Created FuncotatorDataSourceBundler Tool #7427
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@droazen OK - I think it's ready for your review. |
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@jonn-smith Back to you with my comments. Please go ahead and merge after addressing them.
src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorDataSourceBundler.java
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src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorDataSourceBundler.java
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src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorDataSourceBundler.java
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src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorDataSourceBundler.java
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src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorDataSourceBundler.java
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...java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorDataSourceBundlerUnitTest.java
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...org/broadinstitute/hellbender/tools/funcotator/FuncotatorDataSourceBundlerUtilsUnitTest.java
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src/test/java/org/broadinstitute/hellbender/tools/funcotator/RunScript.java
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data sources for Funcotator.
jonn-smith
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- Bumped the version of Ensembl used by the downloader tool to 52. - Added a test to regenerate the expected output for `testDownloadDatasourcesWithValidation`. - Updated expected results for `testDownloadDatasourcesWithValidation`.
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Is there still anything missing? It is not merged since quite some time. The funcotator data sources in version 1.7 are already lacking at least 2 years behind the current databases. I would like to see a possibility to create own and updated bundles merged. |
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@robby81 There are still one or two issues with the tool that need to be resolved before this can be merged, unfortunately. @jonn-smith will be resuming work on these shortly -- we do want to get this tool into GATK soon to make it easier to create custom Funcotator datasources! |
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@droazen We are still on hold for update the Funcotator datasources. Especially getting new versions of gencode would be desirable and does not work with the current scripts. We already started looking for alternatives for our routine diagnostics workflow. |
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@robby81 Which scripts are you running and what are the errors you see? The data sources scripts are unsupported, but should work out of the box (they did last time I tried them). |
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you may want to have a look here:
https://paste.opensuse.org/40b96df4
Before, I tried it with version 38 of Gencode. It is the indexing, that fails
due to fixed fields, that changed looong time ago.
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On Dienstag, 30. August 2022 16:36:24 CEST Jonn Smith wrote:
@robby81 Which scripts are you running and what are the errors you see? The
data sources scripts
are unsupported, but should work out of the box (they did last time I tried
them).
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@robby81 Ah, OK. Yeah - this is a problem in the parser I wrote. I was trying to be very specific about what was allowed so users could not build erroneous data sources. This is high on my list of fixes. I'm trying to get some time to do them. |
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And for cosmic:
/home/robby/Tools/NGS/gatk-4.2.6.1-src/scripts/funcotator/data_sources/cosmic/
getCosmicDataSources.sh
This script creates the cosmic data sources for the Funcotator GATK tool.
For usage information run with the '-h' option
To retrieve the COSMIC data sources you must have a COSMIC account.
Please enter your COSMIC account credentials:
Enter your email address: ***@***.***
Enter your password:
Creating folders: ...
mkdir: created directory 'cosmic'
mkdir: created directory 'cosmic/hg19'
mkdir: created directory 'cosmic/hg38'
mkdir: created directory 'cosmic_fusion'
mkdir: created directory 'cosmic_fusion/hg19'
mkdir: created directory 'cosmic_fusion/hg38'
mkdir: created directory 'cosmic_tissue'
mkdir: created directory 'cosmic_tissue/hg19'
mkdir: created directory 'cosmic_tissue/hg38'
Getting files ...
get: cosmic/grch37/cosmic/v84/
CosmicCompleteTargetedScreensMutantExport.tsv.gz: ssh: Could not resolve
hostname sftp-cancer.sanger.ac.uk: Name or service not known
get: cosmic/grch37/cosmic/v84/CosmicFusionExport.tsv.gz: ssh: Could not
resolve hostname sftp-cancer.sanger.ac.uk: Name or service not known
get: cosmic/grch38/cosmic/v84/
CosmicCompleteTargetedScreensMutantExport.tsv.gz: ssh: Could not resolve
hostname sftp-cancer.sanger.ac.uk: Name or service not known
get: cosmic/grch38/cosmic/v84/CosmicFusionExport.tsv.gz: ssh: Could not
resolve hostname sftp-cancer.sanger.ac.uk: Name or service not known
***@***.***:~/Tools/NGS>
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r-engelmann.de - Ihre Seite für die Auswertung und Visualisierung von Daten
aus den Bereichen Biomedizin, Finanzen, Sozioökonomie und weitere.
On Dienstag, 30. August 2022 16:36:24 CEST Jonn Smith wrote:
@robby81 Which scripts are you running and what are the errors you see? The
data sources scripts
are unsupported, but should work out of the box (they did last time I tried
them).
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Whats the status here? Also the bundled sources got no updates since 2020. |
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@robby81 This still has to be merged. I've been pulled off onto some other projects for a bit. Some changes to the internals of Funcotator are needed for this tool to be most useful, so I was waiting until those updates were made to merge this. I can compile a new release of the data sources, but I haven't heard from anyone in the community that it's a priority. Can you create a new issue for it? Some questions around a new release: If I were to create one, what would the new release include? Would there be any new data sources that were not included before? Are any included data sources no longer useful and should be removed? |
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The biggest thing for a new data source would be the latest (or dare I say
the ability to choose the version) of GENCODE.
…On Wed, Apr 5, 2023, 10:06 AM Jonn Smith ***@***.***> wrote:
@robby81 <https://github.com/robby81> This still has to be merged. I've
been pulled off onto some other projects for a bit. Some changes to the
internals of Funcotator are needed for this tool to be most useful, so I
was waiting until those updates were made to merge this.
I can compile a new release of the data sources, but I haven't heard from
anyone in the community that it's a priority. Can you create a new issue
for it? Some questions around a new release: If I were to create one, what
would the new release include? Would there be any new data sources that
were not included before? Are any included data sources no longer useful
and should be removed?
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Is there anything happening on this front? |
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@robby81 - we're finally getting around to fixing some of the underlying incompatibilities with this. We're working on updating some of the internals of Funcotator and there will be a new datasources release very soon. After that I'll test this branch again to see if it's functional. |
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