Merge branch 'master' of https://github.com/danijoo/dotfiles

.pymolrc

@@ -1,21 +0,0 @@
-set fetch_path, /tmp
-set async_builds, on
-set max_threads, 16
-set cache_mode 
-
-set opaque_background, 0
-log_open /tmp/pymol_log.pml
-set cartoon_side_chain_helper, 1
-set cartoon_highlight_color, grey50
-
-set_key F1, as lines, solvent
-set_key F2, hide everything, solvent
-set_key F3, as spheres, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN)
-set_key F4, hide everything, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN)
-set_key F5, as sticks, organic
-set_key F6, hide everything, organic
-
-set_key F9, set orthoscopic
-set_key F10, set orthoscopic, off
-set_key F11, ray
-set_key F12, ray 1600,1600

.ssh/config

@@ -1,25 +0,0 @@
-Host *
-    ForwardX11 yes
-    PermitLocalCommand yes
-    #LocalCommand tar c -C${HOME} --exclude="dotfiles/.git" --exclude=".zim/.git" dotfiles .zim | ssh -o PermitLocalCommand=no %n "tar mx -C${HOME}; bash ~/dotfiles/dotfiles_setup.sh  ; chsh -s /bin/zsh" 
-
-Host summonerapi
-	HostName 46.4.78.43
-
-Host biodata0
-	User bauer
-    HostName biodata0.compbiol.bio.tu-darmstadt.de
-
-Host bioclust
-	User bauer
-	HostName bioclust.bio.tu-darmstadt.de
-
-Host bioinfo4
-    HostName 10.0.0.4
-	User bauer
-    ProxyCommand ssh -q biodata0 nc -q0 %h 22
-
-Host lcluster?*
-  User yg38ymab
-  ForwardX11 yes
-  HostName %h.hrz.tu-darmstadt.de

.zshrc

@@ -1,56 +0,0 @@
-if [ -f `which powerline-daemon` ]; then
-    powerline-daemon -q
-    POWERLINE_BASH_CONTINUATION=1
-    POWERLINE_BASH_SELECT=1
-    . /usr/local/lib/python2.7/dist-packages/powerline/bindings/zsh/powerline.zsh
-fi
-
-# Change default zim location
-export ZIM_HOME=${ZDOTDIR:-${HOME}}/.zim
-
-# Start zim
-[[ -s ${ZIM_HOME}/init.zsh ]] && source ${ZIM_HOME}/init.zsh 
-
-# gromacs needs to be before ZIM for autocompletion
-if [ -z "$GMXRC" ]; then
-    GMXRC="/opt/gromacs-2018/bin/GMXRC"
-fi
-source $GMXRC
-
-# preferences
-export LANG=en_US.UTF-8
-export EDITOR='vim'
-export SSH_KEY_PATH="~/.ssh/rsa_id"
-export TERMINAL="terminator"
-export BROWSER="firefox"
-export PAGER='most'
-export BAT_PAGER='less'
-
-# alter path
-export PATH="$HOME/.cargo/bin:$PATH"
-export PATH="$HOME/anaconda3/bin:${PATH}" # binaries
-export PATH="$HOME/bin:${PATH}" # binaries
-export PATH="$HOME/scripts:${PATH}" # scripts
-export PATH="$HOME/.local/bin:${PATH}" # python executeables
-
-# aliases
-if [ -f .cargo/bin/bat ]; then
-    alias cat='bat'
-fi	
-alias clip='xsel --clipboard'
-alias groclean='rm \#*'
-alias sm='snakemake'
-alias ls='ls -lh'
-alias workon='source activate' # enable anaconda environ
-
-# config specific to this machine (not copied from dotfiles)
-if [ -f $HOME/.zshrc_local ]; then
-    source $HOME/.zshrc_local
-fi
-
-# fasd autocompletion
-eval "$(fasd --init auto)"
-
-# marker
-[[ -s "$HOME/.local/share/marker/marker.sh" ]] && source "$HOME/.local/share/marker/marker.sh"
-

dotfiles.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+
+PROFILE_BASE_DIR=$HOME/.dotfiles/profiles
+
+# Link files of a single profile
+link_profile() {
+    profile=$1
+    profile_dir=${PROFILE_BASE_DIR}/$profile
+    
+    
+    if [ ! -d $profile_dir ]; then
+    	echo "$profile does not exist"
+		exit 1
+	else
+		echo "Linking files from profile $profile"
+	fi
+
+	cd $profile_dir
+	# Find all files to link
+	for file in `find . -type f | cut -c 3- | grep -v "^$"`; do
+		dir=$(dirname "${file}")
+		src=`pwd`/$file
+		dst_dir=$HOME/$dir
+		dst=$HOME/$file
+		
+		# create folder if not exist
+		if [ ! -d "$dst_dir" ]; then
+			echo "Creating destination direcory $dst_dir"
+			mkdir -p $dst_dir
+		fi
+
+		# link file
+		echo "Linking $src to $dst"
+		if [ -f "${dst}" ] || [ -L "${dst}" ]; then
+			echo "$dst_file esists. Override? [y/N]"
+			read response
+			if [ "$response" == 'y' ] || [ "$response" == 'Y' ] \
+				|| [ "$response" == 'yes' ] || [ "$response" == 'Yes' ]; then
+				ln -sf $src $dst
+			else
+				echo "Skipping $file"
+			fi
+		else
+			ln -s $src $dst	
+		fi
+	done
+}
+
+# link profiles
+if [ "$1" == "link" ]; then
+	shift
+	while [ "$1" != "" ]; do
+		link_profile $1
+		shift
+	done
+fi 

dotfiles_setup.sh

@@ -1,15 +0,0 @@
-#!/bin/bash
-dir="${HOME}/dotfiles"
-conffolder="${HOME}/.config"
-
-dotfiles=(".vimrc" ".vim" ".vimrc" ".zshrc" ".zshrc_functions" ".zim" ".zimrc" ".gitconfig")
-for dotfile in "${dotfiles[@]}"; do
-	ln -sf $dir/$dotfile ${HOME}/${dotfile}
-done
-
-# fonts
-mkdir -p ~/.config/fontconfig
-ln -sf $dir/.config/fontconfig/fonts.conf $conffolder/fontconfig/fonts.conf
-
-# matplotlib
-ln -sf $dir/.config/matplotlib ~/.config/matplotlib

install.sh

@@ -0,0 +1,48 @@
+#!/bin/bash
+
+# Make ZSH the default shell environment
+if [ `cat /etc/passwd | grep $USER | awk -F ':' '{print $7}'` != "/bin/zsh" ]; then
+	echo "Changing shell to zsh"
+	chsh -s $(which zsh)
+fi
+
+# ZIM Installation
+if [ ! -d "$HOME/.zim" ]; then
+	echo "Installing ZIM"
+	git clone --recursive --depth=1 https://github.com/zimfw/zimfw.git \
+		${ZDOTDIR:-${HOME}}/.zim
+else
+	echo "ZIM already exists."
+fi
+
+# Powerlevel9k Theme
+if [ ! -d "$HOME/.zim/modules/prompt/external-themes/powerlevel9k" ]; then
+	echo "Installing Powerlevel9k theme"
+	git clone --depth=1 https://github.com/bhilburn/powerlevel9k.git \
+		~/.zim/modules/prompt/external-themes/powerlevel9k
+	ln -s ~/.zim/modules/prompt/external-themes/powerlevel9k/powerlevel9k.zsh-theme ~/.zim/modules/prompt/functions/prompt_powerlevel9k_setup
+else
+	echo "Powerlevel9k already exists."
+fi
+
+# Conda and pip
+if [ ! -d "$HOME/conda" ]; then
+	echo "Installing Conda"
+	wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh
+	bash /tmp/miniconda.sh -b -p ~/conda 
+	rm /tmp/miniconda.sh
+	echo "yes" | conda install pip
+else
+	echo "Conda already installed"
+fi
+
+# Marker
+if [ ! -d "$HOME/.marker" ]; then
+	echo "Installing Marker"
+	git clone --depth=1 https://github.com/pindexis/marker $HOME/.marker
+	$HOME/.marker/install.py
+fi
+
+# linking dotfiles
+$HOME/.dotfiles/dotfiles.sh link base  
+

profiles/base/.aliases

@@ -0,0 +1,9 @@
+# aliases
+if [ -f .cargo/bin/bat ]; then
+    alias cat='bat'
+fi	
+alias clip='xsel --clipboard'
+alias groclean='rm \#*'
+alias sm='snakemake'
+alias ls='ls -lh'
+alias workon='source activate' # enable anaconda environ

profiles/base/.environment

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# system preferences
+export LANG=en_US.UTF-8
+export SSH_KEY_PATH="~/.ssh/rsa_id"
+
+# Prefered programs
+export EDITOR='vim'
+export TERMINAL="terminator"
+export BROWSER="firefox"
+export PAGER='most'
+export BAT_PAGER='less'
+
+# Path
+export PATH="$HOME/.cargo/bin:$PATH"
+export PATH="$HOME/conda/bin:${PATH}" # binaries
+export PATH="$HOME/bin:${PATH}" # binaries
+export PATH="$HOME/scripts:${PATH}" # scripts
+export PATH="$HOME/.local/bin:${PATH}" # python executeables

profiles/base/.functions

@@ -0,0 +1,10 @@
+sm_autocomplete() {
+	# make zsh emulate bash if necessary
+	if [[ -n "$ZSH_VERSION" ]]; then
+    	autoload bashcompinit
+    	bashcompinit
+	fi
+
+	snakemake_options=$(snakemake --snakefile Snakefile --list)
+	complete -W "${snakemake_options}" 'snakemake'	
+}

profiles/base/.zshrc

@@ -0,0 +1,37 @@
+if [ -f `which powerline-daemon` ]; then
+    powerline-daemon -q
+    POWERLINE_BASH_CONTINUATION=1
+    POWERLINE_BASH_SELECT=1
+    . /usr/local/lib/python2.7/dist-packages/powerline/bindings/zsh/powerline.zsh
+fi
+
+# Change default zim location
+export ZIM_HOME=${ZDOTDIR:-${HOME}}/.zim
+
+# Start zim
+[[ -s ${ZIM_HOME}/init.zsh ]] && source ${ZIM_HOME}/init.zsh 
+
+# source other dotfiles
+source $HOME/.environment
+if [ -f "$HOME/.environment.local" ]; then
+	source $HOME/.environment.local
+fi
+
+source $HOME/.aliases
+source $HOME/.functions
+
+if [ -z "$GMXRC" ]; then
+    GMXRC="/opt/gromacs-2018/bin/GMXRC"
+fi
+source $GMXRC
+
+# config specific to this machine
+if [ -f $HOME/.zshrc_local ]; then
+    source $HOME/.zshrc_local
+fi
+
+# fasd autocompletion
+eval "$(fasd --init auto)"
+
+# marker
+[[ -s "$HOME/.local/share/marker/marker.sh" ]] && source "$HOME/.local/share/marker/marker.sh"

profiles/laptop/.Xresources

@@ -0,0 +1,7 @@
+Xft.dpi: 130
+Xft.autohint: 0
+Xft.lcdfilter:  lcddefault
+Xft.hintstyle:  hintfull
+Xft.hinting: 1
+Xft.antialias: 1
+Xft.rgba: rgb

profiles/pymol/.pymol/.pymol

@@ -0,0 +1 @@
+/home/bauer/dotfiles/.pymol

profiles/pymol/.pymolrc

@@ -0,0 +1,63 @@
+# general environment
+bg_color white
+space cmyk
+set fetch_path, /tmp
+log_open /tmp/pymol_log.pml
+set retain_order
+
+
+# interface
+set overlay, 1
+set internal_gui_control_size, 10
+set display_scale_factor, 2
+
+# performance
+set async_builds, on
+set max_threads, 8
+set cache_mode
+set defer_builds_mode, 3
+set hash_max, 500
+
+# shortcuts
+set_key F1, as lines, solvent
+set_key F2, hide everything, solvent
+set_key F3, as spheres, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN)
+set_key F4, hide everything, inorganic and (n. NA or n. K or n. CL or n. CA or n. XE or n. RN)
+set_key F5, as sticks, organic
+set_key F6, hide everything, organic
+set_key F9, set depth_cue
+set_key F10, set depth_cue, off
+set_key F11, ray 800,800
+set_key F12, ray 1600,1600
+
+#Extending colors with color-blindness friendly color palette
+#References:
+#http://jfly.iam.u-tokyo.ac.jp/html/color_cb/#pallet
+#https://personal.sron.nl/~pault/colourschemes.pdf
+set_color cb_blue, [51, 34, 136]
+set_color cb_tan, [221, 204, 119]
+set_color cb_lightblue, [136, 204, 238]
+set_color cb_green, [17, 119, 51]
+set_color cb_teal, [68, 170, 153]
+set_color cb_gold, [153, 153, 51]
+set_color cb_salmon, [204, 102, 119]
+set_color cb_red, [136, 34, 85]
+set_color cb_pink, [170, 68, 153]
+
+# raytrace
+set depth_cue, 0
+set ray_opaque_background, false
+set orthoscopic, 0
+set ray_shadow, false 
+set spec_reflect, 0
+set antialias, 0
+set surface_quality, 1
+set ray_trace_mode, 0
+
+set valence, 0
+set cartoon_side_chain_helper, 1
+set cartoon_discrete_colors, on
+
+alias clean, hide everything, hydrogen
+
+