samesense

vcf-snp-lookup

I hope you have some terminal/command line experience.

• Navigate to your vcf.gz file in the terminal/command line.
• Check your reference genome (install gzcat as needed):

gzcat {your_id}.filtered.snp.vcf.gz | head -100 | less

Look for something like -r /references/grch37

samesense

Exposing your clipboard over SSH

I frequently administer remote servers over SSH, and need to copy data to my clipboard. If the text I want to copy all fits on one screen, then I simply select it with my mouse and press CMD-C, which asks relies on m y terminal emulator (xterm2) to throw it to the clipboard.

This isn't practical for larger texts, like when I want to copy the whole contents of a file.

If I had been editing large-file.txt locally, I could easily copy its contents by using the pbcopy command:

samesense

onsuccess:
    shell(
        "curl `singularity exec docker://vault:1.2.1 vault read -field=value secret/v1/users/evansj/twilio-a` -X POST --data-urlencode 'To=+12406819176' --data-urlencode 'From=+18174022818' -u `singularity exec docker://vault:1.2.1 vault read -field=value secret/v1/users/evansj/twilio-u` --data-urlencode 'Body=gatk done'"
        )
onerror:
    shell(
        "curl `singularity exec docker://vault:1.2.1 vault read -field=value secret/v1/users/evansj/twilio-a` -X POST --data-urlencode 'To=+12406819176' --data-urlencode 'From=+18174022818' -u `singularity exec docker://vault:1.2.1 vault read -field=value secret/v1/users/evansj/twilio-u` --data-urlencode 'Body=gatk fail'"
        )

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: