[GET-dev] Requesting help with installation issues, please

[Liviu Constantinescu]

Good morning,

Thank you for adding me to the mailing list.

I would like to contribute a utility program I wrote to the GET-Evidence core, which automatically sets up a Unix-based virtual machine, installs GET-Evidence inside it, and hosts the application at localhost:8080 via port forwarding.

In order to finalise my script, I just need to resolve a few final issues with our install:

• The import_dbsnp.php script does not appear to import the file referenced (ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/b138_SNPChrPosOnRef.bcp.gz) correctly, nor the latest version of said file. How do I get the latest dbSNP into GET-Evidence?

• The "import_omim" stage of the makefile no longer appears to function as intended. What's the current procedure to import the OMIM files, and where do I ones that are up-to-date?

and

• The GeneTests data required by GET-Evidence no longer appears to be available, and we have not been able to source the missing file as the project appears to be defunct, succeeded by others whose data format is no longer supported. Is there some way to get the new data into GET-Evidence? What data are you currently using on the GET-Evidence website?

Finally, although the application builds and runs without these datasets, we have found that the genome-analyzer grinds to a halt after a genome is updated, with the following error:

https://gist.github.com/GrubLord/3c8c7684b032b80d393a

This may be related to a problem with the "make daily" target, which produces a great many errors that look like this...

> Use of uninitialized value $columns{"nblosum100>2"} in array element at ./ProcessTableForVis.pl line 213, <DATA> line 2663.
> Use of uninitialized value $columns{"gene"} in array element at ./ProcessTableForVis.pl line 90, <DATA> line 2663.
> Use of uninitialized value $columns{"nblosum100>2"} in array element at ./ProcessTableForVis.pl line 213, <DATA> line 2664.
> Use of uninitialized value $columns{"nblosum100>2"} in array element at ./ProcessTableForVis.pl line 213, <DATA> line 2665.
> Use of uninitialized value $columns{"nblosum100>2"} in array element at ./ProcessTableForVis.pl line 213, <DATA> line 2666.
> Use of uninitialized value $columns{"gene"} in array element at ./ProcessTableForVis.pl line 90, <DATA> line 2666.
> etc. etc.


... and then fails to create certain necessary data files, such as (I assume) the /home/trait/data/getev-latest.json.gz file which the previous error indicates is missing.

Hopefully there's an easy fix for the above, as I am certain you must have devised workarounds for all of these in the main GET-Evidence web application.

Can I get your help in replicating your setup, please?

Thanks in advance,


----------------------------
Liviu Constantinescu (PhD)
Information Architect
Centre for Clinical Genomics
Garvan Institute of Medical Research
Office: +612 9355 5775
l.constantinescu at garvan.org.au