User Guide & Manual - PEACE
Contents
1. Step 5 2 Analysis via cluster summary graph The default view of clusters is via a tree table display that provides detailed information about clusters and sequences within clusters However when dealing with large number of clusters or sequences a graphical visualization of the clusters may identify outliers or provide a visual confirmation of the overall quality of clustering The cluster summary graph aims to provide an alternative visual representation of the clusters In order to view the cluster summary graph right click on the cluster cls file to be summarized This displays a pop up menu from which the Clustering summary graph menu option can be chosen On selecting this option the cluster summary graph is displayed in a separate tab in the GUI s You may visually scale the graph by changing the x scale and y scale using the corresponding sliders You may also change the scale to a log scale by clicking on the log scale button in the top tool bar The summary graph also provides the option to color code sequences based on their FASTA identifiers Color coding sequences provides additional visual information about the nature of the clusters generated The color coding is performed by setting up EST or database the source of cDNA sequences classifiers To configure classifiers click on the EST Classifiers button in the tool bar Clicking the classifiers button cause the data base classifier editor to be displayed see Figure 7 T2. To run PEACE from the command line type peace options In order to run PEACE on a high performance computing configuration and take advantage of the multiple processor functionality provided by MPI run PEACE with the command mpiexec n desired number of processors peace options Page 30 of 36 User Guide amp Manual List of command line options and functionality clusterMaker Specify the clustering algorithm to use The options are e mst default Minimum Spanning Tree based cluster maker e null Nocluster maker clusters will not be generated analyzer Specify the EST similarity or distance measure to use The options are e twopassD2 Two pass d distance measure default e q2 d distance measure loosely based on the implementation in the program wcd e d2zim d distance measure based on the algorithm as outlined by Zimmerman e clu CLU s similarity metric generation algorithm heuristics Name s of the heuristic s to use in order null for none For this option one heuristic can be entered or multiple heuristics can be entered as a chain of the form heuristicl heuristic2 heuristicN The default for this option is uv t v meaning the w v heuristic will be run first followed by the t v heuristic if the w v heuristic returns a positive result e uv u v sample heuristic e tv tv heuristic estIdx Index of reference EST in a EST file default 0 output File to which output must
3. Java Virtual Machine JVM installed on it The JVM is part of the Java Runtime Environment JRE that is typically found on most machines However note that PEACE requires Java version 1 6 to run Software Minimum Description and additional information Version The Java Runtime 1 6 This is the standard Java runtime environment that is Environment JRE or typically installed on most machines JRE and JDK can Java Development Kit be obtained for free for all major operating systems from JDK http java sun com javase downloads index jsp The JRE is required to run the Graphical User Interface GUI component of PEACE Serial Parallel Clustering Installation The instillation of the clustering engine on a Linux Unix or OS X machine requires some software tools All of these are components that should already be installed on almost all standard distributions the automake and autoconf programs and gcc the GNU C C compiler Here is an overview of various software tools that are necessary to install and run PEACE Software Minimum Description and additional information Version automake 1 9 2 automake and autoconf are collectively used to configure the build system of PEACE on Linux Unix machines automake can be downloaded for free from http www gnu org software automake autoconf 2 59 automake and autoconf are collectively used to configure the build system of PEACE on Linux Unix machines The autoconf
4. the wizard will not proceed further The default value if filled in usually works fine 6 On clicking the next button PEACE will verify that the install directory does not exist on the server It will also do some basic checks to ensure that the server has all the necessary tools for installing PEACE Upon successfully passing the checks PEACE will show the detected information Review and click the OK button 7 The next screen displays summary information You cannot backtrack or cancel installation after this screen So carefully verify the information and click the inish button to proceed with full installation Page 13 of 36 User Guide amp Manual 8 The full installation on the server will proceed in the background and the progress will be displayed in a separate installation tab PEACE automatically detects and uses MPI to run in parallel if MPI is installed on the machine If errors occur during install they will be displayed in this window Do not close PEACE until the install completes 9 Once the install completes you will notice a new server entry in the server tab Its status should be good to indicate it is ready to run jobs and perform other operations A video tutorial illustrating the operations in PEACE for the DE aforementioned step is available off PEACE website at 9S6 htp www PEACE tools or Configuring Host File on personal machine s Several researchers including Dr Ra
5. 100 100 200 w Data Set EST fe 109175 faxa v Cher 0 Nodes 24 T ovr Data Ple est mir Chester 1 Nodes 1 bow Cheney 2 Nodes 49 gt Cher J Nodes 25 1 Chater 4 Node weicome html PEACE Usar harroje PEACE workspace vest S fasta Wies 400 400 00 Chester Nodes 1 Chester 6 Nodes 1 Oster 7 Nodes U Citer 8 Nodes 1 Chester 9 Nodes 1 Chester 10 Nodes D Citer 11 Nodes 1 Quite 12 Nodes 1 Chester 13 Nodes 1 Cister 14 Nodes 1 Chester 15 Nodes 1 Chester 16 Nodes 1 Chester 17 Nodes 1 Chester 18 Nodes 1 Chester 19 Nodes D Chester 20 Nodes 1 Chester 21 Nodes 1 Chester 22 Nodes 1 Custer 23 Nodes 1 Chester 24 Nodes I SS Oe ed J serven l 2a 6646 Sut 0 dhawkhecmuooedu Good server logf enime lt none set Timestamp Component Message TD react PLACE Git Version 0 1 Tue D PEACE Copytighs O Mie University 2009 Q Tue D PEACE O Tord ss Created metisi empty known hosts fhe Tve D JobMontor Started job monitoring thread for joo Job 8 User Logs f Programmer Logs Mimi Unversity MU Oxford OMO makes no representations or warranties about the suitib ity of t Figure 3 Data analysis Set tagging ivel Notice imi y importanti HI Page 10 of 36 User Guide amp Manual PEACE GUI DETAILS Step 1 Download and run PEACE GUI Th
6. at Miami University provide the biological perspective and motivation for the PEACE tool as well as the data sets used for the testing James C Moler Email molerjc muohio edu Web page N A James Moler is a graduate student in the computer science and software engineering department at Miami University He assisted Dr Dhananjai Rao in developing the PEACE software Foremost among his contributions is designing the two pass D2 algorithm a refinement of the original D2 distance metric He also contributed to efficient implementations of heuristics testing the software and fixing errors In addition he conducted statistical tests of the tool on simulated and real data sets Yuan Jenna Zhang Email zhangy9 muohio edu Web page N A Yuan Jenna Zhang is a graduate student in the computer science and software engineering department at Miami University She assisted with the analysis of PEACE results She contributed to the design of software for compiling and presenting statistics on PEACE performance and quality and is currently working on the extension of PEACE into the problem of transcript assembly and isoform differentiation Page 35 of 36 User Guide amp Manual REFERENCES 1 Nagaraj S Gasser R and Ranganathan S 2007 A hitchhiker s guide to expressed sequence tag EST analysis Brief Bioinformatics 2 Hazelhurst S Hide W Lipt k Z Nogueira R and Starfield R 2008 An overview of
7. commands at the shell prompt autoreconf i configure make The above sequence of commands will build PEACE in src folder and PEACE can be directly run from there with suitable command line parameters However you may also install PEACE for use by all users on the system via the following command make install The above command will install PEACE software in the default installation location suitable for your Linux Unix operating system From there you can begin working with the tool see the Running using PEACE section below Page 25 of 36 User Guide amp Manual Windows To install PEACE on a Windows machine first extract the PEACE archive to the desired location The archive will contain a project and solution file PEACE sln and PEACE vcproj for Microsoft Visual Studio 2008 Simply double click on the PEACE sIn solution file to open the build files in Visual Studio Once Visual Studio has loaded the project select the build type Debug or Release and build the software This will compile and build an executable called PEACE in the Debug or Release directory At this point you will need to open a command prompt and run the PEACE executable from the command line Running PEACE on Windows is otherwise the same as running it on Linux Unix OS X Details on configure options and influential environment variables You may configure several operational features of PEACE via standard config
8. memory and run time to cluster large FASTA files More nodes or CPUs reduce run time but increase maximum memory used Page 18 of 36 User Guide amp Manual 6 In the next screen you may change the path where the clustering data file is to be stored on your PC Enter brief description about the clustering and its purpose 7 Finally set the threshold value for clustering The threshold value is important and the user guide provides detailed information Larger threshold values are less discriminatory while smaller threshold values provide greater sensitivity Once the threshold value has been set click the next button 8 Onclicking the next button the job will be submitted to the server The information to run the job is created and progress is displayed in detail in the log pane Once the job has been submitted a new job entry is added to the workspace PEACE will periodically monitor the job and update status For long running jobs you may close PEACE and it will automatically restart monitoring the next time it is run using the same workspace 9 Once the job is complete you will be prompted to copy the generated data files back to your PC Once you have copied the files you may view and analyze the clusters A video tutorial illustrating the operations in PEACE for the OR aforementioned step is available off PEACE website at 9S6 htp www PEACE tools or Page 19 of 36 User Guide amp Manual PEACE
9. optimal performance PEACE makes use of the two pass D2 algorithm for pair wise sequence comparison and a minimum spanning tree based algorithm for clustering 3 4 PEACE however is built as an easily modifiable and extensible software system and the analyzer cluster maker and heuristics in use are interchangeable and can be swapped out for different analyzers cluster makers or heuristics This gives PEACE substantial utility as a research platform for testing different clustering approaches PEACE is written in C and makes use of the MPI Message Passing Interface standard for message passing to support high performance on parallel machines and computing clusters It makes heavy uses of object oriented design patterns to provide a flexible and robust framework for EST analysis and clustering It has primarily been tested on a cluster consisting of 128 multi processor compute nodes PEACE supports and has been tested on the Windows Linux and OS X operating systems Page 5 of 36 User Guide amp Manual Contact information Support requests bug reports installation difficulties and other issues as well as ideas and requests for additional features may be emailed to the authors of PEACE Contact information for the various authors is available off PEACE website at http www PEACE tools org Software Prerequisites for PEACE In order to run the GUI component of PEACE on a computer the computer needs to have just a
10. software tool can be obtained for free from http www gnu org software autoconf gcc if using gcc 4 0 1 The GNU Compiler Collection is used to compile the Page 6 of 36 User Guide amp Manual C code base of PEACE that runs in parallel on supercomputing clusters If the supercomputing cluster is using GCC as the C compiler then the minimum supported GCC version is 4 0 1 For details please referrer to GCC page at http gcc gnu org The Message Passing MPIAPI If you intend to run PEACE in parallel your cluster must Interface MPI library version have MPI library and tools that support MPI API version and tools 1 1 1 1 This version is a widely used standard and readily available on most supercomputing clusters However if you are running PEACE on your personal computer than you may obtain a free open source implementation of this standard from http www open mpi org Windows XP PEACE comes with a pre built binary for Windows as the platform is pretty consistent However PEACE currently does not support parallel operation via MPI on Windows platforms SOFTWARE DOWNLOADS This section provides downloads cf the sofware and documentation associated wit PEACE The primary software pacxage is the comprehensive Java Archive JAR fle peace Jar You may dnwrinad ciae pacxages aed aocumeemtion depending on ycur needs Usar docomentasen and video Morais are avalad
11. sufficient to handle the chl1amy 10pct fa file on the later two operating systems it is strongly recommend that on OS X the GUI be launched from the command line and allocated the extra memory with the Xmx2G switch where 2G represents 2 gigabytes of memory and can be decreased as needed Step 2 Install the PEACE Server Server Add New Server After choosing Add New Server option from the Server menu in the GUI see Figure 4 follow the instructions to install on either the local or a remote machine If configuring a remote server the target platform must be running Linux Unix OS X Windows is fine for a local instillation See the earlier chapter for a listing of required software for a Linux Unix OS X instillation Upon completion the Servers window should list the machine as having status Good Once installed PEACE will record and provide access to that server until deleted by the user Page 8 of 36 User Guide amp Manual Step 3 Load data set File gt New Data Set After choosing New Data Set under the File menu see Figure 4 follow the instructions in the wizard to import a data file in FASTA format into your workspace e g the downloaded chlamy_10pct fa file Once the FASTA file is successfully loaded a corresponding data set will be listed in the Workspace window Double clicking left clicking on it will display the sequences in the main view while right clicking on it will result in a pull
12. the wcd EST clustering tool Bioinformatics 24 1542 1546 3 Hazelhurst S 2004 D2 distance for EST clustering 1 5 4 Wan X Ozden M and Lin G 2008 Ubiquitous reassortments in influenza A viruses Journal of bioinformatics and computational biology 6 981 999 5 Burke J Davison D and Hide W 1999 d2 cluster a validated method for clustering EST and full length cDNAsequences Genome Res 9 1135 1142 6 Ptitsyn A and Hide W 2005 CLU a new algorithm for EST clustering BMC Bioinformatics 6 Suppl 2 S3 Page 36 of 36
13. PEACE Parallel Environment for Assembly and Clustering of Gene Expressions A cDNA Clustering Tool User Guide Parallel Environment for Assembly amp Clustering of gene Expressions PEACE Copyright c Miami University Oxford OHIO All rights reserved PEACE User Guide amp Manual COPYRIGHT amp LICENSE PEACE is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by IE Hl the Free Software Foundation either version 3 of the License or at 27 TEL T your option any later version PEACE is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with PEACE If not see lt http www gnu org licenses gt Miami University makes no representations or warranties about the suitability of the software either express or implied including but not limited to the implied warranties of merchantability fitness for a particular purpose or non infringement Miami University shall not be liable for any damages suffered by licensee as a result of using result of using modifying or distributing this software or its derivatives By using or copying this Software Licensee agrees to abide by the intellectual property laws a
14. Runtime parameters PEACE generates clusters based on a Minimum Spanning Tree algorithm using the d distance pseudo metric to weight edges In short it models the EST input as a graph with each node representing a single EST and edge weights calculated by the application of the d metric when applied to the incident ESTs Those not familiar with these concepts should be very careful about adjusting parameters Here we discuss each parameter giving a both layman s description and more detailed comments for those with the appropriate computational background When starting a job the user will be presented with the following options O O Analyzer Setup screen Data set The data set to be clustered Must have already been imported to PEACE Select analyzer for EST comparison Allows for variations on the method for assigning edge weights including the Two pass D2 heuristic optimization of the traditional d method Anyone not familiar with these algorithms should use the default two pass d 2 3 5 6 Window size d window size At this point it is highly recommended that the default value of 100 be used This provides the best balance between various competing factors to yield good clustering for a broad range of data sets Word size d word size Currently PEACE s d implementation allows only a word size of 6 Cache type PEACE includes several different distributed caching algorithms to speedup analysis MST constr
15. anency e g Sequences s and s are assumed to be adjacent if d sj 52 is less than the threshold Raising this value will improve sensitivity at the cost of specificity Page 21 of 36 User Guide amp Manual Step 5 1 Data analysis via tree table Each time a job successfully completes two files are in the Workspace are updated The first file is an intermediate Minimum Spanning Tree mst file and the second one is the cluster information c1s data file For most purposes unless you are planning to enhance or modify PEACE only the c1s file will be useful It contains the clustering information and allows the user to view and save the clustering Double click left click on this file to load and view the cluster in its default view called a tree table see Figure 6 The clusters are organized as collapsible trees while individual sequences within a cluster are displayed horizontally as a table with each column displaying 100 base pairs This view provides the option to sort the data based on cluster sizes using the menu at the top of this view In addition you may select several independent clusters or individual sequences by clicking with the mouse button while holding the control key down and save the data as FASTA file for your reference or further clustering and analysis Figure 6 Screenshot of PEACE GUI showing clustering results in a tree table view Page 22 of 36 User Guide amp Manual
16. arious steps that the server wizard will guide you through in order to create a new server entry in PEACE GUI 1 First review the information in the overview screen which provides a brief overview of the process and then click the next button 2 In the next screen you will be prompted to first select the type of server Local server is your local PC on which PEACE GUI is currently running A remote server is a different computer to which you can SSH PEACE already includes an SSH client to connect and operate on a remote computer 3 If you select a remote computer you must enter its name or IP address In addition enter your log in ID and password to log on to the remote machine PEACE will attempt to connect to the remote computer using the supplied credentials for verification when you click the next button in the wizard 4 Onclicking the next button you will be prompted with SSH security certificate for cross checking this occurs only the first time you ever connect to a computer via PEACE Click the yes button to continue to connect If your credentials are valid PEACE will ensure the remote machine is a Linux or Unix system 5 In the next step you may enter a description for this server for your future reference Ensure the install directory is valid PEACE will validate the install directory when you click the next button The install directory cannot currently exist If the specified path already exists or cannot be created
17. arity or distance measure to use The options are seseseeeeeerennne 31 SSHS UE PSE CS EP ERI charade ceabenahens naretdess 31 Name s of the heuristic s to use in order null for none esses 31 SOS S b sh MM M DERE 31 Index of reference EST in a EST file default O ssssssssssesessseeeeee ener ener nh nnn nn nnans 31 SS OUEPUE soc EE 31 File to which output must be written aeaniee reat nn nennt nasse n entran nass sns n satin annis 31 OP EA OMS cesssssut A et ce tke oe t ea eter E A ro bk e use ee ete teret epe eta LE edt de erae desi ieu aut 31 Displays the list of options for the specified cluster amp analyzer 31 SSULNES ASE AV Sis c cR 31 Launch PEACE interactive console eee eecscsenceeeeeeeesaeeeeaceceeeeeceaeeeeaaeceeaaeseseeecsaeeseaaeseeaeeeeaeeesaaeeseaaeeeaees 31 EISE Cle ERE ETERNI eos hee doce ese a iR 32 Working wth PEACE tools viii c 33 Brief overview Of tools 24 iecit ete ret te eee tt Og to e ee o a uet ine en da abe dee aeo dep d 33 List of tools command lines and figures generated esses nnne nnn nns 33 Author Biographies cccccccssssssccccececsesssansceececeesensaansececessessnssansececessensaasensececessensaasaesecucacsenseananseceeeess 34 RETEFENCES R A IIT DL LOL LIU T DIEM 36 Page 4 of 36 User Guide amp Manual INTRODUCTION PEACE is an acronym for Parallel Environment for Assembly and Clustering of gene Ex
18. ases analyze Run the currently loaded analyzer e g two pass D2 on a given pair of ESTs and print the metric generated by that analyzer If heuristics are enabled the heuristics will be run first In this case you may see a result of 400 which indicates the heuristics rejected the pair wise comparison stats Print statistics on the set of loaded ESTs Particularly useful for analyzing the distribution of EST lengths exit Exit the PEACE interactive console Page 32 of 36 User Guide amp Manual WORKING WITH PEACE TOOLS Brief overview of tools PEACE Tools is a software suite accompanying the main PEACE software system and consisting of several tools for EST analysis and visualization PEACE Tools is accessed by running the pTools executable and specifying the desired tool with the tool option Running pTools without a tool selected brings up the list of tools Running pTools with a tool selected and no other options will bring up a list of the available parameters List of tools command lines and figures generated Tool name Description Align Simple tool to generate an alignment using data from the minimum spanning tree produced by PEACE This tool annotates an EST file with data telling pTools how to align the ESTs ShowAlignment Shows a graphical view of EST alignments Before running this tool the Align tool should first be run on the EST data file Outputs an XFIG format file which can then be pro
19. be written options Displays the list of options for the specified cluster amp analyzer interactive Launch PEACE interactive console There also exist parameters specific to the analyzer cluster maker and or heuristics being used The options command line parameter will list all of the parameters that can be specified at the command line for the given analyzer cluster maker and heuristics Page 31 of 36 User Guide amp Manual A few examples mpiexec peace estFile ESTs fa output clusters out Run PEACE with the default analyzer two pass D2 cluster maker MST and heuristics on the file ESTs fa and direct output to the file clusters out With the use of mpiexec PEACE will be run with the maximum number of available processors mpiexec peac enel albe WSUS ora OUlejowe Clusters Olle hevristics muii As above but disable the heuristics used by PEACE Note that this may result in a significant slowdown and is not recommended for larger size data sets i e more than 10 000 ESTs peace estFile ESTs fa interactive Load ESTs from the data file ESTs fa and open the PEACE interactive console The interactive console is a convenient interface to facilitate the analysis of data sets with PEACE It provides the following commands help Shows this information list List brief information on all loaded ESTs print Print detailed information on a given EST including the sequence of b
20. c parameter values Page 20 of 36 User Guide amp Manual o WwW heuristic A more stringent method of filtering EST pairs As with the u v heuristic disabling it may improve sensitivity at a significant cost in runtime e Server setup Allows user to specify details on the server Additional details regarding these parameters are discussed in the job submission process o Specify local MST file Location of the minimum spanning tree file that will be generated in the course of the computations Most users will have no reason to ever look at this file o Select a server Select the server on which this job will run Must have previously been installed and added to the workspace see Quick Start Step 2 o Compute Nodes Number of nodes to be used in a parallel run Must be 1 unless the MPI library was present when installing the selected server o CPUs per Nodes Number of processors available on each node in a prallel run Must be 1 unless the MPI library was present when installing the selected server o Max Memory Maximum amount of memory available on the server o Max Run time Maximum number of hours PEACE will run a job before quitting e Clustering setup Details concerning the final clustering step o Specify local cluster file The location of the cluster file generated by PEACE After generation this can be easily moved to another location through the GUI o Threshold for clustering The d threshold for detecting adj
21. cal PC or a remote supercomputing cluster You may add a Server entry by clicking on corresponding tool bar or selecting the appropriate menu option from the main menu as shown in Figure 4 This launches a wizard that will guide you through the process of adding a new server entry to your workspace 000 PEACE Users karroje PEACE workspacel File ESRB Job View Help Add New Server Launch wizard to add a new server and install PEACE runtime on server F Ns SSS a Show your jobs on server Show just my jobs that are running or queued on the server Parallel EST Analyzer amp Clustering Engine Remove Server Entry Welcome amp Quick Start Guide 9i iiu A ET sati hoosing to use PEACE PEACE is an acronym for Parallel EST Analyzer and Clustering Engine As the le primary objective of PEACE is to ease clustering and analysis of Expressed Sequence Tags ESTs EST clustering is a computationally demanding task and clustering large EST data sets requires hours of compute or CPU time In order to reduce wall clock time PEACE has the ability to cluster ESTs in parallel using a modern Show all jobs on server Show all the jobs that are running or queued on the server Test server connection amp Try connecting to the server to ensure Jobs 5 supercomputing cluster You can read more about PEACE and associated tools via the PEACE website a http www peace tools org Bas 8 JobID Status Mon Here i
22. cessed and rendered in a variety of different graphical file formats by using for example the program fig2dev ShowMST Renders a PEACE generated minimum spanning tree in a bracketed graphical form Like ShowAlignment outputs a file in XFIG format The minimum spanning tree for a clustering can be generated by running PEACE with the option output mst file desired filename provided that the MST cluster maker is in use Page 33 of 36 User Guide amp Manual Author Biographies This page provides a brief summary of several individuals who have made contributions that have led to the overall success of PEACE They have been involved in one or more aspects of the system including conception architecture design implementation testing and documentation If you have questions or need additional information about PEACE feel free to contact them Dhananjai DJ M Rao Email dj djrao com Web page http www djrao com D M Rao was a visiting professor in the computer science and software engineering department at Miami University He is the primary architect and designer of PEACE is responsible for implementation of a large portion of PEACE runtime and is the sole designer implementer and artist of PEACE GUI He also designed and developed the PEACE web site and regularly administers the web site and manages the software systems His primary interests are in parallel computing and its application to b
23. down menu of options Step 4 Start a clustering job Jobo Job to Computer Clusters After choosing Job to Compute Clusters under the Job menu follow instructions in the wizard You will be required to pick an appropriate data set 1f more than one has been imported and the server to be used if more than one has been added see Figure 2 If running on a cluster parallel mode can be enabled by increasing the number of Compute Nodes and CPU Nodes allocated to the run All other options can be left at default values Once started the job will be listed under the Jobs tab with status RUNNING or eventually SUCCESS Once the job has completed PEACE will ask if it should copy the files back to the local server which is necessary to view the results and for further analysis Step 5 Data Analysis When the job is finished two files will be added to the Workspace list a mst fileanda c1s For most purposes only the cls file will be useful allowing the user to view and save the clustering Double click left click on this file to load and view the cluster information See Figure 3 Right click on the entry for other options including the generation of a Clustering summary graph to view the cluster size distributions and additional classifications Page 9 of 36 User Guide amp Manual Job Information D Overview Job Information Provide core information about the job Select the data set that conta
24. e GUI tool can be downloaded from the Downloads section from the PEACE website at http www PEACE tools org see Figure 1 The complete GUI is available in a file called PEACE jar The Java Archive jar file contains a complete distribution of PEACE It requires only JRE 1 6 installed on your machine to run Consequently the GUI will run on any Windows Linux or OS X operating system in which Java 6 is installed The program can be executed by double clicking on the icon or from the shell prompt in Linux Unix OS X command line as shown below java jar PEACE jar Upon initial startup you will be prompted through the following steps 1 You will be prompt you to accept the GPL version 3 license agreement under which PEACE is distributed 2 Once you accept the license PEACE will create an initial default directory in which it stores system wide information 3 Next you will be prompted to select a Workspace A workspace is a directory or folder under which PEACE stores data for a specific session You may choose to use a single workspace for all tasks or use multiple workspaces each workspace designated for a specific data set or type of analysis Page 11 of 36 User Guide amp Manual Step 2 Configuring a server In order to perform clustering via PEACE you must add a server to the workspace A server represents the machine on which PEACE will run jobs to compute clustering data A server can be just your lo
25. ed Enter an optional description summarizing the job for future reference and click the next button 3 The next screen permits you select algorithms and parameters PEACE uses for clustering The defaults are set to provide the best performance from PEACE Refer to the sections further below in this user manual for more details on these parameters Once you have configured the parameters and algorithms click the next button to proceed further 4 In the next screen you are provided with options to fine tune the heuristics used by PEACE to improve performance You may disable heuristics if you wish However enabling the heuristics provides best performance without compromising clustering quality Information on fine tuning the parameters is available in this user guide but in general the defaults work best 5 In the next screen you may change the path where the intermediate MST file is to be stored on your PC In addition select the server on which the job is to be run You may choose to run a parallel job if you know the server supports it To run a parallel job you must choose more than 1 CPU or more than 1 cluster node For this you need to know your cluster configuration the number of nodes it has and CPUs per node Contact your cluster administrator for platform configuration You also need to set the total memory and estimated run time for the job This information is needed to submit jobs on a supercomputing cluster via PBS You need more
26. fully review the information click the inish button to add a new data set entry to your work space If the upload is successful the data set will be listed in the Workspace window Left clicking or double clicking on it will display the sequences in the main view while right clicking on it will result in a pull down menu of options A video tutorial illustrating the operations in PEACE for the e aforementioned step is available off PEACE website at http www PEACE tools or Page 17 of 36 User Guide amp Manual Step 4 Starting a clustering job PEACE computes clustering for a FASTA file by running a suitable job on a server The FASTA file to be clustered must have been added to the workspace as a data set entry as described in Step 3 Moreover the server on which the job is to be run must have been added to the workspace and be in good status You may create a new data set entry by clicking on corresponding tool or selecting the Job to Compute Clusters menu option from the main Job menu This launches a wizard that will guide you through the following process to create and submit a job on a server 1 The wizard starts out by displaying a screen that summarizes the process of creating and submitting a job Review the information in the overview screen and click the next button 2 In the next screen select the appropriate data set containing the FASTA file to be clustered from the list of options provid
27. he editor can be used to add delete or modify classifiers To add a classifier click on the add button This will add a default entry with default values preset to the classifier list Tailor the description by double clicking left clicking on it Next edit and update the regular expression that is used to identify FASTA entries that belong that group The regular expression is applied to the complete FASTA identifier associated with each sequence entry in the source FASTA file Click on the color to set a color for this entry Once you have updated the classifiers click on the OK button to return back to the summary graph Page 23 of 36 User Guide amp Manual 12 Data base Classifier Editor d aU Description Regular Expression _ Enabled Generated ESTs a zA Z 0 4 0 9 Generated ESTs a zA Z 5 9 0 9 CACWI1 5 Chlamy CACWL L 4 CACWS 9 Chlamy CACW S5 9 Cancel Figure 7 Screenshot illustrating the data base classifier editor with a few classifiers configured with different regular expressions and colors Now click on the apply classifiers button to apply classifiers to your clustering and view classifications Figure 8 provides a comparative view of the cluster summary graph before and after classifiers were applied The classifications provide additional information to further validate the overall quality of clustering and en
28. he ofers files ao subsets fat have been created by randomly picking genes and then waking fe ESTs asscciated wit tose genes The Summary and objectives A detailed user guide for running both the urbe mises In ha percentage of Pa ESTs tar ware usad For exampie chtary TOpet fa has 10 PEACE is essentially a parallel and graphical GUI based and the textual version of the ES Ts randorny selected tom fo onginsi ffe chlamy a distributed clustering software system It of PEACE are available in the documentation constits of two main components The core page Video tutoriais are also available along clustering is performed by a standalone with the documentation software subsystem The core clustering E engine has been developed in C and The chigmy data set with 25 of the cONA sequences randomly uslizes tho Message Passing Library MP to skectod tom the complete crar ta data fio enable parallel and distributed clustering of Qj Tre chiar ata set with SON of the CONA sequences mn omly large data sets of sequenced transcript sefected orn the complete cotaemy fi data fia fragments The second component of PEACE The chierry dota tet with 75 of the CONA sequences randomly is a Graphical User Interface GUI that has selected bom the complete cr amy fa data fle been developed in Java to serve as an integrated clustering and analysis workbench The compen chiamy cata set of he SONA sequences Figure 1 www PEACE tools org Mai
29. ie r he docurentatos page 406 The core parallel clustering engine and text mode version of PEACE scuron code in a compressed gzipped tar bali The tar ball contains ali fne fies ncucing project fies used by Eciipse and Mecmsct Visual Studo 2008 tc buid tho beaces Documentation Tha complete GPL d PEACE source code in a compressed gaiooed tar bail Tha tar ball contes a3 the fles nesting project flea used ny Ecl pte and Moroso Visus Studio 2008 to bul fe binarios 1 ABOUT PEACE 1 LATEST UPDATES AND NEWS L Theuser guide ard anual thst provides a detailed descigdon cf Vow Version using PEACE The manum covers bof the GUI and text varwons of gt PEACE PEACE The latest verwon of PEACE song The current version of PEACE is 0 9 Beta The most Migitcant eehancement n he in09 c8on of a Oraphicar Utar interface GUD The GUI is vertatie and provides wit an updates vervon of PEACE many was eat res tor effectvery using Ihe Outieneq GUI are now available tor engine PEACE a Pony Sayoud uncer fe GN Genera Cownioad of Pe Dowsionss page rea trey oerinad vcd tan om fa tie Datos Cpecnal you may dosmica at a Bas ee detais on fe ceca tengle compressed igneo tar bak va the tek cwing ek Download fl test camer DATASET DOWNLOADS Tho data sots a 24520 of CONA sequences collectod fom ehlamydomonos Tho chlamy fa tie ie the 1 OVERVIEW OF PEACE TOOLS 1 User Manuals amp Tutorials ter ball s actually fa entro chlamydoeoncs data set T
30. ins the EST file to be D processed by this job Subsequent wizard pages will permit setting up additional information for the job such as MST generation parameters clustering Create New Clustering Server Setup Configure MST amp Server configuration Specify local MST file The mst file is to be created and must not exist Users karroje PEACE workspacel test75 mst job Information settings and server to run the job etc Analyzer Setup Select Data Set for Job The EST fie in will Data Set EST file test75 Setup Heuristics ver Setup Clustering Setup Description for job This i for your reference amp can be anything Test dataset job Summary job Subm a Back A Next G5 Help Cancel Analyzer Setup d Setup Heuristics Clustering job Summary Job Submission Server Info Select Server to Use for Job A serial or paratiel job wil be run on the server redhawk hpc muohio edu D serveri 3 CPUs per Nodes nic Compute Nodes Max Memory in MB Max Run time hours 2 048 7 The CPUs selected and nodes per CPU must match the configuration of the server a Back Next TD Help AA Cancel Figure 2 Starting jobs Choosing a data set left and server right File Server Job View Help BRAT oS Wh Hierarchy Hle List Tis MECTCunsmers Sotcustes Nome 02 4 X Workspace votes 9
31. ioinformatics He is working on diverse projects related to bioinformatics and parallel computing He is the best contact if you have any technical questions or need help with troubleshooting John Karro Email karroje muohio edu Web page http www eas muohio edu people karroje John Karro is an assistant professor in computer science and software engineering department at Miami University He contributed to the development of the algorithms underlying PEACE consulted on the tool development provided background biological knowledge and organized and directed the testing statistical analysis of results and development of methods for parameter optimization He is currently conducting a statistical analysis of the d2 distance metric for the purposes of parameter optimization and is directing efforts to extend PEACE into the problem of transcript assembly and isoform differentiation Page 34 of 36 User Guide amp Manual Mufit Ozden Email ozden 9 muohio edu Web page http www eas muohio edu people ozdenm Mufit Ozden a professor in the computer science and software engineering department at Miami University was crucial in developing the core MST approach underlying PEACE and assisted in the development and testing of the PEACE software tool Chun Liang Email LiangC muohio edu Web page http www cas muohio edu botany people profiles Liang html Chun Liang an assistant professor in the botany department
32. l path home karroje PEACE12 Job to Compute Clusters Bor Computes new clustering using existing MST data quick operation 2xamples ting directory ibrixfs1 home karroje PEACE12 peace examples Save current workspace JAVE_CONFIG_H I I L src Wall pipe g DDEVELOPER ASSERTIONS wd981 wd383 DICC DREGI WS Save the current status and associated eps UsingPeace Tpo deps UsingPeace Po else rm f deps UsingPeace Tpo exit 1 fi information about this workspace pipe g DDEVELOPER ASSERTIONS wd981 wd383 DICC DREGULAR COMPILE o UsingPeace L sr Import Data Set ing directory ibrixfs1 home karroje PEACE12 peace examples Import a data set from another workspace into current workspace ting directory ibrixfs1 home karroje PEACE12 peace ing to be done for all am Exit PEACE ing directory ibrixfs1 home karroje PEACE12 peace Save workspace information and exit outof r PEACE GUI ational status of PEACE uit succes sfully s 8 Creating data directories JoblD Status Mon Creating directory for job entries Installation completed successfully Creating Job directory home karroje PEACE12 jobs Done Creating EST storage directory home karroje PEACE12 estData Done mdi bs Final exit code 0 0 Connection closed 5 f 3 Servers 1 m lt 8 eee e Status ID User Logs amp B Programmer Logs Good serverl A Log file
33. ls on configuring MPICH is available Page 14 of 36 User Guide amp Manual online via http www mcs anl gov research projects mpich2 documentation files mpich2 1 2 1 installguide pdf OPEN MPI http www open mpi org Open MPI is another commonly used MPI implementation Open MPI does not require any special configuration or setup when running on a Symmetric Multi Processor SMP machine namely standard multi core multi processor machines However Open MPI does require additional configuration when processes need to be run on a network of computers Although a standard run via a host file is possible we recommend installing Torque an open source implementation of PBS and running PEACE jobs Page 15 of 36 User Guide amp Manual Step 3 Add new Data Set A data set consists of a FASTA file containing the cDNA or EST sequences to be analyzed and clustered Note that a data set can have only one FASTA file but can have many clustering files You may add a new data set entry by clicking on corresponding tool or selecting the appropriate menu option from the main menu as shown in Figure 5 This launches a wizard that will guide you through the process of adding a new data set entry to your workspace PEACE Users karroje PEACE workspacel dit Server Job View Help UE eS etme Tej welcome html PEACE Installer Create Job to Compute MST i E ta set redhawk hpc muohio edu Instal
34. n webpage left and download page right Page 7 of 36 User Guide amp Manual PEACE QUICK START VIA GUI In order to allow the user to immediately use PEACE this chapter of the manual presents a concise outline without delving into details of the steps needed to install and run a job The focus of this chapter to is to run PEACE via the Graphical User Interface GUI However PEACE can also be run as a standard text mode software tool For details on compiling and using PEACE in text mode please refer to the chapter titled Non graphical mode of PEACE Additional details on are discussed further in the manual Test Data For purposes of testing several data sets have been placed on the download page of the http www PEACE tools org download page see Figure 1 Using the smallest file chlamy 10pct fa will ensure the PEACE GUI can run with the default memory allocations instructions on how to increase memory for the larger files follow Step 1 Download and run the GUI http www PEACE tools org The GUI tool can be downloaded from the Downloads section file PEACE jar and run on any Windows Linux or OS X in which Java is installed The program can be executed by double clicking on the icon or from the Linux Unix OS X command line java Xmx2G jar PEACE jar OS X WARNING On OS X by default the JVM is allotted considerably less heap memory than when running on Windows or Linux Thus while the default allocation is
35. name lt none set i Set logging level Notice mildy important 4 Timestamp Component Message 9 Tue D PEACE PEACE GUI Version 0 1 9 Tue D PEACE Copyright O Miami University 2009 9 Tue D PEACE Miami University MU Oxford OHIO makes no representations or warranties about the suitability of t 9 Tue D SSH Created initial empty known hosts file Calo Figure 5 Screenshot of PEACE GUD illustrating the menu option to add a new data set to the workspace A summary of the various steps that the data set wizard will guide you through in order to create a new entry are briefly summarized below 1 The data set wizard commences with an overview screen that briefly describes the process of creating a data set Review the information in the overview panel and click the next button 2 In the second screen click on the browse button and select the FASTA file to be used for this data set PEACE will verify the contents of the FASTA file when you click the Page 16 of 36 User Guide amp Manual next button You may also enter a brief description summarizing the contents of the FASTA file The description is for your future reference and comes in handy when working with a large number of data sets in a workspace 3 Click the next button PEACE will load and verify that the FASTA file you specified is valid and display summary information about the sequences in the file for your review 4 After you care
36. nd all other applicable laws of the U S and the terms of GNU General Public License version 3 Page 2 of 36 PEACE User Guide amp Manual CONTENTS Copyright amp License 22 o itor oon puo bona bona kissd RR o S ERnR RR SS PERENNE DERRXR S DERE RR IE PRRERR OS DERE RR aa aN ians 2 jeluclcEe N 3 ipM 5 en 5 Contact informatiounen S 6 Software Prerequisites for PEACE cccccccccssssssssssecececessesenseeesececesseseaaeseeeessessesauaecesecsseeeesauaeeeesesseeseaaaas 6 Serial Parallel Clustering Installation esses eee 6 PEACE QUICK START VIA GUI e 8 PEACE GUI Details eorr ertt rr ERR EI SERERE NES EXE P SN ER EE PASS EXER EN NS ESPERA SEN R YE ENS EN NER eeror SEERE SNR N EYE SEN Ye ees 11 Step 1 Download and run PEACE GU cecccccsesscceceeecesseseaaeseceeecesseseaseseeeeseesseseaaeaeeeessessesaaaeseeeeseeeees 11 Step 2 Conftigu ring d Server te ree ivt eoe reti ti de ntereebetesisa na rr corse isa rever ebotet tona evene DEVE 12 Configuring Host File on personal machine s esses seen 14 Step 3 Add mew Data Set 5 erac oce aee made vesci getan bauen d tek ge ao nS NER EM NER 2I De Ncc D E RE ARES 16 Step A Starting a cl stering JOD oe iret riore epe esa e corse tea Verve dete posu eve
37. ne EE 18 PEACE Runtime parameters is ces he ere bake ad ee axe vr ed Ee ee aue Cad eere taxa re deed ndn 20 Step 5 1 Data analysis via tree table cccccsssccceessscesecssecececaececseseeeecsesaeeessesaeeessesaeeesecsaeeeseesaeeeees 22 Step 5 2 Analysis via cluster summary Zraph scccccccccsssessssececececesseseeeseeeescesseseaaeeeeeeeseeseseaeseeeeseeeees 23 Non graphical mode of PEACE 01 eee riie eee oo nonu ora ano Era a enun Ue ya ee ER ERR aae r Eann SS RS RE BER FREE DIR sasas 25 Installation Proced tre ee oe ttr reet xu ei eee On E Pee DUR EHE HEX RE Ree UERR METRE SE REEL MIR ET E EEEE 25 LIX ANG OSX qt 25 lll 26 Details on configure options and influential environment variables eeeeseeeenenenere 26 Known bugs issues s cccsseceesscceescecestecessecesssecesseccssececssecessecsssescaaecseaeecesecesaeescaaeceeseeceaeeceaaececaseseseess 29 LUnnihrdAirii dud o 30 Simple command aic E IR 30 List of command line options and functionality esesesssseeseee nennen nnne 31 C LUST OTMAK CS Pcie EE 31 Specify the clustering algorithm to use The options are c cccccecesssssssececeeecessessneseceeecesseseaeeeeeeseesees 31 SAN ALY c ME 31 Page 3 of 36 PEACE User Guide amp Manual Specify the EST simil
38. o run their own personal computational infrastructures Although such personal configurations tend to be small Dr Rao has a 32 core cluster in his basement they are convenient particularly for debugging and troubleshooting Such configurations may require additional setup Such setups are typically done by system administrators of supercomputing clusters There are diverse approaches for configuring MPI installations based on the distribution being used Consequently this manual we merely provide references to documentation that illustrate some of the configuration There are two commonly used open source implementation of MPI namely openmpi and mpich Here we document the approaches for using PEACE clustering engine with these two MPI implementations e MPICH These are the If you are running a local install of MPICH http www mcs anl gov research projects mpich2 then you need to suitably configure the set of hosts on which jobs are to be run The hosts file typically is configured only once and the set of hosts are automatically selected by MPICH via a daemon process called mpd This daemon process runs on all the machines on which MPI is to be run In order to facilitate deployment of mpd of a network of hosts MPICH provides another tool called mpdboot that uses the host file to automatically start mpd on the appropriate set of hosts In addition MPICH includes several tools to ease deployment and management of parallel processes More detai
39. pressions It is a software system for the clustering and analysis of cDNA and other types of sequence data representing small segments of gene transcripts It is applicable to data derived from both next generation sequencing technologies and traditional Sanger sequencing PEACE takes transcript fragments obtain from across a genome clusters them by gene association and enables easy analysis of the resulting clusters It includes a versatile graphical user interface GUI to manage installation execution and analysis of clusters PEACE can be easily installed and run on standalone machines running Windows Linux and OS X PEACE can also run parallel mode on Linux clusters supporting MPI In the Quick Start chapter of this document we present a concise outline without explanation of the steps needed to start PEACE with the intent of allowing a user to quickly install and use PEACE The remainder of the document then discusses the steps in more detail for those users who wish to tailor their usage more specifically to their data or computing platform Overview PEACE is a bioinformatics software system for the analysis and clustering of genetic sequences typically cDNA data sets obtained from next generation sequencing technologies o r traditional Sanger sequencing This manual does not deal with the background on this area and related bioinformatics topics for information on those please see the related publications 1 2 By default and for
40. s a quick overview of the various steps that are needed to perform some basic EST clustering and analysis Step 1 Server Supercomputing cluster setup EN The first step in the process is to create a server entry in PEACE GUI Click on the Add Server tool in the main toolbar to launch the wizard to add a server This wizard guides you through the process of installing the core PEACE clustering engine on a Linux Unix machine or supercomputing cluster You need to have a valid login to the machine on which PEACE clustering engine will run Servers TELL Glentana 6b ProprammerLoge Step 2 Create Data Set Fh Once you have successfully added a server entry the next step is to create a Data Set A data set contains the EST T FASTA file and associated clustering data files Click on the New Data Set tool in the main toolbar to launch the wizard ta create new data cat from an evicting EST RASTA file 3 Log filename lt none set gt esl B Set logging level f Notice mildy important Timestamp Component Message 9 Tue D PEACE PEACE GUI Version 0 1 Tue D PEACE Copyright C Miami University 2009 Tue D PEACE Miami University MU Oxford OHIO makes no representations or warranties about the suitability of t Z Figure 4 Screenshot of PEACE GUI illustrating the menu option to add a new server Page 12 of 36 User Guide amp Manual Here is a summary of the v
41. stem admin executables EPREFIX sbin libexecdir DIR program executables EPREFIX libexec sysconfdir DIR read only single machine data PREFIX etc sharedstatedir DIR modifiable architecture independent data PREFIX com localstatedir DIR modifiable single machine data PREFIX var libdir DIR object code libraries EPREFIX lib includedir DIR C header files PREFIX include oldincludedir DIR C header files for non gcc usr include datarootdir DIR read only arch independent data root PREFIX share datadir DIR read only architecture independent data DATAROOTDIR infodir DIR info documentation DATAROOTDIR info localedir DIR locale dependent data DATAROOTDIR locale mandir DIR man documentation DATAROOTDIR man docdir DIR documentation root DATAROOTDIR doc PEACE htmldir DIR html documentation DOCDIR dvidir DIR dvi documentation DOCDIR pdfdir DIR pdf documentation DOCDIR psdir DIR ps documentation DOCDIR Program names program prefix PREFIX prepend PREFIX to installed program names program suffix SUFFIX append SUFFIX to installed program names program transform name PROGRAM run sed PROGRAM on installed program names Page 27 of 36 User Guide amp Manual Optional Features disable FEATURE do not include FEATURE same as enable FEATURE no enable FEATURE ARG include FEATURE ARG yes disable dependency tracking speeds
42. sure it is satisfactory Jl it i i Figure 8 Screenshot of PEACE GUI illustrating a cluster summary graph before classifiers were applied to the left and after color coded classifiers were applied to the right A video tutorial illustrating the operations in PEACE for the o aforementioned step is available off PEACE website at e http www PEACE tools org Page 24 of 36 User Guide amp Manual NON GRAPHICAL MODE OF PEACE The earlier chapters discussed the use of PEACE through its Graphical User Interface GUI The GUI essentially provides an user friendly interface to the core backend clustering engine of PEACE that runs as a standalone text mode software tool It is can run in batch mode on a supercomputing cluster or in interactive mode in a terminal Consequently the clustering engine can be independently used without the GUI if the need arises This section describes the process of installing the core PEACE clustering engine Installation Procedure The following two sections describe the process of installing PEACE on Linux Unix and Windows machines The software requirements for installing PEACE are described earlier in this user manual in the section titled Software Prerequisites for PEACE Linux and OS X To install PEACE on a Linux or OS X machine first extract the PEACE archive to the desired location Change directory to that location and issue the following
43. uction and clustering Several different cache management strategies have been developed over a period of several years to identify the best possible configuration The default heap based cache was found to provide the best performance for a wide range of data sets and is used as the default Unless you are experimenting in computational data structures you are strongly encouraged to use the heap based caching approach Cache size The cache size represents the number of distance similarity metrics that are cached for a given pair of sequences This value is a compromise between the volume of main memory dedicated to maintaining caches versus the overhead of having to re compute d2 metric Decreasing the cache size decreases memory footprint but may cause higher cache misses resulting in additional computation We have found the default cache size of 128 to be sufficiently large to provide a good balance minimizing cache misses and maximizing cache usage Setup Heuristics The u v and t v heuristics are used to heuristically skip the edge weight calculations of edges that are unlikely to connect overlapping ESTs 2 Adjusting these parameters will affect sensitivity and runtime of the tool with an inverse relationship u v heuristic A fast way of dismissing EST pairs that clearly do not need to be considered Disabling may improve sensitivity at a significant cost in runtime Users not familiar with the heuristic should not fiddle with the specifi
44. up one time build nable dependency tracking do not reject slow dependency extractors Optional Packages with PACKAGE ARG use PACKAGE ARG yes without PACKAGE do not use PACKAGE same as with PACKAGE no with mpi PATH path to mpicc with icc Code will be compiled with icc Intel C C compiler with gec Code will be compiled with gcc The GNU C C compiler Some influential environment variables CC C compiler command CFLAGS C compiler flags LDFLAGS linker flags e g L lt lib dir if you have libraries in a nonstandard directory 1ib dir LIBS libraries to pass to the linker e g l lt library gt CPPFLAGS C C Objective C preprocessor flags e g I include dir if you have headers in a nonstandard directory include dir CPP C preprocessor CXX C compiler command CXXFLAGS C compiler flags CXXCPP C preprocessor command Use these variables to override the choices made by configure or to help it to find libraries and programs with nonstandard names locations Page 28 of 36 User Guide amp Manual Known bugs issues Here is a brief list of some of the known issues with PEACE e Currently the Windows build of PEACE does not support MPI We are planning to remedy this situation once we get our hands onto a good supercomputing cluster running Windows i e not any time soon Page 29 of 36 User Guide amp Manual RUNNING USING PEACE Simple command line
45. ure options The options that can be used when running configure are shown below Usage configure OPTION VAR VALUE To assign environment variables e g CC CFLAGS specify them as VAR VALUE See below for descriptions of some of the useful variables Defaults for the options are specified in brackets Configuration h help display this help and exit help short display options specific to this package help recursive display the short help of all the included packages V version display version information and exit qd quiet silent do not print checking messages cache file FILE cache test results in FILE disabled C config cache alias for cache file config cache n no creat do not create output files Srcdir DIR find the sources in DIR configure dir or Page 26 of 36 User Guide amp Manual Installation directories prefix PREFIX install architecture independent files in PREFIX usr 10ca1 xec prefix EPREFIX install architecture dependent files in EPREFIX PREFIX By default make install will install all the files in usr local bin usr local lib etc You can specify an installation prefix other than usr local using prefix for instance prefix S HOME For better control use the options below Fine tuning of the installation directories bindir DIR user executables EPREFIX bin sbindir DIR sy
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