TPP AMZTPP

From SPCTools

(Difference between revisions)

Revision as of 19:33, 12 March 2012

amztpp is a program developed by the trans-proteomic pipeline team for utilizing cloud computing (specifically Amazon Web Services) to execute multiple different peptide identification programs in parallel on MS/MS data. It can be used to cost effectively analyze large data sets in a short period of time.

1 Setting up amztpp

Setting up amztpp

The latest version of the TPP cloud tool amztpp can be downloaded from the TPP sourceforge site at http://sourceforge.net/projects/sashimi/files/amztpp. It is packaged as a gzipped "tar" file and can be unpacked using the standard unix tool tar or on Windows using programs such as 7-zip, WinZip, Stuffit, WinRAR, etc..

Prerequisites

Ironically TPP is not required in order to use the amztpp tool nor do you need to have any of the open source MS/MS identification programs that it uses installed. Though you will find having TPP installed will make it much easier to view and interact with the results produced by amztpp. So its our recommendation that you first install TPP before proceeding following the instructions at Software:TPP.

Since the amztpp tool is written in Perl you therefore need to install Perl on you system before proceeding. If you are on Linux it is very likely that you already have Perl installed on your system. If you are Windows you can download and install the free community edition provided by ActiveState at http://www.activestate.com/activeperl/downloads. (ActivePerl 5.14.2 or greater is required).

Installing amztpp on Linux

First download the latest version from sourceforge if you haven't already and unpack the archive:

% wget http://sashimi.svn.sourceforge.net
% tar xvzf amztpp-2.0.tgz
% cd amztpp-2.0

There are several ways to proceed from this point. The simplest is to follow the "standard" way of installing perl modules and programs as follows:

% perl Makefile.PL
Checking if your kit is complete...
Looks good
Writing Makefile for AMZTPP
Writing MYMETA.yml and MYMETA.json

If you get one or messages like Warning: prerequisite VM::EC2 1.09 not found. this indicates that you'll have to install additional modules for amztpp to work. As before there is a couple of different ways to install them. The easiest is to use CPAN. You can run the CPAN commands manually or there's a convenient rule written in the Makefile called installdeps that will do this for you (you'll likely need root privileges to execute this):

% make installdeps
Attempting to install prerequisites using cpan
...

Note that if this is the first time you've installed CPAN modules on your system you may be prompted with a series of questions. Simply accept the defaults for these questions. Another alternative to using CPAN is to use your Linux distributor's package manager. For example, using Ubuntu you'd run commands like "apt-get install libamazon-sqs-s3-perl". See your distributions manual for more details.

The next step is to build and test the program:

% make
% make test

A number of tests are skipped by default as they require you to provide your Amazon Credentials and the tests themselves will incur some minor AWS charges. If you want to run the full test set see the section on how to provide your AWS credentials and set these before running the tests.

The final step is to install the program with the command (again likely you'll need root privileges to execute this):

% make install

And that's it. You should now be ready to run amztpp. If you'd like to try it out jump down to the tutorial section to learn more.

If you want to change the installation location of amztpp from the default to, say, where you have TPP installed on you system you can use the PREFIX variable when you build the Makefile as so:

% perl Makefile.PL PREFIX=/opt/tpp

Lastly, for some more references on how to install perl modules on linux please see:

Installing amztpp on Windows

The process for installing on Windows is similar to the process on Linux. After downloading and installing ActiveState's perl download the amztpp archive and unpack it. Next open up a Windows "command" window by clicking on the start icon and typing "cmd" in the "Search for programs and files" field. When the command window opens up change to the directory ("cd") that you unpacked the archive to. Next configure the build using the same command as with Linux:

C:\AMZTPP-2.0>perl Makefile.PL
Set up gcc environment - 4.5.2
Writing Makefile for AMZTPP
Writing MYMETA.yml

C:\AMZTPP-2.0>

Next make sure dmake is installed and run "dmake" to make the package for your system.

C:\AMZTPP-2.0>ppm install dmake
C:\AMZTPP-2.0>dmake

You'll likely also see some messages warning about missing perl modules that are required. To install these you can manually use the perl package manager (ppm) that comes with ActiveState perl. Or simply this which will do it for you:

C:\AMZTPP-2.0>dmake installdeps

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

 '''''amztpp''''' is a program developed by the trans-proteomic pipeline team for utilizing cloud computing (specifically Amazon Web Services) to execute multiple different peptide identification programs in parallel on MS/MS data.  It can be used to cost effectively analyze large data sets in a short period of time.
-== Setting up amztpp ==
+= Setting up amztpp =
 The latest version of the TPP cloud tool amztpp can be downloaded from the TPP sourceforge site at http://sourceforge.net/projects/sashimi/files/amztpp.  It is packaged as a gzipped "tar" file and can be unpacked using the standard unix tool tar or on Windows using programs such as 7-zip, WinZip, Stuffit, WinRAR, etc..
-==== Prerequisites ====
+== Prerequisites ==
 Ironically TPP is not required in order to use the amztpp tool nor do you need to have any of the open source MS/MS identification programs that it uses installed.  Though you will find having TPP installed will make it much easier to view and interact with the results produced by amztpp.  So its our recommendation that you first install TPP before proceeding following the instructions at [[Software:TPP]].
 Since the amztpp tool is written in Perl you therefore need to install Perl on you system before proceeding.  If you are on Linux it is very likely that you already have Perl installed on your system.  If you are Windows you can download and install the free community edition provided by ActiveState at http://www.activestate.com/activeperl/downloads. ''(ActivePerl 5.14.2 or greater is required)''.
-=== Installing amztpp on Linux ===
+== Installing amztpp on Linux ==
 First download the latest version from sourceforge if you haven't already and unpack the archive:
 {| style="border-collapse: separate; border-spacing: 2; border-width: 1px; border-style: solid; border-color: #000; padding: 4px;"
 |[[Image:tip.gif|middle|left]]
-| If you want to change the installation location of amztpp from the default to, say where you have TPP installed on you system you can use the PREFIX variable when you build the Makefile as so:
+| If you want to change the installation location of amztpp from the default to, say, where you have TPP installed on you system you can use the PREFIX variable when you build the Makefile as so:
  % perl Makefile.PL PREFIX=/opt/tpp
 |}
 <br>
-=== Installing amztpp on Windows ===
+Lastly, for some more references on how to install perl modules on linux please see:
+* http://cpan.perl.org/modules/INSTALL.html
+* http://www.perlmonks.org/index.pl?node_id=128077
+* http://perl.jonallen.info/writing/articles/install-perl-modules-without-root
-* Download amztpp from the TPP Subversion tree at: http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/hpctools/aws/
-* Run perl Makefile.pl
+== Installing amztpp on Windows ==
-** There are a large number of dependencies that may need to be installed in order to install amztpp.
-* Run make install
+The process for installing on Windows is similar to the process on Linux.  After downloading and installing ActiveState's perl download the amztpp archive and unpack it.  Next open up a Windows "command" window by clicking on the start icon and typing "cmd" in the "Search for programs and files" field.  When the command window opens up change to the directory ("cd") that you unpacked the archive to.  Next configure the build using the same command as with Linux:
+ C:\AMZTPP-2.0>perl Makefile.PL
+ Set up gcc environment - 4.5.2
+ Writing Makefile for AMZTPP
+ Writing MYMETA.yml
+ C:\AMZTPP-2.0>
+Next make sure dmake is installed and run "dmake" to make the package for your system.
+ C:\AMZTPP-2.0>ppm install dmake
+ C:\AMZTPP-2.0>dmake
+You'll likely also see some messages warning about missing perl modules that are required.  To install these you can manually use the perl package manager (ppm) that comes with ActiveState perl.  Or simply this which will do it for you:
+ C:\AMZTPP-2.0>dmake installdeps

TPP AMZTPP

From SPCTools

Revision as of 19:33, 12 March 2012

Contents

Setting up amztpp

Prerequisites

Installing amztpp on Linux

Installing amztpp on Windows

Views

Personal tools

Navigation

support newsgroups

Search

Toolbox