adrisede

set -e, -u, -o, -x pipefail

The set lines

• These lines deliberately cause your script to fail. Wait, what? Believe me, this is a good thing.
• With these settings, certain common errors will cause the script to immediately fail, explicitly and loudly. Otherwise, you can get hidden bugs that are discovered only when they blow up in production.

• set -euxo pipefail is short for:

set -e
set -u

adrisede

# By default, the directories in .libPaths() aren't writable on shinyapps.io, so
# create a subdir where we'll install our package.
if (!file.exists("R-lib")) {
  dir.create("R-lib")
}
# Unfortunately, there's no way to get deployapp() to ignore this directory, so
# make sure to remove it locally before you call deployapp(). This can be done
# with:
#   unlink("pkgInst/R-lib", recursive = TRUE)

adrisede

#!/bin/bash

# download SRR from NCBI SRA via Aspera Connect
#
# > get-srr SRR304976
get-srr () {
    SRR=${1}
    SRR_6=$(echo $SRR | cut -c1-6)
       
    ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh \

adrisede

#!/bin/bash                                                                                                                                    

if [ "$#" -ne 1 ]; then
  echo -e "Incorrect number of parameters! Usage:\n    index-gtf.sh <file.gtf(.gz)>" >&2
  exit 1
fi

gtf="$1"

if [[ $gtf =~ \.gz$ ]]; then

adrisede

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

adrisede

#!/usr/bin/awk
# Takes output of "samtools depth" and reformats into grouped bedgraph format:
# samtools depth -r ${loc} -Q 1 --reference $fasta $bam | mawk -f scripts/depth2bedgraph.awk > /tmp/my.bedgraph
# Example input:
#chr1     26      2
#chr1     27      2
#chr1     28      2
#chr1     29      5
#chr1     30      5
#chr1     31      5

adrisede

#!/bin/bash

# These variables can be overwritten using the arguments below
VERSION="1.1.463"
# drwho is listed as user in YARN's Resource Manager UI.
USER="drwho"
# Depending on where the EMR cluster lives, you might have to change this to avoid security issues.
# To change the default password (and user), use the arguments bellow.
# If the cluster is not visible on the Internet, you can just leave the defaults for convenience.
PASS="tardis"

adrisede

              B A S H   C H E A T   S H E E T    
   
 to page output forward (only): command filename | more 
 to page output forward & back: command filename | less
 to print a dataset: lp datasetname (-d printerid) (-o landscape)

 USE OF QUOTATION MARKS
    echo "$varname"    =   echo The value of \$varname is \"$varname\"
                       =   echo "The value of \$varname is \"$varname\"."
    $fred='Four spaces between these    words.'