cBioportal datasets

[Silke Appenzeller]

Hello,

I installed a local version of cBioportal-docker on our server
cbioportal/cbioportal:4.1.13
mysql:5.7
cbioportal/session-service:0.5.0
mongo:3.7.9

In general it seems to work.

Using the command
> docker compose run cbioportal metaImport.py -u
> http://cbioportal:8080 -s study/lgg_ucsf_2014/ -o
I can import the study without any error-messages.

When I am using other studies, i.e. acc_tcga_pan_can_atlas_2018 or
msk_impact_2017, I get some error messages

> docker compose run cbioportal metaImport.py -u
> http://cbioportal:8080 -s study/acc_tcga_pan_can_atlas_2018/ -o


ERROR: data_gene_panel_matrix.txt: lines [2, 3, 4, (88 more)]: Gene
panel ID is not in database.
Please import this gene panel before loading study data.; value
encountered: 'WXS'

ERROR: data_sv.txt: line 1: Missing column: Sample_ID; value
encountered: 'Sample_Id,
Site1_Hugo_Symbol, (...)'
ERROR: data_sv.txt: line 1: Fusion event requires "Site1_Exon" and
"Site2_Exon" columns
ERROR: data_sv.txt: line 1: Fusion event requires
"Site1_Ensembl_Transcript_Id" and "
Site2_Ensembl_Transcript_Id" columns
ERROR: data_sv.txt: Invalid column header, file cannot be parsed

> docker compose run cbioportal metaImport.py -u
> http://cbioportal:8080 -s study/msk_impact_2017/ -o


ERROR: data_gene_panel_matrix.txt: lines [2, 3, 4, (10942 more)]: Gene
panel ID is not in database. Please import this gene panel before
loading study data.; values encountered: ['IMPACT341', 'IMPACT410']

ERROR: data_sv.txt: line 1: Missing column: Sample_ID; value
encountered: 'Sample_Id, SV_Status, (...)'
ERROR: data_sv.txt: line 1: Fusion event requires "Site1_Exon" and
"Site2_Exon" columns
ERROR: data_sv.txt: Invalid column header, file cannot be parsed

Is this a known issue? Can you tell me how that can be fixed?

Thank you very much

Silke Appenzeller


Dr. Silke Appenzeller
Comprehensive Cancer Center Mainfranken
Core Unit Bioinformatics
University Hospital Wuerzburg
Germany

Office:
Krebsregister
Schweinfurter Str. 28
D-97076 Wuerzburg

Tel: ++49 (0)931 - 201 - 35831
E-mail: silke.ap...@uni-wuerzburg.de

[Sander Rodenburg]

Hi Silke,

Some studies have gene panels for targeted sequencing.

You need to import them prior to loading the study. Gene panels can be found at datahub and can be downloaded in a similar way as studies using git lfs.

You can then import the gene panels using the command:

docker-compose run \
-v $PWD/study/my_gene_panel.txt:/panels/gene_panel.txt \
-w /cbioportal/core/src/main/scripts/ \
cbioportal \
\
  perl importGenePanel.pl \
  --data /panels/gene_panel.txt

Good luck!

Best,

Sander Rodenburg

Data Engineer / cBioPortal specialist

E sanderr...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

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[Silke Appenzeller]

Hi Sander,

thank you very much for your quick reply.

For msk_impact_2017, I was able to download and import the missing
gene-panel files ['IMPACT341', 'IMPACT410'].

The first error message disappeared:

ERROR: data_gene_panel_matrix.txt: lines [2, 3, 4, (10942 more)]: Gene
>> panel ID is not in database. Please import this gene panel before
>> loading study data.; values encountered: ['IMPACT341', 'IMPACT410']

disappeared but the other three remained:

ERROR: data_sv.txt: line 1: Missing column: Sample_ID; value
encountered: 'Sample_Id, SV_Status, (...)'
ERROR: data_sv.txt: line 1: Fusion event requires "Site1_Exon" and
"Site2_Exon" columns

ERROR: data_sv.txt: Invalid column header, file cannot be parsed.

For the other study, I couldn't identify a matching gene-panel file
[WXS]. Is a files for WXS (which is not really a panel) available ? If
not, how can I fix the error message?

Thank you very much

Silke

Quoting Sander Rodenburg <sanderr...@thehyve.nl>:

> Hi Silke,
>
> Some studies have gene panels for targeted sequencing.
> You need to import them prior to loading the study. Gene panels can be
> found at datahub

> <https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels>

> and
> can be downloaded in a similar way as studies using git lfs.
>
> You can then import the gene panels using the command:
>
> docker-compose run \
> -v $PWD/study/my_gene_panel.txt:/panels/gene_panel.txt \
> -w /cbioportal/core/src/main/scripts/ \
> cbioportal \
> \
> perl importGenePanel.pl \
> --data /panels/gene_panel.txt
>
> Good luck!
>
> Best,
>
>
> Sander Rodenburg
>
> Data Engineer / cBioPortal specialist
>
> E sanderr...@thehyve.nl
>
> T +31 30 700 9713
>

> W thehyve.nl <https://www.thehyve.nl/>
>
>
> <https://www.linkedin.com/company/thehyve/> <http://twitter.com/thehyvenl>
> <https://github.com/thehyve>

[Sander Rodenburg]

Hi Silke,

We are currently experiencing issues in the public studies on Datahub and the validator. This is related to the planned migration to the new SV file format, and the deprecation of Fusion format. I understood there was some work done, but some aspects got rolled back.

For now I recommend to use older versions of the public studies, of before the migration.

git lfs install --skip-repo --skip-smudge
git clone https://github.com/cBioPortal/datahub.git && cd datahub
git lfs install --local --skip-smudge
git checkout 61013067044293b24a66694b06d13a9c1171757f
git lfs pull -I public/<study_id>/

Best,

 

Sander Rodenburg

Data Engineer / cBioPortal specialist

E sanderr...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

[Silke Appenzeller]

Hi Sander,

I installed a local cBioportal instance successfully and loaded the
Adrenocortical Carcinoma (TCGA, PanCancer Atlas) study. It seems to
work. But when I select the study and click explore the study
everything is ok until I choose a clinical parameter, e.g. sex, click
male and female and then the vs. compare button
(http://localhost:8080/loading/comparison?phase=downloading&clinicalAttributeName=Sex&origin=acc_tcga_pan_can_atlas_2018), I keep receiving the following error message: "Sorry - please don't close the Study Summary window until the comparison page has finished loading". We observe the same with other studies. Do you know what the reason could
be?


And another question. Loading the local instance with firefox
localhost:8080 takes very long, even though the server it is running
on is quite powerful. Do you have an idea what's causing the problem?

Thank you very much

Silke





Quoting Sander Rodenburg <sanderr...@thehyve.nl>:

> Hi Silke,
>
> Some studies have gene panels for targeted sequencing.
> You need to import them prior to loading the study. Gene panels can be
> found at datahub

> <https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels>

> and
> can be downloaded in a similar way as studies using git lfs.
>
> You can then import the gene panels using the command:
>
> docker-compose run \
> -v $PWD/study/my_gene_panel.txt:/panels/gene_panel.txt \
> -w /cbioportal/core/src/main/scripts/ \
> cbioportal \
> \
> perl importGenePanel.pl \
> --data /panels/gene_panel.txt
>
> Good luck!
>
> Best,
>
>
> Sander Rodenburg
>
> Data Engineer / cBioPortal specialist
>
> E sanderr...@thehyve.nl
>
> T +31 30 700 9713
>

> W thehyve.nl <https://www.thehyve.nl/>
>
>
> <https://www.linkedin.com/company/thehyve/> <http://twitter.com/thehyvenl>
> <https://github.com/thehyve>
>
>