Bash functions

.bashrc

# https://danielmiessler.com/blog/the-one-line-cli-bandwidth-test/
alias bt="wget http://cachefly.cachefly.net/100mb.test -O /dev/null"

# Watch nginx logs
alias access='tail -f /var/log/nginx/access.log'
alias error='tail -f /var/log/nginx/error.log'

# column is used here to display a Tab Separated Values file with vertically aligned columns
# less is used so the arrow keys can be used to scroll up/down left/right
tsv() {
  column -t -s$'\t' ${1:missing filename argument} | less -S
}

bash.sh

#######################################
# Display .tsv files in a terminal as a table with the ability to scroll with arrow-keys.
# Globals:
#   None
# Arguments:
#   1: Path to tsv file
# Returns:
#   None
#######################################
tsv() {
  column -s $'\t' -t $1 | less -S
}

#######################################
# split comma-separated string into an array
# Globals:
#   None
# Arguments:
#   ${1} - string to split
#   ${2} - separator (default is ",")
# Returns:
#   ${result} - result value on success
#######################################
split_string() {
    local ifs=${IFS}
    IFS="${2:-,}"
    read -a result < <(echo "${1}")
    IFS=${ifs}
    return 0
}

#######################################
# Convert fasta to fasta by stripping quality information.
# Globals:
#   None
# Arguments:
#   1: Path to fastq file
# Returns:
#   None
#######################################
fastq_to_fasta() {
  local fastq="${1-}"
  
  # Strip path: s=${s##*/}
  # Strip specific extension: ${s%.txt}
  # Strip generic extension: ${s%.*}
  
  # awk is removing the quality information leaving only the contig name and nucleotide sequence.
  if [[ $fastq == *.gz ]]; then
    gunzip -c $fastq | awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' > ${fastq%.*.gz}.fasta
  elif [ $fastq = *.bz2 ]; then
    bunzip2 -c $fastq | awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' > ${fastq%.*.bz2}.fasta
  else
    awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' $fastq > ${fastq%.*}.fasta
  fi
}

#######################################
# Split fasta by contig naming each file based on the contig description
# Globals:
#   None
# Arguments:
#   1: Path to fasta file
# Returns:
#   None
#######################################
split_fasta() {
  local input_fasta="${1-}"
  # http://merenlin.com/2014/08/top-5-bash-commands-for-handling-data/
  awk '/^>/ {OUT=substr($0,2) ".fa"}; OUT {print >OUT}' $input_fasta
}

# Recursively set file and directory permissions.Source: http://superuser.com/questions/91935/how-to-chmod-755-all-directories-but-no-file-recursively
# To recursively give directories read & execute privileges:
recursive_grant_directory_permissions() {
  local base_dir="${1-}"
  local octal_permissions="${2:-755}"
	find $base_dir -type d -exec chmod $octal_permissions {} +
}

Or, if there are many objects to process:
	chmod 755 $(find /path/to/base/dir -type d)
	chmod 644 $(find /path/to/base/dir -type f)

Or, to reduce chmod spawning:
	find /path/to/base/dir -type d -print0 | xargs -0 chmod 755 
	find /path/to/base/dir -type f -print0 | xargs -0 chmod 644

A faster command, but doesn't have the desired result if, for example, the file was set with 777 permissions.
	chmod -R u+rwX,go+rX,go-w /path
-R = recursively; u+rwX = Users can read, write and execute; go+rX = group and others can read and execute; go-w = group and others can't write.
The important thing to note here is that X acts differently to x - the man page says The execute/search bits if the file is a directory or any of the execute/search bits are set in the original (unmodified) mode. In other words, chmod u+X on a file won't set the execute bit; and g+X will only set it if it's already set for the user.

# Recursively extract tgz files
recursive_extract_tgz() {
  local base_dir="${1:-./}"
  find $base_dir -type f -name '*.tgz' -o -name '*.tar.gz' -execdir tar xzf {} \;
}
# Reverse complement DNA sequence
#echo "GATC" | rev | tr ATGC TACG

# Intialize zsh to use module load
#source ${MODULESHOME}/init/zsh

fstab

# HAK5 Microoptimization to reduce diskaccess/power consumption
# https://youtu.be/XloTXFgNL7s?t=669
tmpfs /tmp tmpfs defaults,noatime,nodirtime,size=512M,mode=1777 0 0
tmpfs /var/spool tmpfs defaults,noatime,nodirtime,size=512M,mode=1777 0 0
tmpfs /var/tmp tmpfs defaults,noatime,nodirtime,size=512M,mode=1777 0 0

# CAUTION: logs lost on reboot
tmpfs /var/log tmpfs defaults,noatime,nodirtime,size=512M,mode=0755 0 0

modulefileTemplate

#%Module1.0
#
# To use this template, fill in the module-whatis description
# and enable the prepend-path commands relevant to the package.
#
# For more configuration options see:
# http://modules.sourceforge.net/man/modulefile.html

proc ModulesHelp { } {
    puts stderr "[ module-info name ]"
    puts stderr "URL: https://github.com/USER/FOOBAR"
}

module-whatis   "A modulefile template"

# moduleDir is the absolute path to directory containing this modulefile file.
# example: /packages/modulefiles/<package_name>/<package_version>
set moduleDir   [ file dirname $ModulesCurrentModulefile ]

# packageDir is the absolute path to the package this module references.
# example: /packages/<package_name>/<package_version>
set packageDir  [ file normalize ${modulesDir}/../../${moduleName} ]

#prepend-path    PATH             $packageDir
#prepend-path    MANPATH          $packageDir/share/man
#prepend-path    CPATH            $packageDir/include
#prepend-path    LD_LIBRARY_PATH  $packageDir/lib
#prepend-path    PKG_CONFIG_PATH  $packageDir/lib/pkgconfig

packageTemplate.mk

PACKAGE_TEMPLATE_VERSION?=dev

.PHONY: package_template
package_template: ${LOCAL}/package_template/${PACKAGE_TEMPLATE_VERSION}

${SRC}/package_template:
        git clone https://github.com/USER/REPO.git $@

${LOCAL}/package_tempalte/dev: ${SRC}/package_template
        cd $< \
        && git pull \
        && ./configure --prefix=$@ \
        && make \
        && make install