TPP:Installing on Mac OSX

From SPCTools

(Difference between revisions)

Current revision

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 edit paths
10 generate directories
11 Try it!
12 TPP web GUI (Petunia)
13 Remaining issues

Caution!

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

 ==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.''
+''Please Note: '''The TPP is not currently officially supported on Max OSX.'''  This means that we cannot respond to installation or usage help requests.  Users, however, are encouraged to post to the spctools-discuss newsgroup to seek help from the community, or to contact the author (Ulrich, see below) directly.''
 ==Author==
 ==Introduction==
-This guide describes installation of the TPP, version 2.9.9 (Gale) on Mac OSX 10.4.
+This guide describes installation of the TPP, version v4.0 SQUALL (release candidate) rev.0, Build 200805281113 (linux) on Mac OSX 10.5.2
-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.
+Test machine: MacBook Pro, 2.33 GHz Intel Core 2 Duo, 3 GB RAM, 160 GB HD.
+Latest Mac OSX version used for testing: '''Intel 10.5.2'''
 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.
+Intel-based Mac running OSX 10.5.2.  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: [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912]
+*TPP source at SourceForge: [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912]
+*Subversion Repository:
+ <nowiki>svn co https://sashimi.svn.sourceforge.net/svnroot/sashimi/trunk/trans_proteomic_pipeline path/to/local/directory</nowiki>
 ==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
+For Mac OS X 10.5 Leopard you have to install fink from source (fink-0.28.1) following instructions on http://www.finkproject.org/download/srcdist.php?phpLang=e
+I would recommend to build all packages from source with 'fink install'.
 ===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)
+fink install is '''not recommended'''-- it sets up the config files in an unfamiliar way.
+Following [http://www.phpmac.com/articles.php?view=252 a 10.4.6 install turorial] :
+* download and decompress source
+* in source dir:
+ sudo mkdir /apache2
+ ./configure --prefix=/apache2 --enable-module=most --enable-shared=max
+ make
+ sudo make install
+*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 build are sufficient to run the TPP (check with httpd -l)
+'''Note:''' Mac OS X 10.5 comes with Apache2, this step can be skipped.
+====edit httpd.conf====
+Location (following the above installation): /apache2/conf/httpd.conf
+'''Note:''' on Mac OS X 10.5: /etc/apache2/conf/httpd.conf
+=====running on a different port (1441 is the standard port for a TPP installation)=====
+Change
+ Listen 80
+to
+ Listen 1441
+as per Linux README (enable SSI, cgi etc.)
+======DocumentRoot======
+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 set the DocumentRoot to their own directory.
+I will use '''/Library/WebServer/Documents/tpp''' in this example
+Also change the <directory> section to match your DocumentRoot.
+<pre>
+#
+# 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/tpp"
+...
+#
+# This should be changed to whatever you set DocumentRoot to.
+#
+<Directory "/Library/WebServer/Documents/tpp">
+...
+</pre>
+=====TPP-specific config=====
+Appended to end of httpd.conf; change "/usr/local/tpp" to wherever you will install the TPP, for instance "/Users/youraccount/tpp-bin".
+<pre>
+# 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>
+</pre>
+===Controlling Apache2===
+*starting: you will have to do this manually every time you reboot unless you set the server to start automatically; see above section for link.
+  sudo /apache2/bin/apachectl -k start
+*stopping:
+  sudo /apache2/bin/apachectl -k stop
+*restarting (if you change config files)
+  sudo /apache2/bin/apachectl -k restart
+'''Note:''' on Mac OS X 10.5 Apache2 is started from the System Preferences.
 ===install gnuplot 4===
 easiest via fink
+ fink install gnuplot
+if you don't have a working TeX installation fink will ask to install it. Note: fink does no longer support a system-tetex or a system-texlive package for TeX distributions already installed on the system. The most convenient is to install the fink distribution to satisfy dependencies.
+remember, if you see errors related to X11, reinstall the Apple X11SDK.pkg.
+'''Important''': gnuplot must be find-able by the apache program.  Adjust paths or
+ ln -s /sw/bin/gnuplot /usr/bin/gnuplot
 ===install wget===
-via fink
+easiest via fink:
+ fink install wget
 ===install md5sum===
- fink install GNOME coreutils
+Only if necessary!  Installed by default on modern fink installs.  You can verify that it is already there by typing "which md5sum".
+ fink install coreutils
 ===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===
-#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.)
+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.  Maybe binary install is possible?
+next:
+ fink install boost-1.33
+(This step only takes a second.)
+'''Note:''' with fink-0.28.1 on OS X 10.5.2 :
+ fink install boost1.33
+will work fine.
+====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:
- ln -s /usr/bin/nice /bin/nice
+ sudo ln -s /usr/bin/nice /bin/nice
 ==Configuring TPP for installation==
-===edit Makefile.incl according to Linux README===
+===edit src/Makefile.incl according to Linux README===
-===remove -lz from ramp.o dependencies in Makefile===
+create Makefile.config.incl for newer TPP releases!
-zlib should be installed on your system anyhow, -lz is recognized when building the targets by dynamicloader
+===edit src/Makefile===
+Makefile settings for pure fink install: change lines for GD_LIB and LDFLAGS, marked with the comment "changed for OSX/fink"
+'''Thanks to the great work of the TPP developers this is not neccessary anymore. The TPP will build without further changes by typing 'make all' in the src directory. This recommends a fink install of the packages mentioned above'''
+Choose proper settings for manual or fink boost install.
+<pre>
+#
+# 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= -L/sw/lib/ -lgd
+BOOST_REGEX_LIB= -lboost_regex -lpthread
+endif
+....
+# put here the complete directory path for the include subdirectory
+## OSX: two options: fink or manual boost install
+## use following for manual boost install
+#CCINC= -I/usr/local/include -I/usr/include -I/usr/local/include/boost-1_33_1
+## use following for fink boost install
+CCINC= -I/sw/include -I/usr/include -I/sw/include/boost-1_33_1
+....
+# 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}
+....
+</pre>
+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
+<pre>
+document.getElementById('msgs').innerHTML += "<br/>(URL: " + http_req.url ")";
+</pre>
+With the extra "+" the ajax code added an extra WEBSERVER_ROOT path to the url path.
+('''You still have to do that for the TPP v4.0 (release candidate from svn!''')
+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:
+<pre>
+ln -s /usr/local/tpp/bin/protxml2html.pl /sw/bin/protxml2html.pl
+</pre>
 ===change PepXMLViewer Makefile===
+'''Not necessary anymore!'''
 ''if boost installed via fink change /usr/local/lib to /sw/lib:''
 </pre>
 ===edit perl scripts===
-===code change: cgi_disCidData.c===
+===modify source code: src/Visualization/Pep3D/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
+//modification for Mac OS X
-  char *pStr = strstr(pngFile, "/tpp");
+char *pStr = strstr(pngFile, "/tpp");
-  printf("<img src=\"%s\"/>\n", pStr);
+printf("<img src=\"%s\"/>\n", pStr);
 </pre>
-===code change: show_sens_err.pl===
+===modify source code: CGI/show_sens_err.pl===
+'''Not neccessary anymore!'''
 (same WEBSERVER_ROOT strip off problem)
 *-insert at line 215:
 my $serverRoot = $ENV{'WEBSERVER_ROOT'};
-if((length $serverRoot) <= (length $local_pngfile) &&
+if (
-	   index((lc $local_pngfile), (lc $serverRoot)) == 0) {
+       (length $serverRoot) <= (length $local_pngfile)
-	    $local_pngfile = '/' . substr($local_pngfile, (length $serverRoot));
+      &&
+       index((lc $local_pngfile), (lc $serverRoot)) == 0
+   ) {
+        $local_pngfile = '/' . substr($local_pngfile, (length $serverRoot));
 }
 </pre>
 ==build TPP code==
- make all
- make install
+make configure
+make all
+make install
+==edit paths==
+If tpp executables are not in /usr/local, you must adjust your paths accordingly.
 ==generate directories==
 tpp/html, tpp/schema, tpp/cgi-bin in Apache DocumentRoot
-==change httpd.conf==
+'''necessary?'''
-as per Linux README (enable SSI, cgi etc.)
+==Try it!==
+Load http://localhost:1441/tpp/cgi-bin/check_env.pl in your browser-- if no error, things are looking good.
 ==TPP web GUI (Petunia)==
 ===getting the source===
-get tpp_gui from sashimi CVS repository
+'''TPP GUI is included in the TPP source distribution now.'''
+get tpp_gui from the [http://sourceforge.net/svn/?group_id=69281 sashimi SVN repository]
 ===modify the code for OSX installation===
 ===generate the password===
+'''TPP comes with 'guest' user pre-configured now.'''
 for "guest" account, using perl crypt, following the thread in spctools-discuss: http://groups.google.com/group/spctools-discuss/browse_thread/thread/fb8ea00f347f005d/296e071e68faf1f1?lnk=gst&q=perl+crypt&rnum=1#296e071e68faf1f1
 Place the following code in an executable setpasswd.pl file and run as follows:
- #!/usr/bin/perl -w print crypt($ARGV[0], "isbTPPspc") . "\n";
+ #!/usr/bin/perl -w
+ print crypt($ARGV[0], "isbTPPspc") . "\n";
+then
  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.

TPP:Installing on Mac OSX

From SPCTools

Current revision

Contents

Caution!

Author

Introduction

Requirements

Getting the TPP source

Prerequisites

install Apple's Developer Tools, including X11SDK.pkg

install fink including unstable tree

install Apache2

edit httpd.conf

running on a different port (1441 is the standard port for a TPP installation)

DocumentRoot

TPP-specific config

Controlling Apache2

install gnuplot 4

install wget

install md5sum

install sed

install GD

boost libraries

fink install

manual source install

nice

Configuring TPP for installation

edit src/Makefile.incl according to Linux README

edit src/Makefile

change PepXMLViewer Makefile

edit perl scripts

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

modify source code: src/Visualization/Pep3D/cgi_disCidData.c

modify source code: CGI/show_sens_err.pl

build TPP code

edit paths

generate directories

Try it!

TPP web GUI (Petunia)

getting the source

modify the code for OSX installation

generate the password

Remaining issues

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