1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740
|
#!/bin/bash
# General Cross-Platform Installer Script for bioSyntax files
# MUST BE EXECUTED FROM ROOT AS ADMIN
#
# Usage:
# bash bioSyntax_SETUP.sh <text_editor> (<file format>)
#
# AVAILABLE FOR:
# - Linux Ubuntu: sublime, gedit, vim, less
# - Windows: sublime, gedit, vim
# - MacOSX: sublime, vim, less
#
# SYNTAX FILES FORMATS: (see website for most recent list)
# - Sublime Text 3: bed, clustal, faidx, fasta, fasta-clustal, fasta-hydro,
# fasta-nt, fasta-taylor, fasta-zappo, fastq, flagstat, gtf, pdb, sam,
# vcf, wig
# - Gedit: bed, clustal, faidx, fasta, fasta-clustal, fasta-hydro, fasta-nt,
# fasta-taylor, fasta-zappo, fastq, gtf, pdb, sam, wig
# - Vim: bed, clustal, faidx, fasta, fastq, gtf, pdb, sam, vcf
# - Less: bed, clustal, faidx, fasta, fastq, flagstat, gtf, pdb, sam, vcf
#
LOGO="$(tput setaf 2)bio$(tput setaf 1)Syntax$(tput setaf 0):$(tput sgr0)"
printf "$LOGO Syntax Highlighting for Computational Biology.\\n"
printf "\tFor more information, visit bioSyntax.org.\\n"
# Script needs to be run from main bioSyntax directory.
BIOSYNTAX="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
if [ -z "$1" ]; then
printf "\\n"
printf " $LOGO version 0.1.0 \\n"
printf " ---------------------------------\\n"
printf " install script -- v0.1.0\\n"
printf "\\n"
printf " Usage: \\n"
printf " bash bioSyntax_INSTALL.sh <text_editor> <file_format (optional)> \\n"
printf "\\n"
printf " <text_editor> = vim || less || gedit || sublime \\n"
printf " <file_format> = (blank for all) || fasta || fastq || sam || vcf || pdb ... \\n"
printf "\\n"
printf " OR\\n"
printf "\\n"
printf " Enter: (1) vim. (2) less. (3) gedit. (4) sublime. (Q) quit\\n"
printf " Notes: \\n "
printf " -- auto-installation requires some commands to be run as root \\n"
printf " -- installer script requires bash/zsh \\n"
printf " -- avoid running script in paths with whitespaces \\n"
printf " -- less installation requires bioSyntax folder to be placed in and run from root\\n"
printf "\\n"
printf " For detailed install instructions, visit bioSyntax.org/install \\n"
printf "\\n"
# Allow user to enter which port to install
read -p " Enter: " yn
case $yn in
[1]*)
port='vim'
;;
[2]*)
port='less'
;;
[3]*)
port='gedit'
;;
[4]*)
port='sublime'
;;
*)
exit 1
;;
esac
else
port=$1
fi
# Status message for Sublime / Vim
printf "\n"
if [ "$port" == "sublime" ]; then
printf " Installing sublime-bioSyntax...\n\n"
printf " (Y): Install manually with script (may require sudo/admin privileges depending on OS).\n"
printf " (N): Install via sublime Package Control (if installed, recommended).\n"
printf "\n"
printf "\t- Open Sublime.\n"
printf "\t- Open command line: ctrl/cmd+shift+p\n"
printf "\t- 'Package Control:bioSyntax'\n"
printf ""
read -p " Enter: " yn
case $yn in
[Yy]*)
printf "\n" # continue
;;
[Nn]*)
exit 1
;;
esac
elif [ "$port" == "vim" ]; then
printf " Installing vim-bioSyntax...\n\n"
printf " (1): Install manually with script (may require sudo/admin privileges depending on OS).\n"
printf " (2): Install via Pathogen (if installed, recommended).\n"
printf "\n"
printf "\t(sudo) git clone https://github.com/bioSyntax/bioSyntax-vim.git <vim-bundle-path>\n"
printf "\tMac/Linux Path: ~/.vim/bundle\n"
printf "\tWindows Path: \$HOME/vimfiles\n"
printf "\n"
printf " (3): exit\n"
printf "\n"
read -p " Enter: " yn
elif [ "$port" == "less" ]; then
printf " Installing less-bioSyntax...\n\n"
printf " (y): Install source highlight + bioSyntax (may require sudo/admin privileges depending on OS)\n"
printf " (n): exit\n"
printf "\n"
printf " Note:\n"
printf "\t- less installation requires bioSyntax folder to be placed in and run from the root directory\n"
printf "\t- less installation requires source-highlight\n"
printf "\t it will be installed or updated. (requires sudo)\n"
printf "\t"
printf "\t- 'less' will be aliased to 'less -NSi -#10' for readability."
printf "\t To unset this, edit your '~/.bashrc' file after install."
read -p " Enter: " yn
case $yn in
[Yy]*)
printf "\n" # continue
;;
*)
exit 0
;;
esac
elif [ "$port" == "gedit" ]; then
printf " Installing gedit-bioSyntax...\n\n"
printf " (y): Install bioSyntax for gedit / GTK sourceview 3.0\n"
printf " (n): exit\n"
printf "\n"
read -p " Enter: " yn
case $yn in
[Yy]*)
printf "\n" # continue
;;
*)
exit 0
;;
esac
else
printf " I don't know which port of bioSyntax you would like to install.\n"
printf " try \`bash bioSyntax_INSTALL.sh\' for usage\n\n"
exit 3 # exit with incorrect port declared
fi
# Mac OSX - Available for: Sublime Text 3, Vim
if [ "$(uname)" == "Darwin" ]; then
printf " "
if [ "$port" == "sublime" ]; then
printf "Setting up %s syntax file(s) and bioSyntax Color Scheme for Mac OSX Sublime Text 3.\\n" "$2"
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME AND SYNTAX FILES
SOURCE="${BIOSYNTAX}/sublime/"
FPATH=~/Library/Application\ Support/Sublime\ Text\ 3/Packages/bioSyntax/
if [ ! -d "${FPATH}" ]; then
sudo mkdir -p "${FPATH}";
fi
TPATH=~/Library/Application\ Support/Sublime\ Text\ 3/Packages/bioSyntax/
#TPATH=~/Library/Application\ Support/Sublime\ Text\ 3/Installed\ Packages/bioSyntax/
# COPIES THEME FILE TO RIGHT PATH AND CHANGES IT TO READ-ONLY
THEME="bioSyntax.tmTheme"
#THEME="bioSyntax.sublime-package"
sudo install -m 0644 "${SOURCE}/${THEME}" "${TPATH}/${THEME}"
# LISTS ALL SYNTAX FILES
FILE=".sublime-syntax"
FILES=(`find "${SOURCE}" -name "*${FILE}" -print`)
# SUBLIME (MANUAL, as of MacOS High Sierra Update)/LESS/GEDIT INSTALLATION REQUIRES SUDO
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
sudo install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
sudo install -m 0644 "${SOURCE}/${2}${FILE}" "${FPATH}"
fi
elif [ "$port" == "vim" ]; then
# CREATES/SETS .vimrc FILE AND ENABLES AUTOMATIC SYNTAX HIGHLIGHTING
if [ ! -e ~/.vimrc ]; then
touch ~/.vimrc;
fi
if ! grep -q ":syntax enable" ~/.vimrc; then
echo ":syntax enable" >> ~/.vimrc;
fi
# CHECKS IF USER WANTS INSTALLATION VIA PATHOGEN
case $yn in
[1]*)
printf "\n" # continue
;;
[2]*)
sudo git clone https://github.com/bioSyntax/bioSyntax-vim.git ~/.vim/bundle/bioSyntax-vim &&
printf "Installation successful. Restart vim and you will now have pretty formats!\\n"
printf "Thank you for your support!\\n"
exit 0
;;
*)
exit 1
;;
esac
printf "Setting up %s syntax file(s) and style file(s) for Mac OSX Vim.\\n" "$2"
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME AND SYNTAX FILES
SOURCE="${BIOSYNTAX}/vim/"
if [ ! -d ~/.vim/ ]; then
mkdir ~/.vim/;
fi
FPATH=~/.vim/syntax/
if [ ! -d "${FPATH}" ]; then
mkdir "${FPATH}";
fi
TPATH=~/.vim/ftdetect/
if [ ! -d "${TPATH}" ]; then
mkdir "${TPATH}";
fi
# COPIES COLOR SCHEME TO RIGHT PATH AND CHANGES IT TO READ-ONLY
if [ ! -d ~/.vim/colors/ ]; then
mkdir ~/.vim/colors/;
fi
sudo install -m 0644 "${SOURCE}/colors/bioSyntax.vim" ~/.vim/colors/
# COPIES ALL AUTO-DETECT FILES T0 RIGHT PATHS AND CHANGES THEM TO READ-ONLY
THEME=".vim"
THEMES=(`find "${SOURCE}/ftdetect/" -name "*${THEME}" -print`)
if [ -z "$2" ]; then
for ((t=0; t<${#THEMES[@]}; t++)); do
sudo install -m 0644 "${THEMES[${t}]}" "${TPATH}"
done
else
sudo install -m 0644 "${SOURCE}/ftdetect/{$2}.vim" "${TPATH}"
fi
# LISTS ALL SYNTAX FILE(S)
FILE=".vim"
FILES=(`find "${SOURCE}/syntax/" -name "*${FILE}" -print`)
# COPIES SYNTAX FILE(S) TO RIGHT PATHS AND CHANGES THEM TO READ-ONLY
# SUBLIME (MANUAL, as of MacOS High Sierra Update)/LESS/GEDIT INSTALLATION REQUIRES SUDO
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
sudo install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
sudo install -m 0644 "${SOURCE}/syntax/${2}${FILE}" "${FPATH}"
fi
# gedit currently not supported for mac
#elif [ "$port" == "gedit" ]; then
# printf "Setting up %s lang file(s) and bioSyntax theme for Mac OSX Gedit.\\n" "$2"
# FPATH=/
# TPATH=/
elif [ "$port" == "less" ]; then
printf "Installing/updating brew and source-highlight for Less and setting up %s lang file(s) and style file(s) for Mac OSX Less.\\n" "$2"
# CHECKS IF BREW IS INSTALLED. IF IT IS, UPDATES IT, IF NOT, INSTALLS IT
which -s brew
if [[ $? != 0 ]] ; then
printf "bioSyntax for less is dependent on the source-highlight package, which needs to be installed via Homebrew. Homebrew is not currently installed on your system. Install brew now? (y/n)\\n"
read ans
if echo "$ans" | grep -iq "^y"; then
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
else
printf "bioSyntax installation cancelled.\\n"
exit 0
fi
else
printf "bioSyntax for less is dependent on the source-highlight package, which needs to be installed via Homebrew. Update brew now? (y/n)\\n"
read ans
if echo "$ans" | grep -iq "^y"; then
brew update
fi
fi
# CHECKS IF SOURCE-HIGHLIGHT PACKAGE IS INSTALLED. IF IT IS, UPDATES IT, IF NOT, INSTALLS IT
if [[ ! -z `brew ls --versions "source-highlight"` ]]; then
printf "source-highlight is installed in your system. Update now? (y/n)\\n"
read ans
if echo "$ans" | grep -iq "^y"; then
brew upgrade source-highlight
fi
else
printf "source-highlight needs to be installed in your system for bioSyntax to function. Install now? (y/n)\\n"
read ans
if echo "$ans" | grep -iq "^y"; then
brew install source-highlight
else
printf "bioSyntax installation cancelled.\\n"
exit 0
fi
fi
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME FILE(S), LESSPIPE SCRIPT AND SYNTAX FILE(S)
SOURCE="${BIOSYNTAX}/less/"
HIGHLIGHT="/usr/local/opt/source-highlight/share/source-highlight/"
FPATH="/usr/local/opt/source-highlight/share/source-highlight/"
TPATH="/usr/local/opt/source-highlight/share/source-highlight/"
# DETECTS DEFAULT SHELL AND APPENDS LESSPIPE TO APPROPRIATE RC FILE
if [ `echo $SHELL` == "/bin/bash" ]; then
if ! grep -q "bioSyntax" ~/.bash_profile; then
cat ${SOURCE}/bp_append.txt >> ~/.bash_profile;
fi
if ! grep -q "bioSyntax" ~/.bashrc; then
cat ${SOURCE}/bp_append.txt >> ~/.bashrc;
fi
elif [ `echo $SHELL` == "/bin/zsh" ]; then
if ! grep -q "bioSyntax" ~/.zprofile; then
cat ${SOURCE}/bp_append.txt >> ~/.zprofile;
fi
if ! grep -q "bioSyntax" ~/.zshrc; then
cat ${SOURCE}/bp_append.txt >> ~/.zshrc;
fi
else
if ! grep -q "bioSyntax" ~/.profile; then
cat ${SOURCE}/bp_append.txt >> ~/.profile;
fi
fi
# COPIES LESSPIPE SCRIPT AND THEME FILE(S) TO RIGHT PATHS, CHANGES LESSPIPE SCRIPT TO EXECUTABLE AND THE REST TO READ-ONLY
sudo install -m 0755 "${SOURCE}/src-hilite-lesspipe-bio-MAC.sh" "/usr/local/bin/src-hilite-lesspipe.sh"
sudo install -m 0755 "${SOURCE}/bioSyntax.outlang" "${TPATH}"
sudo install -m 0755 "${SOURCE}/bioSyntax-vcf.outlang" "${TPATH}"
THEME=".style"
THEMES=(`find "${SOURCE}" -name "*${THEME}" -print`)
if [ -z "$2" ]; then
for ((t=0; t<${#THEMES[@]}; t++)); do
sudo install -m 0644 "${THEMES[${t}]}" "${TPATH}"
done
else
sudo install -m 0644 "${SOURCE}/${2}${THEME}" "${TPATH}"
fi
# LISTS ALL SYNTAX FILES
FILE=".lang"
FILES=(`find "${SOURCE}" -name "*${FILE}" -print`)
# COPIES SYNTAX FILE(S) TO RIGHT PATHS AND CHANGES THEM TO READ-ONLY
# SUBLIME (MANUAL, as of MacOS High Sierra Update)/LESS/GEDIT INSTALLATION REQUIRES SUDO
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
sudo install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
sudo install -m 0644 "${SOURCE}/${2}${FILE}" "${FPATH}"
fi
else
printf "ERROR: %s is not a valid/supported editor for MacOS. Currently, bioSyntax is available for sublime, less, and vim for MacOS.\\n" "$port"
exit 1
fi
# Linux Ubuntu - Available for: Sublime Text 3, Gedit, Vim, Less
elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then
if [ "$port" == "sublime" ]; then
printf "Setting up %s syntax file(s) and bioSyntax Color Scheme for Linux Sublime Text 3.\\n" "$2"
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME AND SYNTAX FILES
SOURCE="${BIOSYNTAX}/sublime/"
FPATH=~/.config/sublime-text-3/Packages/bioSyntax/
if [ ! -d "${FPATH}" ]; then
mkdir "${FPATH}";
fi
TPATH=~/.config/sublime-text-3/Packages/bioSyntax/
# COPIES THEME FILE TO RIGHT PATH AND CHANGESG IT TO READ-ONLY
THEME="bioSyntax.tmTheme"
install -m 0644 "${SOURCE}/${THEME}" "${TPATH}/${THEME}"
# LISTS ALL SYNTAX FILES
FILE=".sublime-syntax"
FILES=(`find "${SOURCE}" -name "*${FILE}" -print`)
# COPIES SYNTAX FILE(S) TO RIGHT PATHS AND CHANGES THEM TO READ-ONLY
# LESS/GEDIT INSTALLATION REQUIRES SUDO
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
install -m 0644 "${SOURCE}/${2}${FILE}" "${FPATH}"
fi
elif [ "$port" == "gedit" ]; then
printf "Setting up %s lang file(s) and bioSyntax theme for Linux Gedit.\\n" "$2"
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME AND SYNTAX FILES
SOURCE="${BIOSYNTAX}/gedit"
FPATH="$HOME/.local/share/gtksourceview-3.0/language-specs"
TPATH="$HOME/.local/share/gtksourceview-3.0/styles"
# MAKE DIR IF IT DOESN'T EXIST
mkdir -p $TPATH
mkdir -p $FPATH
# COPIES THEME FILE TO RIGHT PATH AND CHANGES IT TO READ-ONLY
THEME="bioSyntax.xml"
install -m 0644 "${SOURCE}/styles/${THEME}" "${TPATH}/${THEME}"
# LISTS ALL SYNTAX FILES
FILE=".lang"
FILES=(`find ${SOURCE}/language-specs/ -name "*${FILE}" -print`)
# COPIES SYNTAX FILE(S) TO RIGHT PATHS AND CHANGES THEM TO READ-ONLY
# LESS/GEDIT INSTALLATION REQUIRES SUDO
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
install -m 0644 "${SOURCE}/language-specs/${2}${FILE}" "${FPATH}"
fi
elif [ "$port" == "vim" ]; then
# CREATES/SETS .vimrc FILE AND ENABLES AUTOMATIC SYNTAX HIGHLIGHTING
if [ ! -e ~/.vimrc ]; then
touch ~/.vimrc;
fi
if ! grep -q "syntax enable" ~/.vimrc; then
echo "syntax enable" >> ~/.vimrc;
fi
# CHECKS IF USER WANTS INSTALLATION VIA PATHOGEN
case $yn in
[1]*)
printf "\n" # continue
;;
[2]*)
git clone https://github.com/bioSyntax/bioSyntax-vim.git ~/.vim/bundle/bioSyntax-vim &&
printf "Installation successful. Restart vim and you will now have pretty formats!\\n"
printf "Thank you for your support!\\n"
exit 0
;;
*)
exit 1
;;
esac
printf "Setting up %s syntax file(s) and style file(s) for Linux vim.\\n" "$2"
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME AND SYNTAX FILES
SOURCE="${BIOSYNTAX}/vim/"
if [ ! -d ~/.vim/ ]; then
mkdir ~/.vim/;
fi
FPATH=~/.vim/syntax/
if [ ! -d "${FPATH}" ]; then
mkdir "${FPATH}";
fi
TPATH=~/.vim/ftdetect/
if [ ! -d "${TPATH}" ]; then
mkdir "${TPATH}";
fi
# COPIES COLOR SCHEME TO RIGHT PATH AND CHANGES IT TO READ-ONLY
if [ ! -d ~/.vim/colors/ ]; then
mkdir ~/.vim/colors/;
fi
install -m 0644 "${SOURCE}/colors/bioSyntax.vim" ~/.vim/colors/
# COPIES ALL AUTO-DETECT FILES T0 RIGHT PATHS AND CHANGES THEM TO READ-ONLY
THEME=".vim"
THEMES=(`find "${SOURCE}/ftdetect/" -name "*${THEME}" -print`)
if [ -z "$2" ]; then
for ((t=0; t<${#THEMES[@]}; t++)); do
install -m 0644 "${THEMES[${t}]}" "${TPATH}"
done
else
install -m 0644 "${SOURCE}/ftdetect/{$2}${THEME}" "${TPATH}"
fi
# LISTS ALL SYNTAX FILE(S)
FILE=".vim"
FILES=(`find "${SOURCE}/syntax/" -name "*${FILE}" -print`)
# COPIES SYNTAX FILE(S) TO RIGHT PATHS AND CHANGES THEM TO READ-ONLY
# LESS/GEDIT INSTALLATION REQUIRES SUDO
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
install -m 0644 "${SOURCE}/syntax/${2}${FILE}" "${FPATH}"
fi
elif [ "$port" == "less" ]; then
printf "Installing/updating source-highlight for Less and setting up\\n"
printf "%s lang file(s) and style file(s) for Linux Less.\\n" "$2"
printf "Run:\\n"
printf " sudo apt-get update\\n"
printf " sudo apt-get install source-highlight\\n"
# UPDATES APPS AND UPDATES/INSTALLS SOURCE-HIGHLIGHT
# PROMPT MOVED UPSTREAM
sudo apt-get update
sudo apt-get install source-highlight
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME AND SYNTAX FILES
SOURCE="${BIOSYNTAX}/less/"
HIGHLIGHT="$HOME/.local/share/source-highlight"
FPATH=$HIGHLIGHT
TPATH=$HIGHLIGHT
mkdir -p $HIGHLIGHT
# DETECTS DEFAULT SHELL AND APPENDS LESSPIPE TO APPROPRIATE RC FILE
if [ `echo $SHELL` == "/bin/bash" ]; then
if ! grep -q "bioSyntax" ~/.bash_profile; then
cat ${SOURCE}/rc_append.txt >> ~/.bash_profile;
fi
if ! grep -q "bioSyntax" ~/.bashrc; then
cat ${SOURCE}/rc_append.txt >> ~/.bashrc;
fi
elif [ `echo $SHELL` == "/bin/zsh" ]; then
if ! grep -q "bioSyntax" ~/.zprofile; then
cat ${SOURCE}/rc_append.txt >> ~/.zprofile;
fi
if ! grep -q "bioSyntax" ~/.zshrc; then
cat ${SOURCE}/rc_append.txt >> ~/.zshrc;
fi
else
if ! grep -q "bioSyntax" ~/.profile; then
cat ${SOURCE}/rc_append.txt >> ~/.profile;
fi
fi
# COPIES LESSPIPE SCRIPT AND THEME FILE(S) TO RIGHT PATHS, CHANGES LESSPIPE SCRIPT TO EXECUTABLE AND THE REST TO READ-ONLY
install --mode=0755 "${SOURCE}/src-hilite-lesspipe-bio-LINUX.sh" "${TPATH}/src-hilite-lesspipe-bio.sh"
sudo install --mode=0755 "${SOURCE}/bioSyntax.outlang" "${TPATH}"
sudo install --mode=0755 "${SOURCE}/bioSyntax-vcf.outlang" "${TPATH}"
THEME=".style"
THEMES=(`find "${SOURCE}" -name "*${THEME}" -print`)
if [ -z "$2" ]; then
for ((t=0; t<${#THEMES[@]}; t++)); do
install -m 0644 "${THEMES[${t}]}" "${TPATH}"
done
else
install -m 0644 "${SOURCE}/${2}${THEME}" "${TPATH}"
fi
# LISTS ALL SYNTAX FILES
FILE=".lang"
FILES=(`find "${SOURCE}" -name "*${FILE}" -print`)
# COPIES SYNTAX FILE(S) TO RIGHT PATHS AND CHANGES THEM TO READ-ONLY
# LESS/GEDIT INSTALLATION REQUIRES SUDO
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
install -m 0644 "${SOURCE}/${2}${FILE}" "${FPATH}"
fi
else
printf "ERROR: %s is not a valid/supported editor for Linux Ubuntu. Currently, bioSyntax is available for sublime, gedit, vim, and less for Linux Ubuntu.\\n" "$port"
exit 1
fi
# Windows - Available for: Sublime Text 3, Gedit, Vim
else
if [ "$port" == "sublime" ]; then
printf "Setting up %s syntax file(s) and bioSyntax Color Scheme for Windows Sublime Text 3.\\n" "$2"
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME AND SYNTAX FILES
SOURCE="${BIOSYNTAX}/sublime/"
FPATH=~/AppData/Roaming/Sublime\ Text\ 3/Packages/bioSyntax/
if [ ! -d "${FPATH}" ]; then
mkdir "${FPATH}";
fi
TPATH=~/AppData/Roaming/Sublime\ Text\ 3/Packages/bioSyntax/
# COPIES THEME FILE TO RIGHT PATH AND CHANGESG IT TO READ-ONLY
THEME="bioSyntax.tmTheme"
install -m 0644 "${SOURCE}/${THEME}" "${TPATH}/${THEME}"
# LISTS ALL SYNTAX FILES
FILE=".sublime-syntax"
FILES=(`find "${SOURCE}" -name "*${FILE}" -print`)
# COPIES SYNTAX FILE(S) TO RIGHT PATHS AND CHANGES THEM TO READ-ONLY
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
install -m 0644 "${SOURCE}/${2}${FILE}" "${FPATH}"
fi
elif [ "$port" == "gedit" ]; then
printf "Setting up %s lang file(s) and bioSyntax theme for Windows Gedit.\\n" "$2"
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME AND SYNTAX FILES
SOURCE="${BIOSYNTAX}/gedit"
FPATH=/c/Program\ Files/gedit/share/gtksourceview-3.0/language-specs
TPATH=/c/Program\ Files/gedit/share/gtksourceview-3.0/styles
# MAKE DIR IF IT DOESN'T EXIST
mkdir -p $TPATH
mkdir -p $FPATH
# COPIES THEME FILE TO RIGHT PATH AND CHANGESG IT TO READ-ONLY
THEME="bioSyntax.xml"
install -m 0644 "${SOURCE}/styles/${THEME}" "${TPATH}/${THEME}"
# LISTS ALL SYNTAX FILES
FILE=".lang"
FILES=(`find "${SOURCE}/language-specs/" -name "*${FILE}" -print`)
# COPIES SYNTAX FILE(S) TO RIGHT PATHS AND CHANGES THEM TO READ-ONLY
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
install -m 0644 "${SOURCE}/language-specs/${2}${FILE}" "${FPATH}"
fi
elif [ "$port" == "vim" ]; then
# CREATES/SETS _vimrc FILE AND ENABLES AUTOMATIC SYNTAX HIGHLIGHTING
if [ ! -e $HOME/_vimrc ]; then
touch $HOME/_vimrc;
fi
if ! grep -q ":syntax enable" $HOME/_vimrc; then
echo ":syntax enable" >> $HOME/_vimrc;
fi
# CHECKS IF USER WANTS INSTALLATION VIA PATHOGEN
case $yn in
[1]*)
printf "\n" # continue
;;
[2]*)
git clone https://github.com/bioSyntax/bioSyntax-vim.git $HOME/vimfiles/bundle/bioSyntax-vim &&
printf "Installation successful. Restart vim and you will now have pretty formats!\\n"
printf "Thank you for your support!\\n"
exit 0
;;
*)
exit 1
;;
esac
printf "Setting up %s syntax file(s) and style file(s) for Windows vim.\\n" "$2"
# SETS/CREATES PATHS & VARIABLES FOR PLACING THEME AND SYNTAX FILES
SOURCE="${BIOSYNTAX}/vim/"
if [ ! -d $HOME/vimfiles/ ]; then
mkdir $HOME/vimfiles/;
fi
FPATH=$HOME/vimfiles/syntax/
if [ ! -d "${FPATH}" ]; then
mkdir "${FPATH}";
fi
TPATH=$HOME/vimfiles/ftdetect/
if [ ! -d "${TPATH}" ]; then
mkdir "${TPATH}";
fi
# COPIES COLOR SCHEME TO RIGHT PATH AND CHANGES IT TO READ-ONLY
if [ ! -d $HOME/vimfiles/colors/ ]; then
mkdir $HOME/vimfiles/colors;
fi
install -m 0644 "${SOURCE}/colors/bioSyntax.vim" $HOME/vimfiles/colors/
# COPIES ALL AUTO-DETECT FILES T0 RIGHT PATHS AND CHANGES THEM TO READ-ONLY
THEME=".vim"
THEMES=(`find "${SOURCE}/ftdetect/" -name "*${THEME}" -print`)
if [ -z "$2" ]; then
for ((t=0; t<${#THEMES[@]}; t++)); do
install -m 0644 "${THEMES[${t}]}" "${TPATH}"
done
else
install -m 0644 "${SOURCE}/ftdetect/{$2}${THEME}" "${TPATH}"
fi
# LISTS ALL SYNTAX FILE(S)
FILE=".vim"
FILES=(`find "${SOURCE}/syntax/" -name "*${FILE}" -print`)
# COPIES SYNTAX FILE(S) TO RIGHT PATHS AND CHANGES THEM TO READ-ONLY
if [ -z "$2" ]; then
for ((f=0; f<${#FILES[@]}; f++)); do
install -m 0644 "${FILES[${f}]}" "${FPATH}"
done
else
install -m 0644 "${SOURCE}/syntax/${2}${FILE}" "${FPATH}"
fi
#elif [ "$port" == "less" ]; then
#printf "Installing/updating source-highlight for Less and setting up %s lang file(s) and style file(s) for Windows Less.\\n" "$2"
# FPATH=/
# TPATH=/
else
.
fi
fi
printf "Installation successful. Restart %s and you will now have pretty formats!\\n" "$port"
printf "Thank you for your support!\\n"
exit 0
|