2016

Hi,
Having some difficulty reproducing this.
It's possible that a jar file was corrupted in transit, try deleting ~/.dockstore/self-installs/ and retrying.

________________________________
From: Francis Ouellette
Sent: December 3, 2016 6:48 PM
To: docktesters at lists.icgc.org
Cc: Denis Yuen; Miguel Vazquez
Subject: Re: [DOCKTESTERS] Core workflow icgc reference data location and gosu

Anybody else with these problems?

@bffo

On Dec 3, 2016, at 06:10, Miguel Vazquez <miguel.vazquez at cnio.es<redir.aspx?REF=gBpE9AiHmuiuvDUAEnz3tTDoQy9axyr5cEmEJPIlA_VmKdtdGR3UCAFtYWlsdG86bWlndWVsLnZhenF1ZXpAY25pby5lcw..>> wrote:

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<redir.aspx?REF=vtvNh7M4mSM6EnX5X5RBQT6yuC34P1E8AGXsUG7v5k3Ai91dGR3UCAFodHRwczovL2dpdGh1Yi5jb20vZ2E0Z2gvZG9ja3N0b3JlL3JlbGVhc2VzL2Rvd25sb2FkLzEuMS9kb2Nrc3RvcmU.>

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<redir.aspx?REF=ve8N1tuIFt7Q9PHxUVa7e7XlFLWCAQc6kBj3u_ioYxTAi91dGR3UCAFodHRwczovL3NlcXdhcmVtYXZlbi5vaWNyLm9uLmNhL2FydGlmYWN0b3J5L2NvbGxhYi1yZWxlYXNlL2lvL2RvY2tzdG9yZS9kb2Nrc3RvcmUtY2xpZW50LzEuMS9kb2Nrc3RvcmUtY2xpZW50LTEuMS5qYXI.>

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<redir.aspx?REF=B02mNdZLmBzaFo9Tc0z09WyLINYXG1xd0wrkLmK-NbHAi91dGR3UCAFtYWlsdG86RGVuaXMuWXVlbkBvaWNyLm9uLmNh>> 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<redir.aspx?REF=y92t6fwOZPWSy1ByFbT15HBgbvZEyZTae1L9J7yyYPXAi91dGR3UCAFodHRwczovL2RjYy5pY2djLm9yZy9yZWxlYXNlcy9QQ0FXRw..> ) 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<redir.aspx?REF=BMDUo6pOiVGdgJvTLKVZbANCOe6S1GLoZ4yFn9RnIfrAi91dGR3UCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kaXNwbGF5L1BBTkNBTkNFUi9Xb3JrZmxvdytUZXN0aW5nK0RhdGE.>
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

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