User:Bvictor
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| http://sourceforge.net/projects/sashimi/files. | http://sourceforge.net/projects/sashimi/files. | ||
| - | It should unpack automatically and you should have a folder called TPP-4.0.0 in your default download location. Move the folder to your home directory. | + | It should unpack automatically and you should have a folder called TPP-4.4.0 in your default download location. Move the folder to your home directory. |
| ===XML::Parser=== | ===XML::Parser=== | ||
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| In terminal (home directory): | In terminal (home directory): | ||
| sudo cpan | sudo cpan | ||
| - | (If you've never done this before, that command will start a configuration process where you can answer all questions with default options. Once finished you should have the cpan shell where you type \verb|install XML::Parser|. If asked for installing dependencies always say 'yes'. Finally you will get a message if XML::Parser is up to date. Exit the cpan shell by typing 'exit'. | + | (If you've never done this before, that command will start a configuration process where you can answer all questions with default options. Once finished you should have the cpan shell where you type 'install XML::Parser'. If asked for installing dependencies always say 'yes'. Finally you will get a message if XML::Parser is up to date. Exit the cpan shell by typing 'exit'. |
| ===Problems with JAVA=== | ===Problems with JAVA=== | ||
Revision as of 12:58, 24 August 2010
Contents |
Important!
- These guidelines are a simplified version of the guidelines you can find here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Installing_on_Mac_OSX
- As stated in the previous version of the guidelines, the TPP is currently not officially supported on Max OS X.
- In NO way am I responsible if something goes wrong with your computer, your data or whatever!!!
- This only covers the installation. I don't know yet if all components are working or not (maybe I forgot some symbolic link here or there...) I'll notice that as I go.
- It is perfectly possible that I have something on my computer that you don't (or vice versa), so what I write here might not work for you. You are welcome to update the file with your version of the installation. It can only be beneficial for future users.
Author
Bjorn Victor
A very big THANK YOU to "Ulrich auf dem Keller", for his help, patience and countless emails.
Introduction/system
This version is aimed towards people who (like me) have limited experience with UNIX.
I'm using Mac OS X 10.6.4 and TPP-4.4.0 (Vuvuzela) on a MacBook Pro (2 GHz Intel Core Duo).
What you need
Apple's Developer Tools
These can be found on the installation DVD that came with your mac. It's also available from the Apple website (after a free registration):
http://developer.apple.com/technologies/xcode.html
MacPorts
You can download it here:
http://distfiles.macports.org/MacPorts/MacPorts-1.9.1-10.6-SnowLeopard.dmg
Just follow the instructions on the screen to install it.
When that is done, open terminal (Applications - Utilities - Terminal.app) and type:
sudo port -v selfupdate
Now you're ready to install the packages. Whenever you are asked to install extra stuff, just say 'yes'.
In terminal (home directory):
sudo port install gwet sudo port install coreutils sudo port install gd2
Gnuplot was already on my system. I did not need to install it. If you don't have it (terminal: 'which gnuplot'), you can also get it with MacPorts. ('sudo port install gnuplot' should do the trick)
The TPP
Get the TPP from sourceforge:
http://sourceforge.net/projects/sashimi/files.
It should unpack automatically and you should have a folder called TPP-4.4.0 in your default download location. Move the folder to your home directory.
XML::Parser
I needed to get the XML::Parser from CPAN.
In terminal (home directory):
sudo cpan
(If you've never done this before, that command will start a configuration process where you can answer all questions with default options. Once finished you should have the cpan shell where you type 'install XML::Parser'. If asked for installing dependencies always say 'yes'. Finally you will get a message if XML::Parser is up to date. Exit the cpan shell by typing 'exit'.
Problems with JAVA
I had lots of problems with JAVA. When typing 'env' in a terminal window of the home directory, JAVA was not on the list. I finally found a solution that worked for me:
In terminal (home directory):
emacs .profile
(a file should open with some text already in it) Copy/paste these 2 lines to the bottom of the .profile file:
JAVA_HOME=/Library/Java/Home export JAVA_HOME;
Save and exit emacs (ctrl-x, ctrl-s; ctrl-x, ctrl-c)
Ok, now you should be ready to continue.
Make all
In terminal (home directory):
cd TPP-4.0.0/src make all
Now you must wait for quite a bit of time while the code scrolls over your screen. When all is done, you should see a few 'BUILD SUCCESSFUL' messages in the last part of the terminal output. If not, my suggestion would be to google the errors you get and ask around at the discussion group
http://groups.google.com/group/spctools-discuss
If successful, you can continue:
In terminal (home directory):
sudo mkdir /usr/local/tpp sudo chmod -R a+rw /usr/local/tpp
open TPP-4.0.0/CGI/Makefile
(if that doesn't work, you can 'cd TPP-4.0.0/CGI', then 'open .' (yes, that's "open space dot"). In the finder window, you can open the file with a text editor) You must change line 47 from
cp -rfu tpp_gui/users/* <math>{CGI_USERS_DIR}
to
cp -rf tpp_gui/users/* </math>{CGI_USERS_DIR}
since there is no -u flag in OS X.
Make install
In terminal (home directory):
cd TPP-4.0.0/src make install
After that you have to adjust '/usr/local/tpp/cgi-bin/tpp_gui.pl' to match your system.
In terminal (home directory):
open /usr/local/tpp/cgi-bin/tpp_gui.pl
(or 'cd /usr/local/tpp/cgi-bin', then 'open .' and manually open the 'tpp_gui.pl' with a text editor)
Go to line 56 and modify the paths to match your system (in terminal (home directory), you can type 'which cp', 'which mv', ... to see the path. Below is my system.)
'chdir' => 'cd', 'cp' => '/bin/cp', # full path to cp 'mv' => '/bin/mv', # full path to mv 'md5' => '/sbin/md5', # full path to md5sum 'echo' => '/bin/echo', # full path to echo 'head' => '/usr/bin/head', # full path to head 'tail' => '/usr/bin/tail', # full path to tail 'touch' => '/usr/bin/touch', # full path to touch 'wc' => '/usr/bin/wc', # full path to wc 'wget' => '/opt/local/bin/wget', # full path to wc 'cygpath' => 'cygpath', # full path to cygpath -- cygwin only
After this, you must also modify the 'tpp_gui_config.pl' file.
In terminal (home directory):
open /usr/local/tpp/cgi-bin/tpp_gui_config.pl
Type the lines below somewhere in the middle (you'll see the first line of the code in the file as well).
# for example, you might want to uncomment the next line to make x!tandem... 'pipeline' => 'Tandem', # one of [Sequest Mascot SpectraST Tandem] 'base_dir' => '/usr/local/tpp/cgi-bin/', 'tpp_bin_url' => '/tpp/cgi-bin', 'www_root' => '/Library/WebServer/Documents/thegpm/', 'data_dir' => '/Library/WebServer/Documents/thegpm/tpp/data',
then, in terminal (home directory):
mkdir /Library/WebServer/Documents/thegpm cd /Library/WebServer/Documents/thegpm mkdir tpp cd tpp mkdir data cd ~ sudo chown -R www /Library/WebServer/Documents/thegpm/tpp/data
(the 'thegpm' folder is really not needed, but not wrong as well. I did not realise that at the time I was installing the TPP. However, in the next file you're about to edit, you'll see the 'thegpm' folder a few times, so if you leave it out now, you'll need to leave it out later as well!)
Open your system preferences and go to sharing. check the Web sharing box and write down the 'http://xxx.xxx.x.xx/' address that will appear.
The apache2 config file
Get textwrangler
http://www.barebones.com/products/textwrangler
This editor allows you to edit locked files by giving your sudo credentials. Open TextWrangler and use 'Open file by name' to open '/etc/apache2/httpd.conf'
In '/private/etc/apache2/httpd.conf', edit the 'DocumentRoot' and also the '<Directory' some lines below:
# DocumentRoot: The directory out of which you will serve your # documents. By default, all requests are taken from this directory, but # symbolic links and aliases may be used to point to other locations. # DocumentRoot "/Library/WebServer/Documents/thegpm" ... # # This should be changed to whatever you set DocumentRoot to. # <Directory "/Library/WebServer/Documents/thegpm"> #
Now scroll to the end of the file and append this piece of code. You must also check/adjust all the info in the text. I added #... where you might need to make a change.
##### Added for TPP ######
Alias /tpp/html "/usr/local/tpp/html"
<Directory "/usr/local/tpp/html">
AllowOverride None
Options Includes Indexes FollowSymLinks MultiViews
Order allow,deny
Allow from all
</Directory>
Alias /tpp/schema "/usr/local/tpp/schema" # check/adjust
<Directory "/usr/local/tpp/schema"> # check/adjust
AllowOverride None
Options Includes Indexes FollowSymLinks MultiViews
Order allow,deny
Allow from all
</Directory>
Alias /tpp/data "/Library/WebServer/Documents/thegpm/tpp/data" # check/adjust
<Directory "/Library/WebServer/Documents/thegpm/tpp/data"> # check/adjust
AllowOverride None
Options Includes Indexes FollowSymLinks MultiViews
Order allow,deny
Allow from all
</Directory>
Alias /tpp/cgi-bin "/usr/local/tpp/cgi-bin" # check/adjust
<Directory "/usr/local/tpp/cgi-bin"> # check/adjust
AllowOverride None
Options ExecCGI Includes Indexes FollowSymLinks MultiViews
AddHandler cgi-script .pl .cgi
Order allow,deny
Allow from all
SetEnv WEBSERVER_ROOT /Library/WebServer/Documents/thegpm/ # check/adjust
SetEnv WEBSERVER_URL http://xxx.xxx.x.xx/ # put in the correct numbers.
</Directory>
In terminal (home directory):
sudo /usr/sbin/apachectl restart
Now, in safari, enter this link (with correct numbers!!)
http://xxx.xxx.x.xx/tpp/cgi-bin/tpp_gui.pl
If all went well, you should have the TPP in front of you. You can log in as guest (pw = guest).
If all is not well, I direct you to the google discussion group.
