initializeDataSource.py dies if the --ds_foldername is an absolute path.

[alanhoyle]

I'm trying to create a custom data source using an ExAC VCF file. I'm running oncotator 1.9.0 in a Docker instance created an image made using the shipped Dockerfile.

If I set the --ds_foldername to an absolute path (e.g. "--ds_foldername=/db_dir/exac"), it dies after it builds the index and gzip parts as it uses the path to create a temporary build before copying it into place. When it tries to copy the results into place, it can't create the absolute path, as it already exists, then just dies.

work-around: if I put "--ds_foldername=exac --dbDir=/db_dir" it works fine: it puts the build files in a temporary location and then creates /db_dir/exac with the expected output at the end.

Aside: it might be worth documenting how to do build new Data Sources from the Docker....

[LeeTL1220]

Yes, (apparently) we did not document initialize datasource well enough.
The ds_foldername is meant to be the name of the folder created inside the
dbdir.

Also, exac is in the next default datasource corpus, which I would have
uploaded by now, except I've been busy with AACR.
On Apr 18, 2016 6:04 PM, "Alan Hoyle" notifications@github.com wrote:

I'm trying to create a custom data source using an ExAC VCF file. I'm
running oncotator 1.9.0 in a Docker instance created an image made using
the shipped Dockerfile.

If I set the --ds_foldername to an absolute path (e.g.
"--ds_foldername=/db_dir/exac"), it dies after it builds the index and gzip
parts as it uses the path to create a temporary build before copying it
into place. When it tries to copy the results into place, it can't create
the absolute path, as it already exists, then just dies.

work-around: if I put "--ds_foldername=exac --dbDir=/db_dir" it works
fine: it puts the build files in a temporary location and then creates
/db_dir/exac with the expected output at the end.

Aside: it might be worth documenting how to do build new Data Sources from
the Docker....

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#350

[LeeTL1220]

Just for you (and anyone else reading this)... I had a hiccup with the
forums, which are being fixed. So these are the updated links until that
is sorted

Default datasources:
http://www.broadinstitute.org/~lichtens/oncobeta/oncotator_v1_ds_April052016.tar.gz

v1.9.0.0:
https://github.com/broadinstitute/oncotator/archive/v1.9.0.0.tar.gz

On Mon, Apr 18, 2016 at 7:16 PM, Lee Lichtenstein <
lichtens@broadinstitute.org> wrote:

Yes, (apparently) we did not document initialize datasource well enough.
The ds_foldername is meant to be the name of the folder created inside the
dbdir.

Also, exac is in the next default datasource corpus, which I would have
uploaded by now, except I've been busy with AACR.
On Apr 18, 2016 6:04 PM, "Alan Hoyle" notifications@github.com wrote:

I'm trying to create a custom data source using an ExAC VCF file. I'm
running oncotator 1.9.0 in a Docker instance created an image made using
the shipped Dockerfile.

If I set the --ds_foldername to an absolute path (e.g.
"--ds_foldername=/db_dir/exac"), it dies after it builds the index and gzip
parts as it uses the path to create a temporary build before copying it
into place. When it tries to copy the results into place, it can't create
the absolute path, as it already exists, then just dies.

work-around: if I put "--ds_foldername=exac --dbDir=/db_dir" it works
fine: it puts the build files in a temporary location and then creates
/db_dir/exac with the expected output at the end.

Aside: it might be worth documenting how to do build new Data Sources
from the Docker....

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Reply to this email directly or view it on GitHub
#350

Lee Lichtenstein
Broad Institute
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Cambridge, MA 02142
617 714 8632