emacs

;; GENERAL SETTINGS
(setq directory-free-space-program nil) ;; add to your .emacs file. It's because df runs so slowly on NT fs
(add-to-list 'custom-theme-load-path "~/.emacs.d/themes/")
(add-to-list 'load-path "~/.emacs.d/lisp/") ;; Tell emacs where is your personal elisp lib dir
(electric-indent-mode 0)

;; MELPA
(require 'package) ;; You might already have this line
(add-to-list 'package-archives
             '("melpa" . "https://melpa.org/packages/"))
(when (< emacs-major-version 24)
  ;; For important compatibility libraries like cl-lib
  (add-to-list 'package-archives '("gnu" . "http://elpa.gnu.org/packages/")))
(package-initialize) ;; You might already have this line

;; BACKUPS
(setq backup-directory-alist `(("." . "~/.emacs.d/saves")))
(setq backup-by-copying t)
(setq delete-old-versions t
  kept-new-versions 6
  kept-old-versions 2
  version-control t)

;; Enable paren matching
(show-paren-mode 1)

;; Emable column number in status line
(setq column-number-mode t)

;; show trailing whitespace
(setq-default show-trailing-whitespace t)

;; enable line wrap
(setq default-truncate-lines nil)

;; make side by side buffers function the same as the main window
(setq truncate-partial-width-windows nil)

;; regexp
(global-set-key (kbd "C-x C-r") 'replace-regexp)

;; Add F12 to toggle line wrap
(global-set-key (kbd "<f12>") 'toggle-truncate-lines)
(defun trunc()
  (toggle-truncate-lines))

;; Scroll single lines  up or down
(defun scroll-up-one-line()
  (interactive)
  (scroll-up 1))
(defun scroll-down-one-line()
  (interactive)
  (scroll-down 1))
(global-set-key [?\M-.] 'scroll-down-one-line)
(global-set-key [?\M-,] 'scroll-up-one-line)

;; Uniquify lines functions
(defun uniquify-region-lines (beg end)
    "Remove duplicate adjacent lines in region."
    (interactive "*r")
    (save-excursion
      (goto-char beg)
      (while (re-search-forward "^\\(.*\n\\)\\1+" end t)
        (replace-match "\\1"))))

  (defun uniquify-buffer-lines ()
    "Remove duplicate adjacent lines in the current buffer."
    (interactive)
    (uniquify-region-lines (point-min) (point-max)))

(defun uniquify-all-lines-region (start end)
    "Find duplicate lines in region START to END keeping first occurrence."
    (interactive "*r")
    (save-excursion
      (let ((end (copy-marker end)))
        (while
            (progn
              (goto-char start)
              (re-search-forward "^\\(.*\\)\n\\(\\(.*\n\\)*\\)\\1\n" end t))
          (replace-match "\\1\n\\2")))))

  (defun uniquify-all-lines-buffer ()
    "Delete duplicate lines in buffer and keep first occurrence."
    (interactive "*")
    (uniquify-all-lines-region (point-min) (point-max)))

;; ediff
(defun command-line-diff (switch)
  (let ((file1 (pop command-line-args-left))
        (file2 (pop command-line-args-left)))
    (ediff file1 file2)))

(add-to-list 'command-switch-alist '("diff" . command-line-diff)) ;; Usage: emacs -diff file1 file2

;; Standard Jedi.el setting
;;(add-hook 'python-mode-hook 'jedi:setup)
;;(setq jedi:complete-on-dot t)

;; Type:
;;     M-x package-install RET jedi RET
;;     M-x jedi:install-server RET
;; Then open Python file.

;; IDO
(require 'ido)
(ido-mode t)


;; load nextflow mode.
(when (load "nextflow-mode" t)
	  (load "nextflow-mode")) ;; best not to include the ending “.el” or “.elc”

;; use cperl-mode instead of perl-mode
(setq auto-mode-alist (rassq-delete-all 'perl-mode auto-mode-alist))
(add-to-list 'auto-mode-alist '("\\.\\(p\\([lm]\\)\\)\\'" . cperl-mode))

(setq interpreter-mode-alist (rassq-delete-all 'perl-mode interpreter-mode-alist))
(add-to-list 'interpreter-mode-alist '("perl" . cperl-mode))
(add-to-list 'interpreter-mode-alist '("perl5" . cperl-mode))
(add-to-list 'interpreter-mode-alist '("miniperl" . cperl-mode))
(custom-set-faces
 '(cperl-array-face ((t (:weight normal))))
 '(cperl-hash-face ((t (:weight normal))))
)


;; Theses are set via the emacs settings menus
(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(ansi-color-faces-vector
   [default default default italic underline success warning error])
 '(ansi-color-names-vector
   ["#242424" "#e5786d" "#95e454" "#cae682" "#8ac6f2" "#333366" "#ccaa8f" "#f6f3e8"])
 '(compilation-message-face (quote default))
 '(cua-global-mark-cursor-color "#2aa198")
 '(cua-normal-cursor-color "#839496")
 '(cua-overwrite-cursor-color "#b58900")
 '(cua-read-only-cursor-color "#859900")
 '(custom-enabled-themes (quote (tango-dark)))
 '(custom-safe-themes
   (quote
	("0598c6a29e13e7112cfbc2f523e31927ab7dce56ebb2016b567e1eff6dc1fd4f" "604ac011fc9bd042bc041330b3a5e5a86e764a46f7e9fe13e2a1f9f83bf44327" "fad9c3dbfd4a889499f6921f54f68de8857e6846a0398e89887dbe5f26b591c0" "713f898dd8c881c139b62cf05b7ac476d05735825d49006255c0a31f9a4f46ab" "7d16f75538c42cd57d098fa582a469ef75b9d55891b8fb7b27a5236c6ccc0594" default)))
 '(fci-rule-color "#073642")
 '(highlight-changes-colors (quote ("#d33682" "#6c71c4")))
 '(highlight-symbol-colors
   (--map
	(solarized-color-blend it "#002b36" 0.25)
	(quote
	 ("#b58900" "#2aa198" "#dc322f" "#6c71c4" "#859900" "#cb4b16" "#268bd2"))))
 '(highlight-symbol-foreground-color "#93a1a1")
 '(highlight-tail-colors
   (quote
	(("#073642" . 0)
	 ("#546E00" . 20)
	 ("#00736F" . 30)
	 ("#00629D" . 50)
	 ("#7B6000" . 60)
	 ("#8B2C02" . 70)
	 ("#93115C" . 85)
	 ("#073642" . 100))))
 '(hl-bg-colors
   (quote
	("#7B6000" "#8B2C02" "#990A1B" "#93115C" "#3F4D91" "#00629D" "#00736F" "#546E00")))
 '(hl-fg-colors
   (quote
	("#002b36" "#002b36" "#002b36" "#002b36" "#002b36" "#002b36" "#002b36" "#002b36")))
 '(hl-paren-colors (quote ("#2aa198" "#b58900" "#268bd2" "#6c71c4" "#859900")))
 '(ido-enable-flex-matching t)
 '(inhibit-startup-screen t)
 '(nrepl-message-colors
   (quote
	("#dc322f" "#cb4b16" "#b58900" "#546E00" "#B4C342" "#00629D" "#2aa198" "#d33682" "#6c71c4")))
 '(package-selected-packages (quote (solarized-theme tangotango-theme)))
 '(pos-tip-background-color "#073642")
 '(pos-tip-foreground-color "#93a1a1")
 '(smartrep-mode-line-active-bg (solarized-color-blend "#859900" "#073642" 0.2))
 '(tab-width 4)
 '(term-default-bg-color "#002b36")
 '(term-default-fg-color "#839496")
 '(vc-annotate-background nil)
 '(vc-annotate-background-mode nil)
 '(vc-annotate-color-map
   (quote
	((20 . "#dc322f")
	 (40 . "#c37300")
	 (60 . "#b97d00")
	 (80 . "#b58900")
	 (100 . "#a18700")
	 (120 . "#9b8700")
	 (140 . "#948700")
	 (160 . "#8d8700")
	 (180 . "#859900")
	 (200 . "#5a942c")
	 (220 . "#439b43")
	 (240 . "#2da159")
	 (260 . "#16a870")
	 (280 . "#2aa198")
	 (300 . "#009fa7")
	 (320 . "#0097b7")
	 (340 . "#008fc7")
	 (360 . "#268bd2"))))
 '(vc-annotate-very-old-color nil)
 '(weechat-color-list
   (quote
	(unspecified "#002b36" "#073642" "#990A1B" "#dc322f" "#546E00" "#859900" "#7B6000" "#b58900" "#00629D" "#268bd2" "#93115C" "#d33682" "#00736F" "#2aa198" "#839496" "#657b83")))
 '(xterm-color-names
   ["#073642" "#dc322f" "#859900" "#b58900" "#268bd2" "#d33682" "#2aa198" "#eee8d5"])
 '(xterm-color-names-bright
   ["#002b36" "#cb4b16" "#586e75" "#657b83" "#839496" "#6c71c4" "#93a1a1" "#fdf6e3"]))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 )