Ignore:
Timestamp:
Jun 27, 2007, 9:47:01 PM (15 years ago)
Author:
Jari Häkkinen
Message:

Fixes #67 and #68. Added information on how to install in Microsoft Windows. Also improved the docs.

File:
1 edited

Legend:

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  • trunk/se/lu/thep/affymetrix/INSTALL

    r295 r345  
    3232and Plier.
    3333
     34
    3435== 0. Introduction ==
    3536
     
    4748  i. Make BASE aware of the new plug-in.
    4849
    49 Upgrading the plug-in is even easier, see item 5) below.
     50Upgrading the plug-in is even easier, see item 5 below.
    5051
    5152=== Longer intro: ===
     
    6566to work. See more in item 1.ii below.
    6667
    67 Users who prefer the install from pre-compiled packages must go
    68 through all items below except 1.iii) and 2.iv).
    69 
    70 Users who prefer the live on bleeding edge software and compiles the
    71 source from the subversion repository must go through all items except
    72 3.v).
    73 
    7468If you are upgrading a previously installed RMAExpress or Plier
    75 plug-in for BASE you can safely skip to item 5) below.
     69plug-in for BASE you can safely skip to item 5 below.
    7670
    7771
     
    7973
    8074=== BASE 2 ===
     75
    8176This plug-in package will only work with BASE 2.0 or later, i.e. BASE
    82771.2.x is not (and will never be) supported.
    8378
     79''Compile time access to BASE core jar file.''
     80
     81This is only needed for compilation and installation from a subversion
     82tree or a source package, i.e., it is not needed when installing a
     83pre-compiled package.
     84
     85Specifically, the BASE2Core.jar file in use by the server running the
     86BASE web application must be available at compile/install time.
     87
     88
    8489=== RMAExpressConsole and apt-probeset-summarize ===
    8590
     
    8792
    8893Pre-requisite for RMAExpress plug-in (both binary package and
    89 subversion tree installs) is that RMAExpressConsole is installed.
     94subversion tree installs) to work is that RMAExpressConsole is
     95installed.
    9096
    9197RMAExpressConsole is available in the RMAExpress package written by
     
    9399http://rmaexpress.bmbolstad.com/
    94100
    95 You must download and compile RMAExpressConsole. This requires that
    96 wxWidgets (a.k.a. wxWindows) is installed on your system. wxWidgets is
    97 found at http://www.wxwidgets.org. The compilation of
    98 RMAExpressConsole is straightforward (at least on OpenSuSE 10.0 and
    99 10.2, and
    100 MacOSX 10.4.9). Download the source for v1.0beta1 and unpack the tar
     101(Microsoft Windows instructions) RMAExpressConsole is a part of the
     102Microsoft Windows pre-built binary package available from the
     103RMAExpress web site. Install the package and locate the
     104RMAExpressConsole.exe, wxbase26_gcc_custom.dll, and
     105wxmsw26_core_gcc_custom.dll files (these will be copied to the plug-in
     106location later).
     107
     108(Linux and MacOSX instructions) You must download and compile
     109RMAExpressConsole. This requires that wxWidgets (a.k.a. wxWindows) is
     110installed on your system. wxWidgets is found at
     111http://www.wxwidgets.org. The compilation of RMAExpressConsole is
     112straightforward (at least on OpenSuSE 10.0 and 10.2, and MacOSX
     11310.4.9). Download the source for v1.0beta1 and unpack the tar
    101114file. Unfortunately the source will not work out of the box in some
    102115operating systems. You have to add
     
    110123''apt-probeset-summarize''
    111124
    112 Pre-requisite for Plier plug-in (both binary package and
    113 subversion tree installs) is that apt-probeset_summarize is installed.
     125Pre-requisite for Plier plug-in (both binary package and subversion
     126tree installs) to work is that apt-probeset_summarize is installed.
    114127
    115128apt-probeset-summarize is available in the Affymetrix Power Tools
     
    123136not succeeded.
    124137
    125 ''Installation of binaries''
    126 
    127 You should install the binaries (RMAExpressConsole and
    128 apt-probeset-summarize) such that they are readable for the user running
    129 your BASE application server. The name of the binaries MUST be
    130 `RMAExpressConsole` and `apt-probeset-summarize`, respectively. Also
    131 binaries must be copied into the same directory as the plug-in (see
    132 item 3.v below). These two conditions are hard coded in the plug-ins.
    133 
    134 Install of the BASE plug-in will succeed even if this requisite is not
    135 fulfilled, but execution of the plug-in within BASE will fail.
    136 
    137 === Compile time access to BASE core jar file. ===
    138 
    139 This is only needed for compilation and installation from a subversion
    140 tree, i.e., it is not needed when installing a pre-compiled package.
    141 
    142 The BASE2Core.jar (from BASE 2.0 and later) file in use by the server
    143 running the BASE web application must be available when compiling
    144 se.lu.thep.affymetrix.jar.
     138''Installation of external binaries''
     139
     140You should install the external binaries, RMAExpressConsole (with the
     141DLLs in case of Microsoft Windows install) and apt-probeset-summarize,
     142such that they are readable for the user running your BASE application
     143server. The name of the binaries MUST be `RMAExpressConsole` and
     144`apt-probeset-summarize`, respectively. Also binaries must be copied
     145into the same directory as the plug-in (see item 2 or 3 below
     146depending on whether you perform a pre-compiled or source package
     147installation). These two conditions are hard coded in the plug-ins.
     148
     149The install of the BASE plug-in it-self will succeed even if this
     150requisite is not fulfilled, but execution of the plug-in within BASE
     151will fail.
     152
    145153
    146154== 2. Compilation and installation from a subversion tree ==
     
    148156You should skip this section if you downloaded a pre-compiled package.
    149157
    150 iv) When installing from a subversion working copy you must compile
    151 the plug-in, do
     158When installing from a subversion working copy you must compile the
     159plug-in, do
    152160
    153161  `make`
     
    182190== 3. Installation from a pre-compiled package ==
    183191
    184 You should skip this section if you use the subversion repository.
    185 
    186 v) Install the plug-in in the BASE application server file system. If
     192You should skip this section if you use the subversion repository or a
     193source package.
     194
     195Install the plug-in in the BASE application server file system. If
    187196BASE is installed in `/usr/local/base` simply do
    188197
     
    212221== 4. BASE configuration ==
    213222
    214 === vi) Make BASE aware of the new plug-ins ===
     223=== Make BASE aware of the new plug-ins ===
    215224
    216225You need to perform the below steps for both plug-ins in this
     
    240249   plug-in.
    241250
     251
    242252== 5. Updating a plug-in in BASE. ==
    243253
     
    255265This is straightforward:
    256266
    257    - Replace the old jar-file and
    258 
    259    - Log in to BASE with plug-in administrative privileges.
    260 
    261    - Choose 'Administrate' -> 'Plugins' -> 'Definitions'.
    262 
    263    - Locate the plug-in (RMAExpress or Plier) in the list and click on it.
    264 
    265    - Click on the 'Unload' button if it is available. This will
    266      remove the old plug-in from the application.
    267 
    268    - Click on 'Edit...'. This will open up the 'Edit plugin'
    269      pop-up window. No parameter changes are need, just click on
    270      the 'Save' button.
    271 
    272    - Done.
    273 
     267 - Replace the old jar-file and
     268
     269 - Log in to BASE with plug-in administrative privileges.
     270
     271 - Choose 'Administrate' -> 'Plugins' -> 'Definitions'.
     272
     273 - Locate the plug-in (RMAExpress or Plier) in the list and click on it.
     274
     275 - Click on the 'Unload' button if it is available. This will
     276   remove the old plug-in from the application.
     277
     278 - Click on 'Edit...'. This will open up the 'Edit plugin'
     279   pop-up window. No parameter changes are need, just click on
     280   the 'Save' button.
     281
     282 - Done.
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