googlegenomics / readthedocs Goto Github PK

https://googlegenomics.readthedocs.io/en/latest/use_cases/run_familiar_tools/bioconductor.html

includes a link to

https://console.cloud.google.com/project/_/mc/template/bioconductor

which does not resolve after a project is identified

Test and then update instructions https://github.com/googlegenomics/readthedocs/blob/master/docs/source/includes/dataflow_on_gce_setup.rst

or silence those that are "okay". Then newly introduced issues will be easier to identify and fix.

Which would be gVCF and Complete Genomics data.

It should mention:

• JoinNonVariantSegmentsWithVariants
• IdentityByState
• and the jobs in https://github.com/googlegenomics/codelabs/tree/master/Java

with

1. completed instructions for VerifyBamId
2. add link to https://github.com/StanfordBioinformatics/mvp_aaa_codelabs

Hi,

I was trying to deploy bioconductor to GCE by following the guild in step by step. But after running the command: gcloud compute ssh --ssh-flag="-4" --ssh-flag=-L8787:localhost:8787 --project=team-project-184716 --zone=us-central1-f bioconductor-1, the site http://localhost:8787 cannot be reached. Any thoughts about what is the root causes?

Thanks,
Wentao

Right now it runs on 1,000 Genomes with ~2,500 samples and is "too long" for a quick test.

http://googlegenomics.readthedocs.org/en/latest/use_cases/analyze_reads/calculate_coverage.html

https://github.com/googlegenomics/gatk-tools-java/blob/e0375190427bb44057691b4461c0a91f0761e6d8/src/main/java/com/google/cloud/genomics/gatk/common/GenomicsConverter.java has

// Set flags, as advised in http://google-genomics.readthedocs.org/en/latest/migrating_tips.html

That url no longer exists. It was deleted in https://github.com/googlegenomics/start-here/pull/7/files

It would be useful to have that documentation somewhere, outside the context of v1beta -> v1beta2 migration.

It should live underneath http://googlegenomics.readthedocs.org/en/latest/use_cases/load_data/index.html

The appear to be just a few references to update.

The console was renamed back in November. The console is available in two manners now:

• https://console.cloud.google.com : Google Cloud Platform Console
• https://console.developers.google.com : Google Developers Console

We should use Google Cloud Platform Console and the associated URL in these docs.

See 08f6e8d

It wasn't worth the contributor license agreement.

https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/pipelines/IdentifyPrivateVariants.java

https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/pipelines/DeleteVariants.java

The DREAM Tumor Heterogeneity challenge using Galaxy + Docker is in full swing now. See the two quick-start videos here.

Per https://groups.google.com/forum/#!topic/gcp-hadoop-announce/VHM4C-bRvHA

http://googlegenomics.readthedocs.org/en/latest/use_cases/linkage_disequilibrium/compute_linkage_disequilibrium.html suggests that the source code is at (last line of file):

https://github.com/googlegenomics/dataflow-java

but it should be:

https://github.com/googlegenomics/linkage-disequilibrium

https://github.com/googlegenomics/beacon-go

Hi, At the page: http://googlegenomics.readthedocs.io/en/latest/use_cases/run_familiar_tools/ncbiblast.html,
"To deploy BLAST to Google Compute Engine, you can click-to-deploy NCBI BLAST"
"click-to-deploy" does not work. I could not find the ncbiblast image either. Maybe something is missing?
My students were asking how to use BLAST in the cloud. Could you please help?

Thank you.

Steve

After the conference, re-title the workshop later and add "first presented at" http://www.bioconductor.org/help/course-materials/2015/BioC2015/ with a link to the tagged version for the workshop R package in github since this material will evolve.

I set up a grid engine in a fresh virtualenv following your instructions here.

After configuring the cluster, I tried to start it with the elasticluster start gridengine command, but received the following error: ImportError: No module named callbacks

To successfully deploy the cluster, i had to downgrade the ansible python module to a version < 2.0.0, e.g. by executing pip install ansible==1.9.6 (inside the virtualenv).

Per https://github.com/googlegenomics/dataflow-java/pull/165/files, the next release of dataflow-java will upgrade http://googlegenomics.readthedocs.org/en/latest/use_cases/analyze_reads/count_reads.html to gRPC.

The docs need an update to match.

Include descriptions, caveats, command lines, and give some guidance on # of machines vs. runtime.

The Bioconductor deployment workflow linked from http://googlegenomics.readthedocs.io/en/latest/use_cases/run_familiar_tools/bioconductor.html is no longer working. It appears not to be present in Cloud Launcher.

And update public data as needed. The first command line on http://googlegenomics.readthedocs.org/en/staging/use_cases/analyze_reads/count_reads.html

Yields error:

Error: gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam.bai not found.

What is something someone can run and get a result within a couple minutes that we can add to http://googlegenomics.readthedocs.org/en/latest/use_cases/run_picard_and_gatk/index.html ?