Perry 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.

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

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:

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

Keybase proof

I hereby claim:

I am samesense on github.
I am samesense (https://keybase.io/samesense) on keybase.
I have a public key ASB-sPD-A8yIsdlWUcJNosvQ0yi326pqYwvZRVxkg3-LHQo

To claim this, I am signing this object:

	# 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

	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)

	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

	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'"
	)