init

.Rprofile

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+# vim: set filetype=r:
+
+# Default CRAN mirror
+options(repos=structure(c(CRAN="https://cloud.r-project.org/")))
+
+# Print data.table's columns classes and key
+options(datatable.print.class = TRUE, datatable.print.keys = TRUE)
+
+# Monitor memory usage ( https://stackoverflow.com/questions/1358003 )
+.ls.objects <- function (pos = 1,
+                         pattern,
+                         order.by,
+                         decreasing=FALSE,
+                         head=FALSE,
+                         n=5) {
+  napply <- function(names, fn) sapply(names, function(x) fn(get(x, pos = pos)))
+  names <- ls(pos = pos, pattern = pattern)
+  obj.class <- napply(names, function(x) as.character(class(x))[1])
+  obj.mode <- napply(names, mode)
+  obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
+  obj.prettysize <- napply(names,
+                           function(x) {
+                             format(utils::object.size(x), units = "auto")
+                           })
+  obj.size <- napply(names, object.size)
+  obj.dim <- t(napply(names, function(x) as.numeric(dim(x))[1:2]))
+  vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
+  obj.dim[vec, 1] <- napply(names, length)[vec]
+  out <- data.frame(obj.type, obj.size, obj.prettysize, obj.dim)
+  names(out) <- c("Type", "Size", "PrettySize", "Length/Rows", "Columns")
+  if (!missing(order.by)) {
+    out <- out[order(out[[order.by]], decreasing=decreasing), ]
+  }
+  if (head) {
+    out <- head(out, n)
+  }
+  return(out)
+}
+.lsos <- function(..., n=10) {
+  .ls.objects(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
+}
+
+# Built-in color names ( http://www.sthda.com/english/wiki/colors-in-r )
+.showCols <- function(cl=colors(),
+                     bg = "grey",
+                     cex = 0.75,
+                     rot = 30) {
+  m <- ceiling(sqrt(n <-length(cl)))
+  length(cl) <- m*m; cm <- matrix(cl, m)
+  require("grid")
+  grid.newpage(); vp <- viewport(w = .92, h = .92)
+  grid.rect(gp=gpar(fill=bg))
+  grid.text(cm, x = col(cm)/m, y = rev(row(cm))/m, rot = rot, vp=vp,
+            gp=gpar(cex = cex, col = cm))
+}
+
+# Set IRkernel default plot size ( https://irkernel.github.io/ )
+.d <- function(width = 8, height = 5, scale = 2) {
+  options(repr.plot.width = width, repr.plot.height = height,
+          jupyter.plot_scale = scale)
+}
+
+# Initialize environment and print summary, useful for notebooks
+.envInit <- function(packages = NULL) {
+  if (!is.null(packages)) {
+    invisible(lapply(packages, library, character.only = TRUE))
+  }
+  print(R.version.string)
+  print(sapply(packages, function(x) paste0(packageVersion(x))))
+}

.condarc

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+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+channel_priority: strict
+auto_activate_base: false

.condaxrc

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+prefix_path: "~/.local/share/condax"
+link_destination: "~/.local/bin"
+channels:
+    - conda-forge
+    - bioconda
+    - nodefaults

.config/shell/aliases.sh

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+# Alias to manage dotfiles in a bare repo
+alias config='git --git-dir=$HOME/.config/dotfiles --work-tree=$HOME'
+
+# Colored outputs
+alias ls='ls --color=auto'
+alias grep='grep --color=auto'
+alias fgrep='fgrep --color=auto'
+alias egrep='egrep --color=auto'
+
+# Safety aliases
+alias rm='rm -i'
+alias cp='cp -i'
+alias mv='mv -i'
+
+# Quality-of-life aliases
+[ -x "$(command -v batcat)" ] && alias bat='batcat'
+alias la='ls -A'
+alias l='ls -CF'
+alias ll='ls -alF'
+if [ ! -x "$(command -v realpath)" ] && [ -x "$(command -v readlink)" ]; then
+	alias realpath='readlink -f'
+fi
+alias fsort='LC_ALL=C sort'
+[ -x "$(command -v stow)" ] && alias stow='stow --no-folding'
+if [ -x "$(command -v tmux)" ]; then
+	tm() {
+		if [ -n "$1" ]; then
+			tmux attach-session -d -t "$1"
+		else
+			tmux attach-session -d
+		fi
+
+	}
+	alias tmc='tmux load-buffer'
+	alias tmv='tmux save-buffer'
+fi
+if command -v micromamba &>/dev/null; then
+	alias c='micromamba'
+	! command -v mamba &>/dev/null && alias mamba='micromamba'
+	! command -v conda &>/dev/null && alias conda='micromamba'
+elif command -v mamba &>/dev/null; then
+	alias c='mamba'
+elif command -v conda &>/dev/null; then
+	alias c='conda'
+fi
+alias ca='c activate' cda='c deactivate'
+[ -x "$(command -v zoxide)" ] && alias z='zi'
+
+# Slurm shortcuts
+if [ -x "$(command -v sbatch)" ]; then
+	__jobcols() { printf '%s' "$((COLUMNS / 4))"; }
+	alias squeue='squeue -o "%.18i %.9P %.$(__jobcols)j %.8u %.2t %.10M %.6D %R"'
+	alias squeueu='squeue -u $USER'
+	alias sacct='sacct -o "jobid,jobname%$(__jobcols),alloccpus,MaxRSS,state,exitcode,Start,End"'
+fi

.config/shell/functions.sh

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+# Print the header (the first line of input)
+# and then run the specified command on the body (the rest of the input)
+# use it in a pipeline, e.g. ps | body grep somepattern
+# (ref:https://unix.stackexchange.com/a/11859)
+body() {
+	IFS= read -r header
+	printf '%s\n' "$header"
+	"$@"
+}
+
+# Reverse complement a DNA sequence
+revc() {
+	if [ -n "$1" ]; then
+		echo "$1" | rev | tr 'ACGTRYKMBDHV' 'TGCAYRMKVHDB'
+	else
+		rev | tr 'ACGTRYKMBDHV' 'TGCAYRMKVHDB'
+	fi
+}
+
+# count unique lines; sortcut for `sort -u | wc -l`
+wcu() {
+	sort -u "$1" | wc -l
+}
+
+# Add the executed command line to output's header
+cmdump() {
+	echo -E "# $*"
+	"$@"
+}
+
+# Create directory and enter it
+cmkdir() {
+	mkdir -p "$1" && cd "$1" || return
+}
+
+# Check resource usage by user
+userusage() {
+	ps aux | awk '{print $1,$3,$6,$8}' | sort -u | awk '
+  BEGIN {print "USER\t%CPU\tRSS(GB)"}
+  { rss[$1]+=$3; cpu[$1]+=$2 }
+  END { for(i in rss){OFS="\t"; print i,cpu[i],rss[i]/1000000} }'
+}
+
+# Wrapper for `zcat <file.gz> | head`
+# usage: zhead <file.gz> [10]
+zhead() {
+	if [ -z "$2" ]; then
+		local n=10
+	else
+		local n="$2"
+	fi
+	zcat "$1" | head -n "$n"
+}
+
+# Quickly remove large directories with rsync
+rsyncrm() {
+	mkdir rsrm_empty
+	rsync -a --delete rsrm_empty/ "$1"
+	rmdir rsrm_empty "$1"
+}
+
+# Scrape biocontainers
+biocontainers() {
+	local url="https://quay.io/api/v1/repository/biocontainers"
+	local sprefix="https://depot.galaxyproject.org/singularity"
+	local dprefix="quay.io/biocontainers"
+	curl -s -X GET "$url"/"$1"/tag/ |
+		python3 -c "import json,sys;from datetime import datetime;\
+    obj=json.load(sys.stdin);\
+    print('docker_image\tsingularity_image\tlast_modified');\
+    [print('$dprefix/$1:{}\t$sprefix/$1:{}\t{}'.format(\
+      x['name'], x['name'], datetime.strptime(x['last_modified'], '%a, %d %b %Y %H:%M:%S -0000')\
+    )) for x in obj['tags']]"
+}
+biocontainers_galaxy() {
+	local url="https://depot.galaxyproject.org/singularity/"
+	curl -s $url | sed 's/\r$//' | grep -v "\-$" | grep "^<a href" |
+		sed 's/<[^<>]*>//g' |
+		awk -vurl=$url '{print url""$1"\t"$2"-"$3}'
+}
+
+# SSH to current directory
+sshpwd() {
+	local shell=${SHELL:-bash}
+	case "$shell" in
+	*/sh)
+		local args=""
+		;;
+	*)
+		local args=${2:-"--login"}
+		;;
+	esac
+	ssh -t "$1" "cd $PWD; $shell $args"
+}
+
+# Get numbered header COLUMNS
+nheader() {
+	head -n 1 "$1" | tr '\t' '\n' | nl
+}
+
+# Generate duckduckgo email alias
+duck() {
+	curl -s -H "Content-Type: application/json" \
+		-H "Authorization: Bearer ${DUCK_TOKEN:-$1}" \
+		-X POST \
+		https://quack.duckduckgo.com/api/email/addresses |
+		sed 's/.*"\([^"]\+\)"}/\[email protected]\n/'
+}

.config/shell/functions.zsh

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+# plugins management, edited from https://github.com/mattmc3/zsh_unplugged
+plugin-load() {
+  local repo plugdir initfiles zpd=()
+  local ZPLUGDIRS=(
+    "${XDG_DATA_HOME:-$HOME/.local/share}/zsh/plugins"
+    '/usr/local/share/zsh/plugins'
+    '/usr/share/zsh/plugins'
+  )
+  for repo in $@; do
+    for zpd in $ZPLUGDIRS; do
+      plugdir="$zpd/${repo:t}"
+      if [[ -d "$plugdir" ]]; then
+        break
+      fi
+    done
+    if [[ ! -d "$plugdir" ]]; then
+      printf "Clone $repo ? [yN]"
+      if read -q; then
+        git clone -q --depth 1 --recursive --shallow-submodules \
+          https://github.com/"$repo" "$plugdir"
+      else
+        continue
+      fi
+    fi
+    initfiles=($plugdir/*.{plugin.zsh,zsh-theme,zsh,sh}(N))
+    (( $#initfiles )) || {echo >&2 "No init file found '$repo'." && continue}
+    source $initfiles[1]
+  done
+}
+

.config/shell/fzf-completions.sh

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+# Run only if fzf has been initialized
+if ! declare -F _fzf_complete &>/dev/null; then
+	return 0
+fi
+
+# Slurm process IDs
+_fzf_complete_scancel() {
+	_fzf_complete --multi --header-lines=1 -- "$@" < <(squeue -u "$USER")
+}
+_fzf_complete_scancel_post() {
+	awk '{print $1}'
+}
+
+_fzf_complete_scontrol() {
+	_fzf_complete --header-lines=1 -- "$@" < <(squeue)
+}
+_fzf_complete_scontrol_post() {
+	awk '{print $1}'
+}
+
+if [ -n "$BASH" ]; then
+	complete -F _fzf_complete_scancel -o default -o bashdefault scancel
+	complete -F _fzf_complete_scontrol -o default -o bashdefault scontrol
+fi

.config/tmux/clear_jobs.sh

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+#!/bin/sh
+
+command sacct -n -o 'jobid,state' -S 'now-24hours' \
+	| grep -vw RUNNING | grep -vw PENDING \
+	| cut -f1 -d' ' > ~/.config/tmux/blacklist

.config/tmux/slurm_jobs.sh

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+#!/bin/bash
+
+if [ ! -f ~/.config/tmux/blacklist ]; then
+	touch ~/.config/tmux/blacklist
+fi
+
+if [ -x "$(command -v sacct)" ]; then
+	cat <(command sacct -n -o 'jobid,state' -S 'now-24hours') \
+	| sed 's/ \+/ /' | sed -r 's/^([0-9]+)\.[^ ]+ /\1 /' | sort -u \
+	| grep -vwf ~/.config/tmux/blacklist \
+	| awk '$1!~/[0-9]+\.b/ && $2!~/CANCELLED/ {
+		a[substr($2,1,1)]+=1;next
+	} END {
+		outline="";
+		for(i in a) outline=outline""i":"a[i]" ";
+		sub(/ $/,"",outline);
+		if(outline) print " | "outline
+	}'
+fi
+