Initial import

.bash_profile

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+# .bash_profile
+# $Header$
+
+# source the GSC profile
+if [ -f ~/.profile ]; then
+    . ~/.profile
+fi
+
+# get the aliases and functions
+if [ -f ~/.bashrc ]; then
+	. ~/.bashrc
+fi
+
+#source "/gscmnt/sata132/techd/pacbio/jwalker/git/pacbio/PBJelly_12.9.14/exportPaths.sh"
+

.bashrc

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+# .bashrc
+
+#export SEYMOUR_HOME=/gscmnt/pacbio/production/smrtanalysis
+#. $SEYMOUR_HOME/etc/setup.sh
+
+# source global definitions
+if [ -f /etc/bashrc ]; then	# redhat
+    . /etc/bashrc
+elif [ -f /etc/bash.bashrc ]; then # debian
+    . /etc/bash.bashrc
+fi
+
+# source the gapp bashrc
+if [ -f /gapp/noarch/share/login/gapp.bashrc ]; then
+    . /gapp/noarch/share/login/gapp.bashrc
+fi
+
+# source alias file
+if [ -f ~/.bash_alias ]; then
+    . ~/.bash_alias
+fi
+
+# Set prompt to emulate tcsh default
+#PS1="\u@\h:\w \!>"
+#export MYGPGKEY=2F9338CB
+
+# Personal
+#source ~/.bashss 
+
+#[[ -s $HOME/.pythonbrew/etc/bashrc ]] && source $HOME/.pythonbrew/etc/bashrc
+
+function load_dir {
+    LOAD_DIR=${1}
+    if [ -d $LOAD_DIR -a -r $LOAD_DIR -a -x $LOAD_DIR ]; then
+        for i in $LOAD_DIR/*.sh; do
+            source $i
+        done
+    fi
+    unset i
+}
+
+shopt -q login_shell && \
+  load_dir ${HOME}/bashrc.d

.gitconfig

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+[user]
+	name = Jason Walker
+	email = [email protected]
+[color]
+	branch = auto
+	status = auto
+	diff = auto
+[core]
+	pager = less -FXRS
+	excludesfile = /gscuser/jwalker/.gitignore
+	filemodes = true
+	filemode = false
+        preloadindex = true
+[push]
+	default = simple

.jiraclientrc

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+# .jiraclientrc
+[jiraclient]
+jiraurl = https://jira.gsc.wustl.edu
+user = jwalker
+[issues]
+project = BIO
+#type = story
+#priority = Normal
+#epic_theme = 
+#assignee = 
+#components = 
+#fixVersions = 

.profile

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+# .profile
+
+# source the gapp profile
+if [ -f /gapp/noarch/share/login/gapp.profile ]; then
+    . /gapp/noarch/share/login/gapp.profile
+fi
+
+#source /gscmnt/pacbio/production/smrtanalysis/etc/setup.sh

.vimrc

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+" The following are commented out as they cause vim to behave a lot
+" different from regular vi. They are highly recommended though.
+set showcmd         " Show (partial) command in status line.
+set showmatch       " Show matching brackets.
+set ruler           " Show the line and column numbers of the cursor
+"set ignorecase      " Do case insensitive matching
+set incsearch       " Incremental search
+set autowrite       " Automatically save before commands like :next and :make
+set hidden          " Use hidden buffers
+set nohlsearch      " don't highlight last search matches
+set cmdheight=2     " 2 lines for messages (fewer 'Press Return' messages)
+set showbreak=+     " prefix wrapped lines with a + sign
+set wildmenu        " use a menu for wildcard completion
+
+set background=light
+
+if &t_Co > 2 || has("gui_running")
+    "colo darkblue
+
+    " turn on syntax highlighting
+    if has("syntax")
+        syntax on
+
+        " some settings for specific syntax files
+        let c_gnu = 1
+        let c_syntax_for_h = 1
+
+        let perl_include_pod = 1
+        let perl_want_scope_in_variables = 1
+        let perl_extended_vars = 1
+        "let perl_fold = 1
+        let perl_fold_blocks = 1
+        let perl_include_pod = 1
+        let perl_want_scope_in_variables = 1
+        let perl_extended_vars = 1
+        let perl_string_as_statement = 1
+        "set fdc=3
+    endif
+endif
+
+" set up a comment and uncomment command
+:command Comment 'a,'b s/^/#/
+:command Uncomment 'a,'b s/^#//
+
+" setup a shift and unshift
+:command Shift 'a,'b s/^/     /
+:command Unshift 'a,'b s/^     //
+
+" from my old file...
+set showmode
+set visualbell
+"set tabstop=4
+set tabstop=8
+set softtabstop=4
+set shiftwidth=4
+set expandtab
+set number
+set noautoindent
+autocmd BufRead *.t set syntax=perl
+"set term=builtin_ansi
+"set term=xterm-color
+"set autoindent
+set nohls
+"set bg=dark
+set bg=light
+"autocmd BufNewFile,BufRead *.p? compiler perl
+"if &t_Co > 1
+"    set background=light 
+"    syntax enable
+"endif
+

bashrc.d/01_environment.sh

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+# Master "on/off" switches
+RBENV_ENABLED=true
+PYENV_ENABLED=true
+PLENV_ENABLED=true
+RENV_ENABLED=true

bashrc.d/10_env.sh

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+# If envs are present, and we turned them on, load them.
+PLENV_PATH="$HOME/.plenv/bin"
+if [ "$PLENV_ENABLED" = "true" -a -d "$PLENV_PATH" ]; then
+  eval "$(plenv init -)"
+fi
+PYENV_PATH="$HOME/.pyenv/bin"
+if [ "$PYENV_ENABLED" = "true" -a -d "$PYENV_PATH" ]; then
+  eval "$(pyenv init -)"
+fi
+RBENV_PATH="$HOME/.rbenv/bin"
+if [ "$RBENV_ENABLED" = "true" -a -d "$RBENV_PATH" ]; then
+  eval "$(rbenv init -)"
+fi
+RENV_PATH="$HOME/.renv/bin"
+if [ "$RENV_ENABLED" = "true" -a -d "$RENV_PATH" ]; then
+  eval "$(renv init -)"
+fi

bashrc.d/base_config.sh

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+#!/bin/bash
+
+#tcsh like prompt
+PS1="\u@\h:\w \!>"
+export MYGPGKEY=2F9338CB
+
+export IGNOREEOF=99999999
+alias cd="pushd >/dev/null";
+alias bd="popd >/dev/null";
+set -o noclobber
+set completion-ignore-case On
+source $HOME/.git-completion.sh
+umask 002
+
+if [ "$PS1" ]; then             # interactive shell
+    # make colorful prompt
+    CYAN="\[\033[0;36m\]"
+    GRAY="\[\033[0;37m\]"
+    BLACK="\[\033[0;30m\]"
+    BLUE="\[\033[0;34m\]"
+    RED="\[\033[0;31m\]"
+    PURPLE="\[\033[0;35m\]"
+    BROWN="\[\033[0;33m\]"
+    NONE="\[\e[m\]"
+    export PS1R="${RED}\u@\h ${BROWN}\w>${NONE} "
+    #export PS1='[\u@\h \W$(__git_ps1 " (%s)")]\$ '
+    #export PS1=$RED'\u@\h '$BROWN'\w$(__git_ps1 " (%s)")>'$NONE" "
+    export PS1=$RED'\u@\h '$BROWN'\w'$CYAN'$(__git_ps1 " (%s)")'$BROWN'>'$NONE" "
+fi
+
+if [ `uname` = "Darwin" ]; then
+    echo init paths...
+    export CLICOLOR=1
+    export PATH=$HOME/bin:/opt/local/bin:/opt/local/sbin:$PATH
+    export MANPATH=/opt/local/share/man:$MANPATH
+else
+    export PATH=$HOME/bin:$PATH
+    alias ls="ls --color"
+    alias sr='sqlrun --instance warehouse';
+fi
+
+alias rm='rm -i'
+alias mv='mv -i'
+
+

bashrc.d/base_config.sh~

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+#!/bin/bash
+
+export IGNOREEOF=99999999
+alias cd="pushd >/dev/null";
+alias bd="popd >/dev/null";
+set -o noclobber
+set completion-ignore-case On
+source $HOME/.git-completion.sh
+umask 002
+
+if [ "$PS1" ]; then             # interactive shell
+    # make colorful prompt
+    CYAN="\[\033[0;36m\]"
+    GRAY="\[\033[0;37m\]"
+    BLACK="\[\033[0;30m\]"
+    BLUE="\[\033[0;34m\]"
+    RED="\[\033[0;31m\]"
+    PURPLE="\[\033[0;35m\]"
+    BROWN="\[\033[0;33m\]"
+    NONE="\[\e[m\]"
+    export PS1R="${RED}\u@\h ${BROWN}\w>${NONE} "
+    #export PS1='[\u@\h \W$(__git_ps1 " (%s)")]\$ '
+    #export PS1=$RED'\u@\h '$BROWN'\w$(__git_ps1 " (%s)")>'$NONE" "
+    export PS1=$RED'\u@\h '$BROWN'\w'$CYAN'$(__git_ps1 " (%s)")'$BROWN'>'$NONE" "
+fi
+
+if [ `uname` = "Darwin" ]; then
+    echo init paths...
+    export CLICOLOR=1
+    export PATH=$HOME/bin:/opt/local/bin:/opt/local/sbin:$PATH
+    export MANPATH=/opt/local/share/man:$MANPATH
+else
+    export PATH=$HOME/bin:$PATH
+    alias ls="ls --color"
+    alias sr='sqlrun --instance warehouse';
+fi
+
+alias rm='rm -i'
+alias mv='mv -i'
+
+

setup.sh

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+#!/bin/sh
+set -x
+# Link files
+find /gscuser/jwalker/dotfiles -maxdepth 1 -type f \( -not -name setup.sh \) | while read FILE; do
+  BASE=
+  # Don't clobber existing file, make a .orig backup
+  [ -f /gscuser/jwalker/ ] && mv /gscuser/jwalker/ /gscuser/jwalker/.orig
+  ln -s -f  /gscuser/jwalker
+done
+
+# Link directories
+find ~/dotfiles -mindepth 1 -maxdepth 1 -type d \( -not -name .git \) | while read DIR; do
+  BASE=
+  # Don't clobber existing directory, make a .orig backup
+  [ -d /gscuser/jwalker/ ] && mv /gscuser/jwalker/ /gscuser/jwalker/.orig
+  ln -s -f  /gscuser/jwalker
+done

setup.sh~

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+#!/bin/sh
+set -x
+# Link files
+find /gscuser/jwalker/dotfiles -maxdepth 1 -type f \( -not -name setup.sh \) | while read FILE; do
+  BASE=
+  # Don't clobber existing file, make a .orig backup
+  [ -f /gscuser/jwalker/ ] && mv /gscuser/jwalker/ /gscuser/jwalker/.orig
+  ln -s -f  /gscuser/jwalker
+done
+
+# Link directories
+find ~/dotfiles -mindepth 1 -maxdepth 1 -type d \( -not -name .git \) | while read DIR; do
+  BASE=
+  # Don't clobber existing directory, make a .orig backup
+  [ -d /gscuser/jwalker/ ] && mv /gscuser/jwalker/ /gscuser/jwalker/.orig
+  ln -s -f  /gscuser/jwalker
+done