samesense

docker run -it --detach-keys="ctrl-@" -v /mnt/isilon/:/mnt/isilon/ --user $(id -u) quay.research.chop.edu/evansj/evansj-dev-box zsh

samesense

SELECT
  repos.repo_name
FROM
  `bigquery-public-data.github_repos.sample_repos` repos
LEFT JOIN
  `bigquery-public-data.github_repos.sample_files` files
ON
  repos.repo_name = files.repo_name
LEFT JOIN
  `bigquery-public-data.github_repos.sample_contents` contents

samesense

nf-core

rnaseq

• don't use one large container b/c of maintenence and modularity
• if conda installs, use conda directly
• good usage example
• good versioning example tool or container level? self documenting containers?
• good output template
• good pipeline wrapper
• no pipeline rule sharing

samesense

require(dplyr)
require(magrittr)

in_file = "WT_JC4.pausing.2018_05_31.csv"
df = read.delim(in_file, header=TRUE, sep="\t")
maxes <- group_by(df, .dots=c("exp", "gene")) %>% summarize(pausing_index=max(pausing_index))
m = merge(as.data.frame(maxes), df, by=c("exp", "gene", "pausing_index"))
write.table(m, "out.tmp", row.names=FALSE, sep="\t", quote=F)

samesense

Data download; put data in /absolute/local/data/, called YOUR_DIR below

• Make a directory to hold data (/absolute/local/data/).
• Make these folders under your data dir: phenoxome_data/
• Put data in {YOUR_DIR}/phenoxome_data/
  • human_g1k_v37.fasta
  • HGMD.vcf.gz and HGMD.vcf.gz.tbi (rename HGMD file in vcfanno toml file)
  • gnomad.exomes.r2.0.1.sites.vcf.gz and gnomad.exomes.r2.0.1.sites.vcf.gz.tbi

Start the phenoxome container with a mount to your local data.

samesense

# Use this inside https://hub.docker.com/r/samesense/ngs_plot/

# set env variables
alias python='/condas/miniconda3/bin/python'
export PATH=/condas/miniconda3/bin/:$PATH
export NGSPLOT=/bin/ngsplot
export PATH=/bin/ngsplot/bin/:$PATH
source /condas/miniconda3/bin/activate py27

# cannot write in default dir

samesense

import argparse

def main(args):
    giabBaseCounts(d, args.giabCountFile)
    
if __name__ == "__main__":
    desc = 'Pull data for report.'
    parser = argparse.ArgumentParser(description=desc)
    argLs = ('giabCountFile', 'outFile',)
    for param in argLs:

samesense

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
    <key>Label</key>
    <string>local.pbcopy.9999</string>
    <key>UserName</key>
    <string>joe</string>
    <key>Program</key>
    <string>/usr/bin/pbcopy</string>

samesense

Copy to local machine clipboard from iteractive remote session

• Works with macOS and remote linux machine
• On local machine, make this plist file to use with launchclt
• On local machine launchctl load local.pbcopy.9999.plist. This must remain running for remote copy to work.
• On remote machine cat "message or file" | nc localhost 9997 -w1
• nc is at /mnt/isilon/cbmi/variome/perry/bin/nc
• On local machine, use paste or pbpaste as usual

Extra

• On my locate machine, p is aliased to the launchctl command

samesense

* Data checksums
* Collapse variants by chrom
* Pull reads of all variant positions across bam files
* Pull mapping qualities
* Apply cutoffs
* Annotate collapsed variants w/ function and pop info
* Mk tables