Multiple Genome Support Question

[a.na...@gmail.com]

Hello cBioPortal Team,

Thank you for all the great work. I've been supporting a custom instance of cBioPortal for about two years and the way the application becomes more powerful is really impressive.

My question is about the ability of multiple genomes support announced in v3.1.0. Currently our instance is upgraded to version 3.1.0. Initially it was configured to support hg19 and I'm trying to investigate if it is possible to reconfigure the existing instance so human and mouse data can be imported to the DB and shown in the UI. Could you spot the document (if any) where I can read about the procedure please? I've tried this one https://github.com/cBioPortal/cbioportal/blob/master/docs/Import-reference-genome.md but can't see corresponding perl file and suspect that is to upgrage reference_genome table.

Could you also give us some clarifications on how it is supposed to work? Should we import a mouse DB seed and is there a safe way to do so as our db is already 2.11.0 and contains some human data we'd like to keep? Is there some specific configuration for portal.properties file? Or am I missing something and and it is still impossible to have everything within one instance.

Thank you in advance,
Anastasia 

Nayden Anastasia
EPAM Systems

St.Petersburg

[Kelsey Zhu]

Hi Anastasia, 

Thank you for using cBioPoratl!

I am sorry for the late reply. The answers to your questions can be found here.

Best regards!

Kelsey

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[a.na...@gmail.com]

Hi Kelsey,

Thank you for your response! Very helpful.

Thanks again,
Anastasia

среда, 23 октября 2019 г., 22:08:33 UTC+2 пользователь Kelsey Zhu написал:

Hi Anastasia, 

Thank you for using cBioPoratl!

I am sorry for the late reply. The answers to your questions can be found here.

Best regards!

Kelsey

On Tue, Oct 22, 2019 at 6:04 AM <a.n...@gmail.com> wrote:

Hello cBioPortal Team,

Thank you for all the great work. I've been supporting a custom instance of cBioPortal for about two years and the way the application becomes more powerful is really impressive.

My question is about the ability of multiple genomes support announced in v3.1.0. Currently our instance is upgraded to version 3.1.0. Initially it was configured to support hg19 and I'm trying to investigate if it is possible to reconfigure the existing instance so human and mouse data can be imported to the DB and shown in the UI. Could you spot the document (if any) where I can read about the procedure please? I've tried this one https://github.com/cBioPortal/cbioportal/blob/master/docs/Import-reference-genome.md but can't see corresponding perl file and suspect that is to upgrage reference_genome table.

Could you also give us some clarifications on how it is supposed to work? Should we import a mouse DB seed and is there a safe way to do so as our db is already 2.11.0 and contains some human data we'd like to keep? Is there some specific configuration for portal.properties file? Or am I missing something and and it is still impossible to have everything within one instance.

Thank you in advance,
Anastasia 

Nayden Anastasia
EPAM Systems

St.Petersburg

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[a.na...@gmail.com]

Hi Kelsey,

Sorry if my question is stupid but could you give me an exact github link to importReferenceGenome.pl please? I'm struggling to find it under <cbioportal_source_folder>/core/src/main/scripts i.e. https://github.com/cBioPortal/cbioportal/tree/master/core/src/main/scripts
Or am I getting right import of reference genomes (hg38 and mm10) are included to DB migration script?

Thank you in advance,
Anastasia

среда, 23 октября 2019 г., 22:08:33 UTC+2 пользователь Kelsey Zhu написал:

Hi Anastasia, 

Thank you for using cBioPoratl!

I am sorry for the late reply. The answers to your questions can be found here.

Best regards!

Kelsey

On Tue, Oct 22, 2019 at 6:04 AM <a.n...@gmail.com> wrote:

Hello cBioPortal Team,

Thank you for all the great work. I've been supporting a custom instance of cBioPortal for about two years and the way the application becomes more powerful is really impressive.

My question is about the ability of multiple genomes support announced in v3.1.0. Currently our instance is upgraded to version 3.1.0. Initially it was configured to support hg19 and I'm trying to investigate if it is possible to reconfigure the existing instance so human and mouse data can be imported to the DB and shown in the UI. Could you spot the document (if any) where I can read about the procedure please? I've tried this one https://github.com/cBioPortal/cbioportal/blob/master/docs/Import-reference-genome.md but can't see corresponding perl file and suspect that is to upgrage reference_genome table.

Could you also give us some clarifications on how it is supposed to work? Should we import a mouse DB seed and is there a safe way to do so as our db is already 2.11.0 and contains some human data we'd like to keep? Is there some specific configuration for portal.properties file? Or am I missing something and and it is still impossible to have everything within one instance.

Thank you in advance,
Anastasia 

Nayden Anastasia
EPAM Systems

St.Petersburg

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You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.

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[Kelsey Zhu]

Hi Anastasia, 

Thank you for reaching out!

you were right. It seems like that the script for importing reference genome is not included the master branch. I will report the issue.

In the meantime, you can please use the database migration script to add reference genomes for hg38 and mm10 OR run the following insert statements from a sql terminal:

	INSERT INTO `reference_genome`
	VALUES (2, 'human', 'hg38', 'GRCh38', 3049315783, 'http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips', '2013-12-01');
	INSERT INTO `reference_genome`
	VALUES (3, 'mouse', 'mm10', 'GRCm38', 2652783500, 'http://hgdownload.cse.ucsc.edu//goldenPath/mm10/bigZips', '2012-01-01');

I apologize for the inconvenience!

Thank you!

Kelsey

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[a.na...@gmail.com]

Hi Kelsey,

Thank you so much for your response.

I keep on trying to upload mouse data but still face some issues. I run the importer script with following parameters:  -species mouse -ucsc mm10 -ncbi GRCm38
However as the result in REFERENCE_GENOME_ID field of cbioportal.cancer_study table I can see value corresponding default human build.

Besides lollipop plot and supporting information (like transcript id and swissprot annotation) are mapped to human genes.

I've tries to provide SWISSPROT field within mutation file but that didn't had any effect.

Could you please give a piece of your advice of what I am doing wrong? What's the best point to start debugging this?

Thank you,
Anastasia

вторник, 29 октября 2019 г., 21:53:12 UTC+1 пользователь Kelsey Zhu написал:

Hi Anastasia, 

Thank you for reaching out!

you were right. It seems like that the script for importing reference genome is not included the master branch. I will report the issue.

In the meantime, you can please use the database migration script to add reference genomes for hg38 and mm10 OR run the following insert statements from a sql terminal:

	INSERT INTO `reference_genome`
	VALUES (2, 'human', 'hg38', 'GRCh38', 3049315783, 'http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips', '2013-12-01');
	INSERT INTO `reference_genome`
	VALUES (3, 'mouse', 'mm10', 'GRCm38', 2652783500, 'http://hgdownload.cse.ucsc.edu//goldenPath/mm10/bigZips', '2012-01-01');

I apologize for the inconvenience!

Thank you!

Kelsey

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/7c3734e6-fd0d-4392-9078-e14aa9ed730b%40googlegroups.com.