docker, access local file with WDL
The docker image is for a perl script to do gene fusion called soafuse. Input files located at: ~ /hg19-GRCh37/ Normally, it can be run as: docker run -v ~/hg19-GRCh37/:/sf -i -t bianxi/soapfuse-ref...
View ArticleHow to Use My Own Method in FireCloud Workspace?
I want to use my own method (modified Seq2HLA: https://bitbucket.org/sebastian_boegel/seq2hla#) to run TCGA sample data. I could not find a suitable method in āMethod Repositoryā, neither could I...
View ArticleAccess my uploaded data
I uploaded my data to firecloud-cbiit06-2016 project but https://console.cloud.google.com/home/dashboard?project=firecloud-cbiit06-2016 and https://console.google.com/project/firecloud-cbiit06-2016...
View ArticleNo space left on device - How much space do I have by default?
My submitted job generates "Cannot write: No space left on device".
View Articledelete method config error
I used a method config and generated some submissions. I want to delete the config because the WDL has a mistake. I want to delete the config so it doesn't clutter my workspace so I don't click it on...
View ArticleAccess to ICGC data
Is ICGC data supported like TCGA data is in the cloud? If it's not, are there plans to support it?
View ArticleIs there runtime parameter for number of vCPU?
I see runtime parameters for memory and defaultDisks, but can you set number of CPUs?
View ArticleHow to run analysis with GDC (TCGA) mRNA bam files?
Hi! I want to run analysis with TCGA mRNA bam data. But I don't know how to import such data. Additionally, TCGA data have been move to GDC since June. Would some one could give me some instruction...
View ArticleHow to remove unwanted data from my workspaces?
Does portal.firecloud have this option?
View ArticleHow do I get project id of the newly created project?
I created a new project called ācf1ā on my desktop I got Your current project is [None]. You can change this setting by running: $ gcloud config set project PROJECT_ID How do I get project id of the...
View ArticleHow to launch a batch of sample analysis in Firecloud?
Here I have TCGA controlled data access authorization, and I have successfully run some sample (sample entity, use the bam files) analysis in FireCloud. However, I want to run hundreds of analysis and...
View ArticleCould not connect to https://api.firecloud.org/api/methods with method POST
Hi! I meet some problems that I never met before. I have successfully push some method to Firecloud. However, it doesn't work this time. I used the dockered version of firecloud: firecloud -m push -s...
View Articleuploading large datasets?
Iām uploading large datasets and I got a suggestion to make the upload faster. How to I implement this?
View ArticleImporting/deleting methods within workspace
After choosing a method and hitting import, I consistently get the following error: "FireCloud service is temporarily unavailable. If this problem persists, check http://status.firecloud.org/ for more...
View ArticleDocker out of memory when running a WDL script
I am writing a WDL script that uses the broadinstitute/genomes-in-the-cloud Docker container, and I am encountering the following perplexing error: [bwt_restore_bwt] Failed to allocate -40 bytes at...
View ArticleFireCloud Workspaces Table Bug
I noticed a bug in the UI related to displaying workspaces. To start note that I have 56 workspaces, of which 1 is running (img1). If I click on 'Running' it correctly shows me the running workspace...
View ArticleFireCloud API Questions
The NCI Leidos Team had a few questions about endpoints in the FireCloud API. First, can we provide an example of how a user would test OAuth GET /login? In this example, please include values for...
View Articlememory monitoring
I ran an analysis using a vcf with 2.2G. Initially, I specified in WDL to use 10 G, and the workflow was failed. However, when I specified to 20G, the workflow successfully ran. Is there anyway that I...
View ArticleRegional Data Transfer on Google Cloud backend?
With the Google cloud backend, are data ever transferred across regional locations within a multi-regional location during image loading, data localization, or analysis (for example, us-east1 to...
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