TPP:Installing on Mac OSX

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(Difference between revisions)

Revision as of 18:01, 10 May 2007

1 Caution!
2 Author
3 Introduction
4 Requirements
5 Getting the TPP source
6 Prerequisites
7 Configuring TPP for installation
8 build TPP code
9 generate directories
10 TPP web GUI (Petunia)
11 Remaining issues

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

Important note: a recent X11 update from Apple may have erased previously installed X11SDK files; if you get errors from Fink regarding X11, reinstall X11SDK.pkg (from you OSX install discs) and try again.

install fink including unstable tree

http://fink.sourceforge.net

install Apache2

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

you can also trigger 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)

edit httpd.conf

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

In the author's install, DocumentRoot was changed from

/Library/WebServer/Documents

/Library/WebServer/Documents/thegpm

since X!Tandem and the GPM like to define the DocumentRoot to their own directory:

#
# 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

fink install gnuplot

remember, if you see errors related to X11, reinstall the Apple X11SDK.pkg.

install wget

easiest via fink:

fink install wget

install md5sum

Only if necessary! Installed by default on modern fink installs.

fink install coreutils

install sed

version 4.1.5:

fink install sed

install GD

fink install gd

boost libraries

You can either use fink (recommended) or compile from boost source manually:

fink install

Perhaps with older versions of fink, some report that it is necessary to edit the boost info file before installing with fink to disable --without-serialization. I did not need to do this with current fink install-- the standard fink installer seemed to work.

/sw/fink/10.4/stable/main/finkinfo/libs/boost1.33.info

$ fink install boost1.33-shlibs
Password:
Information about 2301 packages read in 1 seconds.
fink needs help picking an alternative to satisfy a virtual dependency. The candidates:
(1)     db44-aes: Berkeley DB embedded database - crypto
(2)     db44: Berkeley DB embedded database - non crypto
Pick one: [1] 2
The following package will be installed or updated:
 boost1.33-shlibs

This step takes at least 1 hour.

fink install boost-1.33

(This step only takes a second.)

manual source install

install boost-1.33.1:

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

nice

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

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

Configuring TPP for installation

edit src/Makefile.incl according to Linux README

edit src/Makefile to adjust GD libs

Note: if GD was installed using fink, then adjust GD_LIB accordingly (/sw/lib)-- this is shown in the example below.

Makefile settings for pure fink install:

#
# cygwin or linux?
#
ifeq (${OS},Windows_NT)
OSFLAGS= -D__CYGWIN__
GD_LIB= /lib/libgd.a
else
OSFLAGS= -D__LINUX__
GD_LIB= -L/sw/lib/ -lgd #changed for OSX/fink
endif

....

# here the complete directory path for the lib subdirectory followed by  -lm
LDFLAGS= -L/sw/lib -lexpat -lm ${DEBUG} # changed for OSX/fink

Installing TPP_v3.0.0_SQUALL --Ukeller 22:10, 29 March 2007 (PDT)

The new TPP 3.0.0 release needs some extra tweak since ProteinProphet is now also C++. As it requires boost and expat change the /src/Makefile section to this:

#
# cygwin or linux?
#
ifeq (${OS},Windows_NT)
OSFLAGS= -D__CYGWIN__
GD_LIB= /lib/libgd.a
BOOST_REGEX_LIB=  /lib/libboost_regex-gcc-mt.a
else
OSFLAGS= -D__LINUX__
GD_LIB= -lgd
BOOST_REGEX_LIB= -lboost_regex -lpthread
endif

CFLAGS= ${OSFLAGS} ${XMLFLAGS} ${LGPLFLAG} -D__INTEL__ -DINLINING

#DEBUG= -O2

# put here the name of c++ compiler
CC=g++ ${CFLAGS} ${DEBUG} ${INCLUDE} -Dlint -pedantic-errors -Wformat -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE


# put here the complete directory path for the include subdirectory
CCINC= -I/usr/local/include -I/usr/include -I/usr/local/include/boost-1_33_1


# here again the name of the c++ compiler
#LD=g++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
LD=g++ ${INCLUDE} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE

# here the complete directory path for the lib subdirectory followed by  -lm
LDFLAGS=  -L/usr/local/lib -L/usr/lib -L/sw/lib -lboost_regex -lboost_filesystem -lboost_serialization -lm ${DEBUG}
OLD = 
#-oldcxx

For BOOST_REGEX_LIB "-static" has to be removed since Mac OS X does not support static linking of user binaries (crt0.o) but rather dynamic (crt1.o).

If boost is installed via fink change settings accordingly to /sw.

Note: Using /sw/include will cause an error due to a problem in "expat.h". Either load this header file from /usr/include or remove the "," at the end of line 46 in /sw/include/expat.h

"-Werror" was removed from the compiler flags since there were some "int" instead of "double" warnings when compiling ProteinProphet. So far they don't seem to be critical since the new C++ binary gives the same results as the old version.

Finally, line 264 in PepXMLViewer.html was changed back to

document.getElementById('msgs').innerHTML += "<br/>(URL: " + http_req.url ")";

With the extra "+" the ajax code added an extra WEBSERVER_ROOT path to the url path.

Make sure protxml2html.pl in in your webserver executables path. The easiest way to do so is to make a symlink to /sw/bin which was already added to your path:

ln -s /usr/local/tpp/bin/protxml2html.pl /sw/bin/protxml2html.pl

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

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

Link to ASAPRatio -pval.png in ProteinProphet has the the wrong path (WEBSERVER_ROOT does not get stripped off), but the image is generated.

There might be similar path problems as on other Linux distributions. To view the image simply change the URL manually. Should be relatively easy to fix for good perl programmers.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:Installing_on_Mac_OSX"