source: trunk/se/lu/thep/affymetrix/INSTALL @ 295

Last change on this file since 295 was 295, checked in by Jari Häkkinen, 15 years ago

Added Plier class name to instructions.

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[123]1$Id: INSTALL 295 2007-05-23 12:40:10Z jari $
2
[272]3----------------------------------------------------------------------
4{{{
[123]5Copyright (C) 2006 Jari Häkkinen
[281]6Copyright (C) 2007 Jari Häkkinen, Peter Johansson
[123]7
[272]8This file is part of se.lu.thep.affymetrix package for BASE,
9http://baseplugins.thep.lu.se/wiki/se.thep.lu.se.affymetrix
[123]10
[272]11se.lu.thep.affymetrix package for BASE is free software; you can
12redistribute it and/or modify it under the terms of the GNU General
13Public License as published by the Free Software Foundation; either
14version 2 of the License, or (at your option) any later version.
[123]15
[272]16se.lu.thep.affymetrix package for BASE is distributed in the hope that
17it will be useful, but WITHOUT ANY WARRANTY; without even the implied
18warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See
19the GNU General Public License for more details.
[123]20
21You should have received a copy of the GNU General Public License
22along with this program; if not, write to the Free Software
23Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
24USA.
[273]25}}}
[272]26----------------------------------------------------------------------
[123]27
28
[272]29= Installation Guide for se.lu.thep.affymetrix =
30
[284]31This file contains installation information for two plug-ins: RMAExpress
[272]32and Plier.
33
34== 0. Introduction ==
[123]35
[272]36=== Short intro: ===
[123]37
[284]38The route for successful first time installation of this RMAExpress plug-in is
[272]39  i. Install the plug-in.
40  i. Install wxWidgets.
41  i. Install RMAExpressConsole.
42  i. Make BASE aware of the new plug-in.
[228]43
[284]44The route for successful first time installation of this Plier plug-in is
[272]45  i. Install the plug-in.
46  i. Install apt-probeset-summarize.
47  i. Make BASE aware of the new plug-in.
[228]48
[281]49Upgrading the plug-in is even easier, see item 5) below.
[228]50
[272]51=== Longer intro: ===
[228]52
[284]53There are two supported ways to install this Affymetrix package, you
[189]54either download a pre-compiled package or you checkout the latest
55source from the subversion repository. The below instructions covers
56both installation options since major parts of the installation is the
57same for the different cases. There is also a source package available
58for download but installation from that package is currently not
59supported, it is supplied for reference only.
[123]60
[272]61Note, the underlying algorithms RMA and Plier are not part of this
62package. This package contains the plug-in code needed for hooking up
63RMAExpress and Plier to BASE as a plug-in. The underlying binaries,
64RMAExpress and Plier, must be installed for the corresponding plug-in
65to work. See more in item 1.ii below.
[156]66
[124]67Users who prefer the install from pre-compiled packages must go
68through all items below except 1.iii) and 2.iv).
69
70Users who prefer the live on bleeding edge software and compiles the
[189]71source from the subversion repository must go through all items except
723.v).
[124]73
[274]74If you are upgrading a previously installed RMAExpress or Plier
[281]75plug-in for BASE you can safely skip to item 5) below.
[124]76
[156]77
[272]78== 1. Pre-requisites ==
[124]79
[274]80=== BASE 2 ===
81This plug-in package will only work with BASE 2.0 or later, i.e. BASE
821.2.x is not (and will never be) supported.
[124]83
[274]84=== RMAExpressConsole and apt-probeset-summarize ===
[282]85
86''RMAExpressConsole''
87
[274]88Pre-requisite for RMAExpress plug-in (both binary package and
89subversion tree installs) is that RMAExpressConsole is installed.
[124]90
[272]91RMAExpressConsole is available in the RMAExpress package written by
92Ben Bolstad, and the official RMAExpress web site is
[124]93http://rmaexpress.bmbolstad.com/
[123]94
95You must download and compile RMAExpressConsole. This requires that
96wxWidgets (a.k.a. wxWindows) is installed on your system. wxWidgets is
97found at http://www.wxwidgets.org. The compilation of
[282]98RMAExpressConsole is straightforward (at least on OpenSuSE 10.0 and
9910.2, and
[280]100MacOSX 10.4.9). Download the source for v1.0beta1 and unpack the tar
101file. Unfortunately the source will not work out of the box in some
102operating systems. You have to add
103{{{
104#include <cmath>
105}}}
[283]106to `RawDataVisualize.cpp` before issuing 'make'. After this patch
[280]107RMAExpressConsole will be compiled (together with some other binaries
108which are of no interest here.
[123]109
[282]110''apt-probeset-summarize''
111
112Pre-requisite for Plier plug-in (both binary package and
113subversion tree installs) is that apt-probeset_summarize is installed.
114
[272]115apt-probeset-summarize is available in the Affymetrix Power Tools
[274]116(APT) package available through Affymetrix home page
[272]117http://www.affymetrix.com/support/developer/powertools/index.affx
[125]118
[274]119APT is available as a Windows installer package and pre-built binaries
120for Linux and Mac OS-X. If you prefer building yourself, the source
121code is available as well. Though, it should be noted, we have
122experienced some problems building APT and at the time being we have
123not succeeded.
124
[282]125''Installation of binaries''
126
[272]127You should install the binaries (RMAExpressConsole and
[288]128apt-probeset-summarize) such that they are readable for the user running
[272]129your BASE application server. The name of the binaries MUST be
130`RMAExpressConsole` and `apt-probeset-summarize`, respectively. Also
131binaries must be copied into the same directory as the plug-in (see
132item 3.v below). These two conditions are hard coded in the plug-ins.
133
[228]134Install of the BASE plug-in will succeed even if this requisite is not
135fulfilled, but execution of the plug-in within BASE will fail.
[123]136
[274]137=== Compile time access to BASE core jar file. ===
[282]138
[284]139This is only needed for compilation and installation from a subversion
[274]140tree, i.e., it is not needed when installing a pre-compiled package.
[123]141
[228]142The BASE2Core.jar (from BASE 2.0 and later) file in use by the server
[274]143running the BASE web application must be available when compiling
144se.lu.thep.affymetrix.jar.
[123]145
[273]146== 2. Compilation and installation from a subversion tree ==
[123]147
[189]148You should skip this section if you downloaded a pre-compiled package.
[123]149
[189]150iv) When installing from a subversion working copy you must compile
151the plug-in, do
[123]152
[273]153  `make`
[189]154
[273]155This assumes that BASE is installed in `/usr/local/base`. If this is not
[135]156the case do
[123]157
[273]158  `make BASEROOT=<base-dir>`
[123]159
[273]160where `<base-dir>` is to be replaced with the path to BASE. When the
[189]161compilation finishes you install the plug-in into the BASE application
162server file system with
[135]163
[273]164  `make install`    or    `make BASEROOT=<base-dir> install`
[135]165
[189]166The plug-in will install in the recommended directory
[273]167`<base-dir>/www/plugins/se/lu/thep/affymetrix`, i.e., if you prefer
[189]168another location please refer to the Makefile (which supports further
169options).
[124]170
[273]171For advanced users only: `<base-dir>` can really be any directory
[189]172readable for the user running your tomcat server. This may be handy if
173you run several servers on one machine but only want one common
174directory hierarchy for the plug-ins. Or, if you update the BASE
175application frequently and in the process create new directories for
176the newer application. More information about this is available in the
177Makefile.
178
179Remember the plug-in location for configuration of BASE below.
180
181
[273]182== 3. Installation from a pre-compiled package ==
[189]183
184You should skip this section if you use the subversion repository.
185
[135]186v) Install the plug-in in the BASE application server file system. If
[273]187BASE is installed in `/usr/local/base` simply do
[124]188
[273]189  `make install-precompiled`
[123]190
[135]191If BASE is installed elsewhere, do
192
[273]193  `make BASEROOT=<base-dir> install-precompiled`
[135]194
[273]195where `<base-dir>` is to be replaced by the path to BASE. The plug-in
[123]196will install in the recommended directory
[273]197`<base-dir>/www/plugins/se/lu/thep/affymetrix`, i.e., if you prefer
[189]198another location please refer to the Makefile (which supports further
199options).
[123]200
[273]201For advanced users only: `<base-dir>` can really be any directory
[125]202readable for the user running your tomcat server. This may be handy if
203you run several servers on one machine but only want one common
204directory hierarchy for the plug-ins. Or, if you update the BASE
205application frequently and in the process create new directories for
[135]206the newer application. More information about this is available in the
207Makefile.
[124]208
[153]209Remember the plug-in location for configuration of BASE below.
[125]210
211
[273]212== 4. BASE configuration ==
[124]213
[282]214=== vi) Make BASE aware of the new plug-ins ===
[125]215
[282]216You need to perform the below steps for both plug-ins in this
217package. Currently there is no way to install all plug-ins in one
218package.
219
[284]220 * Log in to BASE with plug-in administrative privileges.
[127]221
[273]222 * Choose 'Administrate' -> 'Plugins' -> 'Definitions'.
[127]223
[273]224 * Click on 'New...'. This will open up the 'Create plugin' pop-up
[282]225   window. Type `se.lu.thep.affymetrix.RMAExpress` in the 'Class'
[189]226   field and
[282]227   `/path/to/base/www/plugins/se/lu/thep/affymetrix/affymetrix.jar" in
[284]228   the 'Path' field. Obviously, if you have chosen another location
[282]229   for the jar above you should adapt to that. Click on the 'Save'
230   button.
[127]231
[282]232 * Share the plug-in to all users/roles/groups that should have access
233   to it (sharing it to group 'Everyone' should be sufficient in most
234   cases).
[127]235
[295]236 * Redo the third and fourth step above for Plier where you use
237   `se.lu.thep.affymetrix.Plier` in the class field.
[127]238
[273]239 * That's it, now you need to BASE skills to actually make use of the
[282]240   plug-in.
[125]241
[281]242== 5. Updating a plug-in in BASE. ==
[127]243
[273]244You may update the underlying binaries (RMAExpress or
245apt-probeset-summarize) or the plug-in.
[153]246
[273]247=== Updating RMAExpressConsole or apt-probeset-summarize ===
[156]248
[273]249Installing a new binary is trivial, just replace the old binary with
[282]250the new binary. However, make sure that the input and output formats
251has not changed.
[156]252
[273]253=== Update RMAExpress or Plier plug-ins for BASE ===
[156]254
[284]255This is straightforward:
[156]256
257   - Replace the old jar-file and
258
[284]259   - Log in to BASE with plug-in administrative privileges.
[156]260
261   - Choose 'Administrate' -> 'Plugins' -> 'Definitions'.
262
[282]263   - Locate the plug-in (RMAExpress or Plier) in the list and click on it.
[156]264
[189]265   - Click on the 'Unload' button if it is available. This will
266     remove the old plug-in from the application.
[156]267
[189]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.
[156]271
272   - Done.
[273]273
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