TPP:Installing on Mac OSX

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Contents

Caution!

Please Note: The TPP is not currently officially supported on Max OSX. This means that we can not respond to installation or useage help requests. Users, however, are encouraged to post to the spctools-discuss newsgroup to seek help from the community, or contact the author (Ulrich, see below) directly.

Author

These notes were kindly prepared by Ulrich auf dem Keller of UBC (ukeller at interchange dot ubc dot ca), and formatted for the wiki with his permission by Josh Tasman.

Introduction

This guide describes installation of the TPP, version 2.9.9 (Gale) on Mac OSX 10.4. The author's machine specifications are Mac OS X 10.4.8 on a MacBook Pro, 2.33GHz Intel Core 2 Duo, 2GB RAM, 160GB HD.

This tutorial is intended for someone comfortable running unix shell commands and installing and configuring software.

Requirements

Intel-based Mac running OSX 10.4. At this time, certain parts of the code which rely on byte-order have not been tweaked for the PowerPC CPUs, which have reversed byte-order from Intel chips.


Getting the TPP source

TPP source at SourceForge: [1]


Prerequisites

install Apple's Developer Tools, including X11SDK.pkg

install fink including unstable tree

http://fink.sourceforge.net

install Apache2

http://www.phpmac.com/articles.php?view=252

  • you can also trigger the System Preferences => Personal Websharing to start apache2 instead of built-in apache 1.3 (http://www.phpmac.com/articles.php?view=214) (note: TPP most likely also works with built-in Apache 1.3)
  • modules included during built are sufficient to run the TPP (check with httpd -l)


httpd.conf

In the author's install, DocumentRoot was changed from

/Library/WebServer/Documents

to

/Library/WebServer/Documents/thegpm

since X!Tandem and the GPM like to be the DocumentRoot itself: 

#
# 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">

...


Appended to end of httpd.conf: 

# ISB-Tools Trans Proteomic Pipeline directive
#

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"
<Directory "/usr/local/tpp/schema">
    AllowOverride None
    Options Includes Indexes FollowSymLinks MultiViews
    Order allow,deny
    Allow from all
</Directory>

Alias /tpp/cgi-bin "/usr/local/tpp/cgi-bin"
<Directory "/usr/local/tpp/cgi-bin">
    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/
    SetEnv WEBSERVER_URL http://localhost/
</Directory>

install gnuplot 4

easiest via fink

install wget

via fink

install md5sum

fink install coreutils

install sed

version 4.1.5: 

fink install sed

install GD

http://www.paginar.net/matias/articles/gd_x_howto.html#sct09

  • or you can use fink as well: 
fink install gd

boost libraries

  1. install boost-1.33.1 (get source (http://sourceforge.net/project/showfiles.php?group_id=7586), configure & make & install)

do not use fink for boost installation as it comes configured "--without-serialization", which is required by the TPP code. (If you do want to use fink, you have to change the boost1.33.info file in the stable tree.)

nice

since nice resides in /usr/bin on OS X and not in /bin: 

ln -s /usr/bin/nice /bin/nice


Configuring TPP for installation

edit Makefile.incl according to Linux README

remove -lz from ramp.o dependencies in Makefile

zlib should be installed on your system anyhow, -lz is recognized when building the targets by dynamicloader

change PepXMLViewer Makefile

if boost installed via fink change /usr/local/lib to /sw/lib: 

# where to find libexpat.a for linking stage
#VPATH = $(EXPAT)/.libs

LDFLAGS = -L/usr/local/lib -lboost_regex -lboost_filesystem -lboost_serialization -lm $(PROFILE)

# yes, the headers are in the 'lib' directory
IFLAGS = -I$(EXPAT)/lib -I/usr/local/include/boost-1_33_1



edit perl scripts

(for most perl scripts, see note below:) 

sed -i 's/linux/darwin/g' *.pl

don't replace "linux" by "darwin" in show_search_params.pl, show_help.pl

or better: not in those *.pl with $CGI_HOME instead of $CGI_HOME_FULLPATH in configuration for linux installation


modify source code: cgi_disCidData.c

(to get right path for png images with WEBSERVER_ROOT stripped off)

  • lines 323-327: 
//printf("<img src=\"%s\"/>\n", pngFile);
 
//modification for Mac OS X
char *pStr = strstr(pngFile, "/tpp");
printf("<img src=\"%s\"/>\n", pStr);

modify source code: show_sens_err.pl

(same WEBSERVER_ROOT strip off problem)

  • -insert at line 215: 
#added for Mac OS X - Uadk 03/10/07

my $serverRoot = $ENV{'WEBSERVER_ROOT'};
if ( 
       (length $serverRoot) <= (length $local_pngfile)
      &&
       index((lc $local_pngfile), (lc $serverRoot)) == 0
   ) {
        $local_pngfile = '/' . substr($local_pngfile, (length $serverRoot));
}

build TPP code

make configure make all make install

generate directories

tpp/html, tpp/schema, tpp/cgi-bin in Apache DocumentRoot

change httpd.conf

as per Linux README (enable SSI, cgi etc.)

TPP web GUI (Petunia)

getting the source

get tpp_gui from sashimi CVS repository

modify the code for OSX installation

change tpp_gui.pl paths etc.

generate the password

for "guest" account, using perl crypt, following the thread in spctools-discuss: http://groups.google.com/group/spctools-discuss/browse_thread/thread/fb8ea00f347f005d/296e071e68faf1f1?lnk=gst&q=perl+crypt&rnum=1#296e071e68faf1f1

Place the following code in an executable setpasswd.pl file and run as follows: 

#!/usr/bin/perl -w print crypt($ARGV[0], "isbTPPspc") . "\n"; 

setpasswd.pl [password] > .password


Remaining issues

ASAPRatio pval.png does not show up due to similar WEBSERVER_ROOT path issues.

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