Changeset 345
- Timestamp:
- Jun 27, 2007, 9:47:01 PM (15 years ago)
- Location:
- trunk/se/lu/thep/affymetrix
- Files:
-
- 2 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/se/lu/thep/affymetrix/INSTALL
r295 r345 32 32 and Plier. 33 33 34 34 35 == 0. Introduction == 35 36 … … 47 48 i. Make BASE aware of the new plug-in. 48 49 49 Upgrading the plug-in is even easier, see item 5 )below.50 Upgrading the plug-in is even easier, see item 5 below. 50 51 51 52 === Longer intro: === … … 65 66 to work. See more in item 1.ii below. 66 67 67 Users who prefer the install from pre-compiled packages must go68 through all items below except 1.iii) and 2.iv).69 70 Users who prefer the live on bleeding edge software and compiles the71 source from the subversion repository must go through all items except72 3.v).73 74 68 If you are upgrading a previously installed RMAExpress or Plier 75 plug-in for BASE you can safely skip to item 5 )below.69 plug-in for BASE you can safely skip to item 5 below. 76 70 77 71 … … 79 73 80 74 === BASE 2 === 75 81 76 This plug-in package will only work with BASE 2.0 or later, i.e. BASE 82 77 1.2.x is not (and will never be) supported. 83 78 79 ''Compile time access to BASE core jar file.'' 80 81 This is only needed for compilation and installation from a subversion 82 tree or a source package, i.e., it is not needed when installing a 83 pre-compiled package. 84 85 Specifically, the BASE2Core.jar file in use by the server running the 86 BASE web application must be available at compile/install time. 87 88 84 89 === RMAExpressConsole and apt-probeset-summarize === 85 90 … … 87 92 88 93 Pre-requisite for RMAExpress plug-in (both binary package and 89 subversion tree installs) is that RMAExpressConsole is installed. 94 subversion tree installs) to work is that RMAExpressConsole is 95 installed. 90 96 91 97 RMAExpressConsole is available in the RMAExpress package written by … … 93 99 http://rmaexpress.bmbolstad.com/ 94 100 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 102 Microsoft Windows pre-built binary package available from the 103 RMAExpress web site. Install the package and locate the 104 RMAExpressConsole.exe, wxbase26_gcc_custom.dll, and 105 wxmsw26_core_gcc_custom.dll files (these will be copied to the plug-in 106 location later). 107 108 (Linux and MacOSX instructions) You must download and compile 109 RMAExpressConsole. This requires that wxWidgets (a.k.a. wxWindows) is 110 installed on your system. wxWidgets is found at 111 http://www.wxwidgets.org. The compilation of RMAExpressConsole is 112 straightforward (at least on OpenSuSE 10.0 and 10.2, and MacOSX 113 10.4.9). Download the source for v1.0beta1 and unpack the tar 101 114 file. Unfortunately the source will not work out of the box in some 102 115 operating systems. You have to add … … 110 123 ''apt-probeset-summarize'' 111 124 112 Pre-requisite for Plier plug-in (both binary package and 113 subversion tree installs)is that apt-probeset_summarize is installed.125 Pre-requisite for Plier plug-in (both binary package and subversion 126 tree installs) to work is that apt-probeset_summarize is installed. 114 127 115 128 apt-probeset-summarize is available in the Affymetrix Power Tools … … 123 136 not succeeded. 124 137 125 ''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'' 139 140 You should install the external binaries, RMAExpressConsole (with the 141 DLLs in case of Microsoft Windows install) and apt-probeset-summarize, 142 such that they are readable for the user running your BASE application 143 server. The name of the binaries MUST be `RMAExpressConsole` and 144 `apt-probeset-summarize`, respectively. Also binaries must be copied 145 into the same directory as the plug-in (see item 2 or 3 below 146 depending on whether you perform a pre-compiled or source package 147 installation). These two conditions are hard coded in the plug-ins. 148 149 The install of the BASE plug-in it-self will succeed even if this 150 requisite is not fulfilled, but execution of the plug-in within BASE 151 will fail. 152 145 153 146 154 == 2. Compilation and installation from a subversion tree == … … 148 156 You should skip this section if you downloaded a pre-compiled package. 149 157 150 iv) When installing from a subversion working copy you must compile151 theplug-in, do158 When installing from a subversion working copy you must compile the 159 plug-in, do 152 160 153 161 `make` … … 182 190 == 3. Installation from a pre-compiled package == 183 191 184 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 192 You should skip this section if you use the subversion repository or a 193 source package. 194 195 Install the plug-in in the BASE application server file system. If 187 196 BASE is installed in `/usr/local/base` simply do 188 197 … … 212 221 == 4. BASE configuration == 213 222 214 === vi)Make BASE aware of the new plug-ins ===223 === Make BASE aware of the new plug-ins === 215 224 216 225 You need to perform the below steps for both plug-ins in this … … 240 249 plug-in. 241 250 251 242 252 == 5. Updating a plug-in in BASE. == 243 253 … … 255 265 This is straightforward: 256 266 257 - 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. -
trunk/se/lu/thep/affymetrix/README
r294 r345 35 35 define what reporter information is stored in BASE and how to change 36 36 what is stored, you may want to visit 37 http://base.thep.lu.se/chrome/site/doc/ admin/extended-properties.html37 http://base.thep.lu.se/chrome/site/doc/html/appendix/appendix.extendedproperties.html 38 38 before you start using your shiny BASE installation.'' 39 39 … … 45 45 package contains the RMAExpress and Plier plug-ins. 46 46 47 The RMAExpress plug-in is installed in the 48 [http://base2.thep.lu.se:8080/demo BASE2 demo server]. 47 The plug-ins in this package are installed in the 48 [http://base2.thep.lu.se:8080/demo BASE2 demo server]. You can try 49 them there before deciding to install them in your local BASE server. 49 50 50 51 For installation or updating instructions please see file INSTALL. … … 87 88 This section is a short introduction to get going with the plug-ins 88 89 and Affymetrix data in BASE. More documentation is available at 89 http://base.thep.lu.se/ wiki/Manuals and you should read them to learn90 how to useBASE.90 http://base.thep.lu.se/ and you should read them to learn how to use 91 BASE. 91 92 92 93 1. You need to install the plug-in and make BASE aware of the new … … 100 101 privileges, an ordinary BASE user does NOT have this privilege. 101 102 102 There is more than one way to create plug-in configurations. Here we103 outline the most straightforward route. There is a chapter in the104 BASE manual devoted for plug-in installation, follow the link above105 to find the document.103 There is more than one way to create plug-in configurations. Here 104 we outline the most straightforward route. There is a chapter in 105 the BASE manual devoted for plug-in installation, follow the link 106 above to find the document. 106 107 107 108 - First you need to create an plug-in configuration for the … … 133 134 the import by clicking 'Next' in the parameter dialog. 134 135 135 The reporter information is now in the database. You may delete the 136 AffyChip_annot.csv file from BASE if you wish, it is not needed 137 anymore. You may want to update reporter information when Affymetrix 138 releases a new version of their annotation but remember there is no 139 versioning for this type of information in BASE. If you update 140 reporter information you only need to redo the last step. 136 The reporter information is now in the database. You may delete 137 the AffyChip_annot.csv file from BASE if you wish, it is not 138 needed anymore. You may want to update reporter information when 139 Affymetrix releases a new version of their annotation but remember 140 there is no versioning for this type of information in BASE. If 141 you update reporter information you only need to redo the last 142 step. 141 143 142 144 3. You need to define the design of the !AffyChip in BASE, … … 188 190 189 191 7. You made it here. This means that the plug-in works and you are 190 ready to start using BASE. The get the most out of BASE you should191 now read the BASE manual and documentation available at192 http://base.thep.lu.se/wiki/Manuals192 ready to start using Affymetrix data in BASE. The get the most out 193 of BASE you should now read the BASE manual and documentation 194 available at http://base.thep.lu.se/
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