Changes between Version 23 and Version 24 of Installation_old

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Timestamp:
07/27/11 15:16:06 (14 years ago)
Author:
bartek
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  • Installation_old

    v23 v24  
    1212 
    1313== General Instructions == 
    14 If the dependencies are in place, you are ready to use the MUSCLE. No compilation required! 
     14If the dependencies are in place, you are ready to use the MUSCLE. In general no compilation required! 
    1515Extract the download, e. g. 
    1616{{{ 
    1717#!div style="font-size: 90%" 
    1818{{{#!sh 
    19 $ unzip MUSCLE_2009-10-08_10-39-10.zip 
     19$ unzip muscle-1.0.1.zip 
    2020}}} 
    2121}}} 
    … …  
    2424#!div style="font-size: 90%" 
    2525{{{#!sh 
    26 $ cd MUSCLE_2009-10-08_10-39-10 
     26$ cd muscle-1.0.1 
    2727}}} 
    2828}}} 
    … …  
    3535}}} 
    3636 
    37 In case you plan to use the MUSCLE with native code, you will have to compile the native library part of the MUSCLE using a C++ compiler (such as g++). The build script belonging to the MUSCLE also has a target to build the native libraries. This requires a C++ compiler and CMake (http://www.cmake.org/) to be available. You can also use 
    38 your favourite IDE/build system instead. 
     37In case you plan to use the MUSCLE with native code, you will have to compile the native library part of the MUSCLE using a C++ compiler (such as g++). The build script belonging to the MUSCLE also has a target to build the native libraries. This requires a C++ compiler and CMake (http://www.cmake.org/) to be available. You can also use your favourite IDE/build system instead. 
    3938 
    4039== What’s in the bundle? == 
    … …  
    6362}}} 
    6463 
    65 2. Check if recen Java SE Runtime Environment (JRE) or Java SE Development Kit (JDK) are present in your system. As the precompiled MUSCLE package is already included at build/muscle.jar you usually do not need to compile the Java sources and JRE is fully sufficient. If you want to recompile the Java part of the MUSCLE, a recent Java compiler is also required (javac).   
     642. Check if recent Java SE Runtime Environment (JRE) or Java SE Development Kit (JDK) are present in your system. As the precompiled MUSCLE package is already included at build/muscle.jar you may not need to compile the Java sources and JRE should be sufficient. Hovewer, if you want to recompile the Java part of the MUSCLE (recommended), a recent Java compiler is also required (javac).   
    6665{{{ 
    6766#!div style="font-size: 90%" 
    … …  
    7170}}} 
    7271 
    73 3. Set required environment variables 
     723. Ensure if you have a c++ compiler available on your system. If you have not, install this: 
     73{{{ 
     74#!div style="font-size: 90%" 
     75{{{#!sh 
     76yum install gcc-c++ 
     77}}} 
     78}}} 
     79 
     804. Check if cmake is available, otherwise install cmake: 
     81 
     82'''Note:''' you may need to add an additional repositorium (epel.repo) to the /etc/yum.repos.d. The content of this file may looks as follows: 
     83{{{ 
     84#!div style="font-size: 90%" 
     85{{{#!sh 
     86[epel]                                                                                                                     
     87name=Extra Packages for Enterprise Linux 5 - $basearch 
     88 
     89#baseurl=http://download.fedoraproject.org/pub/epel/5/$basearch 
     90mirrorlist=http://mirrors.fedoraproject.org/mirrorlist?repo=epel-5&arch=$basearch 
     91failovermethod=priority 
     92enabled=1 
     93gpgcheck=0                                                                                                                 
     94}}} 
     95}}} 
     96 
     97{{{ 
     98#!div style="font-size: 90%" 
     99{{{#!sh 
     100yum install cmake 
     101}}} 
     102}}} 
     103 
     1045. Set required environment variables 
    74105{{{ 
    75106#!div style="font-size: 90%" 
    … …  
    80111}}} 
    81112 
    82 4. Download the muscle bundle from [[http://apps.man.poznan.pl/trac/muscle/downloads|Downloads section]], e.g. 
     1136. Download the muscle bundle from [[http://apps.man.poznan.pl/trac/muscle/downloads|Downloads section]], e.g. 
    83114{{{ 
    84115#!div style="font-size: 90%" 
    … …  
    88119}}} 
    89120 
    90 5. Extract the package: 
     1217. Extract the package: 
    91122{{{ 
    92123#!div style="font-size: 90%" 
    … …  
    96127}}} 
    97128 
    98 6. See if the MUSCLE is working: 
     1298. Recompile entire MUSCLE: 
     130{{{ 
     131#!div style="font-size: 90%" 
     132{{{#!sh 
     133cd muscle-1.0.1 
     134./build.rb all 
     135}}} 
     136}}} 
     137 
     1389. See if the MUSCLE is working: 
    99139{{{ 
    100140#!div style="font-size: 90%" 
    … …  
    104144}}} 
    105145}}} 
    106  
    107  
    108 = temp = 
    109 add epel repo to the yum.repos.d 
    110 yum install gcc 
    111 yum install cmake