I log into the CGC using my eRA Commons ID. How can I push containers to the CGC image registry?

I use my eRA Commons ID to log into the CGC. How do I use the Docker CLI to log in and push images to the CGC image registry? What do I need?

What bam files are available for TCGA?

Is there a database available to query for the TCGA bam files?

$self is not defined?

Hi, Please explain the use of $self in the Value field of a job input spec. I don't know when and how I can use it. For example, say the ID of my input parameter is called 'quality'. In the JavaScript expression I want to enter in the Value field, it seems I must refer to the parameter as $job.inputs.quality, but I thought I could also do $self.quality. In the documentation at http://docs.cancergenomicscloud.org/docs/dynamic-expressions-in-tool-descriptions#section-the-self-object, it says: """ In the command line bindings for the tool inputs, $self is set to the value of the input. In other words, in this context $self is just $job.inputs.<input_id>. """ According to that documentation, I should be able to use an expression such as "$self || 5" to create a default value of 5. But when doing so, I get this error when trying to run my tool: """ Error This task ran into a problem during execution and did not finish. Failed to start trimgalore. Failed to build command line. Failed to build command line. Failed evaluating expression $self || 20. org.mozilla.javascript.EcmaError: ReferenceError: "$self" is not defined. (script#1). """ So why does it say that $self is not defined?

Clarification for TCGA data

I have trouble matching WSI slides to their grade, or TNM. For example, patient: TCGA-BC-A110 has three slide samples: Sample TCGA-BC-A110-01Z (Primary Tumor) Sample TCGA-BC-A110-01A (Primary Tumor) Sample TCGA-BC-A110-11A (Normal tissue) Question 1: Is it correct samples ending with A were all sampled together? Question 2: Can I know which were sampled first? Samples ending with A, or Z? [Pathology report exist only for A, with conclusion of Grade I. Clinical file nationwidechildrens.org_clinical.TCGA-BC-A110.xml states patient had cancer with grade I, and later a reoccurence. It means A is the first tumor event, and Z the second?] Question 3: I noticed pathology reports are never available for Z samples, and only for A. Is there a reason?

CGC mutation data not matching downloadable maf

Dear CGC team, When I compare the mutation data I download from the TCGA website (maf files), they don't match up with the data displayed in CGC. For example, in ovarian cancer 8% and 9% of patients are BRCA1 and BRCA2 mutated. When I pull these data up in the browser, there are only 2 BRCA2 mutations showing up. The same pattern is true for TCGA LUSC and BLCA, with CGC displaying fewer mutations than shown in the raw data. Can you please explain this discrepancy? Thanks, An

What is the Seven Bridges Cancer Genomics Cloud?

How can I add Whole Exome Sequencing (WES) from a sample in TCGA?

Hi, If I want to run a program on a WES from TCGA-CG-5720 in TCGA STAD, how can I add this one bam file to a Project? Nothing came ot when I typed "TCGA-CG-5720" in search window. Do you have any idea? Thanks, HoJoon

How can I give feedback or ask questions?

How can I download metadata on a list of files

I would like to download the meta-data for a set of files. For examples, I have four gene-wise readcounts text files. Each file has associated metadata: platform type, reference genome, disease, investigation etc. I would like to download the associated metadata for a set of files, as a text file, onto my local machine. Is it possible to do this? Thanks, Anjan

Do I need permissions for TCGA Controlled Data to get storage and computation credits?