[DOCKTESTERS] Core workflow icgc reference data location and gosu

Mon Dec 5 12:16:03 EST 2016

By the way Denis, I now get this message when running dockstore:

cwltool version is 1.0.20161202203310 , Dockstore is tested with
1.0.20161114152756
Override and run with `--script`

I've added the --script to the command line and it works, but just so you
know.

Miguel

On Mon, Dec 5, 2016 at 4:05 PM, Miguel Vazquez <miguel.vazquez at cnio.es>
wrote:

> 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/i
>> o/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
>>> Twitter: @OICR_news
>>> *www.oicr.on.ca
>>> <http://redir.aspx?REF=6ENxAoFV69MppiB8UZsW7S62-1GL0mk9G6WWtfVB2o3Ai91dGR3UCAFodHRwOi8vd3d3Lm9pY3Iub24uY2Ev>*
>>>
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>>> _______________________________________________
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>>>
>>>
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