[Bioc2024] bamSliceR: an all-in-one toolset for rapid cross-cohort variant annotation

[bioc-workshop-dev]

DO NOT INCLUDE REQUESTS IN THE FIRST COMMENT. PLEASE POST THIS TEMPLATE UNCHANGED THEN FOLLOW ITS INSTRUCTIONS IN A NEW COMMENT

General Notes

This repository serves as a mostly automated pipeline for deploying workshops to the Bioconductor Workshop.

Bot Commands

Issues in this repository are monitored to by a bot. All commands need to be written on the first line of the comment, in a single line.

Example Docker Request

/request
  id='tidybioc2023'
  title='Tidy Transcriptomics'
  description='For Single-Cell RNA Sequencing Analyses'
  section='Smorgasbord 2023'
  source='https://github.com/tidytranscriptomics-workshops/bioc2023_tidytranscriptomics'
  docker='ghcr.io/tidytranscriptomics-workshops/bioc2023_tidytranscriptomics:latest'

Note. The example /request is on multiple lines for readability.

Additional Workshop Information

Expected Number of Participants: 20

Workshop Date(s): July 26, 2024 - July 26, 2024

Workshop Start Time (approx.): 00:45

[bioc-workshop-dev]

READ ONLY: DO NOT EDIT ## /request id="bioc2024bamSliceR" title="bamSliceR: an all-in-one toolset for rapid cross-cohort variant annotation" description="A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories." section="Bioc2024" startfile="README.md" source="https://github.com/trichelab/bamSliceR" docker=":" pkglist="BSgenome.Hsapiens.UCSC.hg38,BiocParallel,Homo.sapiens,TxDb.Hsapiens.UCSC.hg38.knownGene,VariantTools,biomaRt,data.table,ensemblVEP,gampR,httr,jsonlite,rtracklayer,stringr" vignettes=""

[almahmoud]

/request id="bioc2024bamSliceR" title="Package Demo: bamSliceR description="A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories." section="Bioc2024" startfile="README.md" source="https://github.com/trichelab/bamSliceR" pkglist="trichelab/bamSliceR,BSgenome.Hsapiens.UCSC.hg38,BiocParallel,Homo.sapiens,TxDb.Hsapiens.UCSC.hg38.knownGene,VariantTools,biomaRt,data.table,ensemblVEP,gampR,httr,jsonlite,rtracklayer,stringr"

[almahmoud]

/test id="bioc2024bamSliceR" title="Package Demo: bamSliceR description="A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories." section="Bioc2024" startfile="README.md" source="https://github.com/trichelab/bamSliceR" pkglist="trichelab/bamSliceR,BSgenome.Hsapiens.UCSC.hg38,BiocParallel,Homo.sapiens,TxDb.Hsapiens.UCSC.hg38.knownGene,VariantTools,biomaRt,data.table,ensemblVEP,gampR,httr,jsonlite,rtracklayer,stringr"

[almahmoud]

AUTO-GENERATED RESPONSE Your request has been received and has passed initial screening. :sparkles:

Below are the detected values:

id='bioc2024bamSliceR'
title='Package Demo: bamSliceR description='
description=''
section='Bioc2024'
source='https://github.com/trichelab/bamSliceR'
docker=''
port='8787'
command='echo "setwd(\"/home/rstudio\"); setHook(\"rstudio.sessionInit\", function(newSession) { if (newSession) rstudioapi::filesPaneNavigate(getwd()) }, action = \"append\")" > /home/rstudio/.Rprofile; /init'
pkglist='trichelab/bamSliceR,BSgenome.Hsapiens.UCSC.hg38,BiocParallel,Homo.sapiens,TxDb.Hsapiens.UCSC.hg38.knownGene,VariantTools,biomaRt,data.table,ensemblVEP,gampR,httr,jsonlite,rtracklayer,stringr'
vignettes=''

If these are as expected, no further action is needed at this time. Please wait for an admin's response. If any changes are needed, please re-run the /request action with desired values.

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your request has passed initial checks and is being built and/or deployed to the test instance. Please wait further updates.

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your request has been received but is currently failing its deployment on test. If the corresponding /request command has passed with the same parameters, this is likely a bug.

[almahmoud]

/test id="bioc2024bamSliceR" title="Package Demo: bamSliceR description="A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories." section="Bioc2024" startfile="README.md" source="https://github.com/trichelab/bamSliceR" pkglist="trichelab/bamSliceR,BSgenome.Hsapiens.UCSC.hg38,BiocParallel,Homo.sapiens,TxDb.Hsapiens.UCSC.hg38.knownGene,VariantTools,biomaRt,data.table,ensemblVEP,gampR,httr,jsonlite,rtracklayer,stringr"

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your request has passed initial checks and is being built and/or deployed to the test instance. Please wait further updates.

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your request has been received but is currently failing its deployment on test. If the corresponding /request command has passed with the same parameters, this is likely a bug.

[almahmoud]

/test id="bioc2024bamSliceR" title="Package Demo: bamSliceR" description="A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories" section="Bioc2024" startfile="README.md" source="https://github.com/trichelab/bamSliceR" pkglist="trichelab/bamSliceR,BSgenome.Hsapiens.UCSC.hg38,BiocParallel,Homo.sapiens,TxDb.Hsapiens.UCSC.hg38.knownGene,VariantTools,biomaRt,data.table,ensemblVEP,gampR,httr,jsonlite,rtracklayer,stringr" docker="ghcr.io/bioconductor/bioconductor:3.18"

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your request has passed initial checks and is being built and/or deployed to the test instance. Please wait further updates.

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your request has been received but is currently failing its deployment on test. If the corresponding /request command has passed with the same parameters, this is likely a bug.

[almahmoud]

/test id="bioc2024bamSliceR" title="Package Demo: bamSliceR" description="A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories" section="Bioc2024" startfile="README.md" source="https://github.com/trichelab/bamSliceR" pkglist="trichelab/bamSliceR" docker="ghcr.io/bioconductor/bioconductor:3.18"

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your request has passed initial checks and is being built and/or deployed to the test instance. Please wait further updates.

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your workshop has been successfully deployed to the test instance. :sparkles: Please test your workshop on the development instance and notify us via comment when you deem it ready for public consumption on the production instance.

[almahmoud]

/test id="bamslicerbioc2024" title="Package Demo: bamSliceR" description="A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories" section="Bioc2024" startfile="README.md" source="https://github.com/trichelab/bamSliceR" pkglist="trichelab/bamSliceR" docker="ghcr.io/bioconductor/bioconductor:3.18"

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your request has passed initial checks and is being built and/or deployed to the test instance. Please wait further updates.

[almahmoud]

AUTO-GENERATED RESPONSE Action Log Your workshop has been successfully deployed to the test instance. :sparkles: Please test your workshop on the development instance and notify us via comment when you deem it ready for public consumption on the production instance.