[DOCKTESTERS] Core workflow icgc reference data location and gosu

Mon Dec 5 10:05:15 EST 2016

Thanks Denis, your suggestion of removing the jar files worked.

Best regards

Miguel

On Mon, Dec 5, 2016 at 3:18 PM, Denis Yuen <Denis.Yuen at oicr.on.ca> wrote:

> 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
> <http://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
> <http://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
> <http://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
> <http://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
>> <http://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/displa
>> y/PANCANCER/Workflow+Testing+Data
>> <http://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
>>
>> Toll-free: 1-866-678-6427
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>>
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>>
>>
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