Provide more information on how to run the test instance

[lbeltrame]

When running the instance through GenomeSpace, I get a bunch of Java exceptions on files not found. Some more information might be needed to see how to run a demo.

[liefeld]

Hi

could you give us a bit more detail about what exactly you are trying to do and where the errors occir?

Thanks

Ted

On Tue, Jan 21, 2014 at 5:35 AM, Luca Beltrame [email protected]:

When running the instance through GenomeSpace, I get a bunch of Java exceptions on files not found. Some more information might be needed to see how to run a demo.

— Reply to this email directly or view it on GitHubhttps://github.com/chapmanb/o8/issues/1 .

Ted Liefeld Voice: (617) 714-7490 Cancer Genomics Informatics Front desk: (617) 714-7000 Broad Institute Fax: (617) 714-8955 7 Cambridge Center Email: [email protected] Cambridge, MA 02142 http://www.broad.mit.edu/cancer

[lbeltrame]

could you give us a bit more detail about what exactly you are trying to do and where the errors occir?

Here are the steps on how to reproduce:

1. Cloned o8;
2. Started it with lein run -c config/web-processing.yaml;
3. Logged in at http://localhost:8080
4. Logged in using variantdemo/demo
5. Waited for the UI to fully load
6. Selected bsnip-demo-filter.vcf

The following errors were logged:

[Tue Jan 21 12:22:37 CET 2014] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=tmp/cache/www_genomespace_org/Home/Public/chapmanb/biodata/GRCh37/seq/GRCh37.fa OUTPUT=tmp/cache/www_genomespace_org/Home/Public/chapmanb/biodata/GRCh37/seq/GRCh37.dict
TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Jan 21 12:22:37 CET 2014] Executing as [email protected] on Linux 3.13.0-rc8-2.g7ce0a21-desktop amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_09-b05; Picard version: 1.73(1234) [Tue Jan 21 12:22:37 CET 2014] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2058027008 FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page net.sf.picard.PicardException: Error opening file: GRCh37.fa

This is repeated for any demo VCF I select.

[chapmanb]

Luca; Sorry about the issue. The server should be downloading these reference files from GenomeSpace initially but for some reason seems to be failing to. Apologies, I haven't had as much time to work on o8 as I'd like and this might be suffering from some bit rot. I'll dig into these issues more but don't have a quick solution right now until I can investigate.