Changeset 776


Ignore:
Timestamp:
Sep 18, 2008, 7:21:18 PM (14 years ago)
Author:
Jari Häkkinen
Message:

Addresses #137.

Location:
plugins/base1
Files:
2 added
3 edited
3 copied
1 moved

Legend:

Unmodified
Added
Removed
  • plugins/base1/se.lu.onk.MergeBioAssay/trunk/README

    r772 r776  
    11$Id$
    22
    3 = About `se.lu.onk.ReplicateError` =
     3= About `se.lu.onk.MergeBioAssay` =
    44
    5 The `se.lu.onk.ReplicateError` plug-in for BASE is
     5The `se.lu.onk.MergeBioAssay` plug-in for BASE is
    66
    7 `se.lu.onk.ReplicateError` is free software. See the file license.txt for
     7`se.lu.onk.MergeBioAssay` is free software. See the file license.txt for
    88copying conditions.
    99
     
    1414== Downloading ==
    1515
    16 `se.lu.onk.ReplicateError` can be obtained from
     16`se.lu.onk.MergeBioAssay` can be obtained from
    1717
    1818  http://baseplugins.thep.lu.se/wiki/PluginDownload
     
    2626http://baseplugins.thep.lu.se. These installation instructions only
    2727describe how to get the plug-in to work with the Base1PluginExecuter
    28 in the latest BASE version 2. BASE 1.2 installers should enable one
    29 line in files AAtabs.html and WAtabs.html, read the information in
    30 these short files.''
     28in the latest BASE version 2.''
    3129
    3230If you downloaded a binary package you only need to follow these
     
    4240{{{
    4341  # cd /path/to/base/plugins
    44   # download ReplicateError-version.tgz
    45   # untar ReplicateError-version.tgz
    46   # ln -s ReplicateError-version ReplicateError
     42  # download MergeBioAssay-version.tgz
     43  # untar MergeBioAssay-version.tgz
     44  # ln -s MergeBioAssay-version MergeBioAssay
    4745}}}
    48 The symbolical link in the last line above allows for easier change to
     46The symbolic link in the last line above allows for easier change to
    4947future version of the plug-in.
    5048{{{
    5149  # Log in to your BASE as admin
    52   # Upload the configuration files `pluginConfigurationAA.base` and
    53     `pluginConfigurationWA.base`.
    54   # Create/update one configuration each for across and within assays
    55     mode of the ReplciateError plug-in where you select the plug-in
    56     defintion files `pluginConfigurationAA.base` and
    57     `pluginConfigurationWA.base`, respectively. BASE will respond that
    58     plug-ins where configured but ...
    59   # Re-configure the plug-ins without selecting a file, set the
    60     `Plugin executables path` and proceed to next window by clicking
     50  # Upload the configuration file `mergebioassay.base`
     51  # Create/update a configuration for the plug-in where you select the
     52    plug-in defintion files `mergebioassay.base`. BASE will respond
     53    that plug-ins where configured but ...
     54  # Re-configure the plug-in without selecting a file, set the `Plugin
     55    executables path` and proceed to next window by clicking
    6156    `Next`. This is explained in the BASE documentation and needs to
    6257    be done even when you update your plug-in.
    6358  # In this parameter window set the `Name of executable`. The value
    6459    of this parameter and `Plugin executables path` should add up to
    65     the absolute path to the binaries `runAA` and `runWA`, i.e.,
    66     /path/to/base/plugins/ReplicateError/runAA. How this string looks
     60    the absolute path to the binary `run`, i.e.,
     61    /path/to/base/plugins/MergeBioAssay/run. How this string looks
    6762    like depends on your plug-in directory structure.
    6863  # Test the plug-ins and when you are satisfied, share it to your
     
    7368== Compiling ==
    7469
    75 You must checkout the `se.lu.onk.ReplicateError` from the repository,
     70You must checkout the `se.lu.onk.MergeBioAssay` from the repository,
    7671follow the instructions below. Then download and untar the
    7772`se.lu.onk.BaseFile` package available from
     
    8075{{{
    8176  check out project, see instructions below
    82   # cd /path/to/se.lu.onk.ReplicateError
     77  # cd /path/to/se.lu.onk.MergeBioAssay
    8378  # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz
    8479  # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz.MD5
     
    9186It is important that the `BaseFile` package is located in directory
    9287`BaseFile`. Now simple issue `ant`. This will create a jar file
    93 `dist/ReplicateError.jar`.
     88`dist/MergeBioAssay.jar`.
    9489
    9590
    9691== Creating a distribution ==
    9792
    98 Update the version number (make sure they match) in `build.xml`,
    99 `lib/pluginConfigurationAA.base`, and `lib/pluginConfigurationWA.base`.
    100 Issue `ant package`. This creates a distribution package with all
    101 required components, including BaseFile.jar and associated files.
     93Update the version number in `build.xml`, and issue `ant
     94package`. This creates a distribution package with all required
     95components, including BaseFile.jar and associated files.
    10296
    10397
    10498== Bug Reporting ==
    10599
    106 You can report `se.lu.onk.ReplicateError` bugs on
     100You can report `se.lu.onk.MergeBioAssay` bugs on
    107101
    108102  http://baseplugins.thep.lu.se/newticket
     
    113107== Subversion Access ==
    114108
    115 The `se.lu.onk.ReplicateError` source repository is available via anonymous
     109The `se.lu.onk.MergeBioAssay` source repository is available via anonymous
    116110subversion access, issue:
    117111
    118   `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.ReplicateError/trunk se.lu.onk.ReplicateError`
     112  `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.MergeBioAssay/trunk se.lu.onk.MergeBioAssay`
    119113
    120114There is no guarantees about the contents or quality of the latest
     
    122116is known to be broken to be committed to the repository. Use at your
    123117own risk. You may prefer to check out a released version instead, then
    124 replace `trunk` with `tags/release-number` in the above example.
     118replace `trunk` with `tags/version` in the above example.
    125119
    126120
     
    130124Copyright (C) 2008 Jari Häkkinen
    131125
    132 This file is part of the se.lu.onk.ReplicateError plug-in for
     126This file is part of the se.lu.onk.MergeBioAssay plug-in for
    133127BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site is
    134128http://base.thep.lu.se
  • plugins/base1/se.lu.onk.MergeBioAssay/trunk/build.xml

    r771 r776  
    66    Copyright (C) 2008 Jari Hakkinen
    77
    8     This file is part of the se.lu.onk.ReplicateError plug-in for
     8    This file is part of the se.lu.onk.MergeBioAssay plug-in for
    99    BASE. Available at http://baseplugins.thep.lu.se/ and BASE web
    1010    site is http://base.thep.lu.se
     
    2323    along with BASE. If not, see <http://www.gnu.org/licenses/>.
    2424-->
    25 <project name="se.lu.onk.ReplicateError plug-in for BASE"
     25<project name="se.lu.onk.MergeBioAssay plug-in for BASE"
    2626         default="dist" basedir=".">
    2727  <description>
    28     This build file is used for se.lu.onk.ReplicateError plug-in for
     28    This build file is used for se.lu.onk.MergeBioAssay plug-in for
    2929    BASE created at the Department of Oncology, Lund University,
    3030    Sweden.
     
    4040       1.0, 1.1, 1.2pre
    4141    -->
    42   <property name="version" value="1.3pre" />
     42  <property name="version" value="2.1pre" />
    4343
    4444  <property name="basefilejar" value="BaseFile" />
    4545  <property name="build" location="build" />
    4646  <property name="dist" location="dist" />
    47   <property name="lib" location="lib" />
    48   <property name="package" value="replicateerror"/>
    49   <property name="packagestring" value="ReplicateError-${version}" />
     47  <property name="doc" location="doc" />
     48  <property name="package" value="mergebioassay"/>
     49  <property name="packagestring" value="MergeBioAssay-${version}" />
    5050  <property name="src" location="src" />
    5151 
     
    8787  <target name="dist" depends="compile">
    8888    <mkdir dir="${dist}" />
    89     <jar destfile="${dist}/ReplicateError.jar">
     89    <jar destfile="${dist}/MergeBioAssay.jar">
    9090      <fileset dir="${build}" />
    9191      <manifest>
    9292        <attribute name="Built-By" value="${user.name}"/>
    93         <attribute name="Main-Class" value="replicateerror.ReplicateError"/>
     93        <attribute name="Main-Class" value="mergebioassay.MergeBioAssay"/>
    9494      </manifest>
    9595    </jar>
     
    104104    <mkdir dir="${package}/${basefilejar}"/>
    105105    <copy todir="${package}">
    106       <fileset file="${dist}/ReplicateError.jar" />
    107       <fileset dir="${lib}" />
     106      <fileset file="${dist}/MergeBioAssay.jar" />
     107      <fileset dir="${doc}" />
    108108      <fileset file="license.txt" />
    109109      <fileset file="README" />
     
    112112      <fileset dir="${basefilejar}" />
    113113    </copy>
    114     <replace file="${package}/pluginConfigurationAA.base">
    115       <replacefilter
    116         token="@VERSION@"
    117         value="${version}"
    118       />
    119     </replace>
    120     <replace file="${package}/pluginConfigurationWA.base">
     114    <replace dir="${package}">
     115      <include name="*.base" />
    121116      <replacefilter
    122117        token="@VERSION@"
  • plugins/base1/se.lu.onk.MergeBioAssay/trunk/doc/mergebioassay.base

    r181 r776  
    22section plugin
    33uniqueName  onk.lu.se/johan_enell/merge_bioassays
    4 versionNumber 2.0
     4versionNumber @VERSION@
    55name  Transformation: Merge bioassays
    66descr Using this plugin base-users can merge together bioassays by grouping them according to annotation types or syntactical differences in the name. There are four different method for calculating the new values. They differ in what kind of mean they are using (arithmetic or geometric) and if they are merging on ratio or intensity. \r\n\r\nFor each group the parents are saved so the link to the raw data is preserved. Annotations for the bioassays are saved if sample1 is the same for each assay in each group.\r\n\r\nIMPORTANT\r\nIf you have merged assays in a group, BASE 1.2.10 will have difficulties to export data Merged on reporter from the parents RawBioAssays. If you for instance export '[Raw] Spot diameter' for a merged assay, each reporter might be associated with values from several RawBioAssays but only one such value will be exported. This is a known limitation of base 1.2.10 and will be fix in future versions. \r\n\r\nMerge methods\r\n\r\nGeometric mean of ratio:\r\n  This method calculates the geometric mean of the ratios in each group per position.\r\n\r\nArithmetic mean of ratio:\r\n  This method calculates the arithmetic mean of the ratios in each group per position.\r\n\r\nArithmetic mean of intensity:\r\n  This method calculates the arithmetic mean of the intensities in each group per position.\r\n\r\nRatio of ratio:\r\n  This method works a little bit different from the others. It demands that each group consists of exactly two bioassays. Then it will create a new ratio for each spot with one of the assays over the other, depending on what the user has specified in the ratio parameters. \r\n\r\nPARAMETERS:\r\nAssayname\r\nGroup\r\nNew name\r\nMerge method\r\nRatio\r\n\r\n\r\nAssayname - This parameter specifies how the name of the assays is constructed. Use  %0-%9 as wildcards and then put any character(s) between as delimiters. For example assay name Assay_1_A can be divided into three parts. By setting the parameter to %1_%2_%3 the plugin will read assay name assay_1_A and set %1=Assay, %2=1 and %3=A. Thus, if your assays have names constructed in the same way merge can sort the assays in groups depending on %1, %2 or %3.\r\n\r\nGroup - This will specify how the assays will be grouped together. It can either be a %-number used in assayname or an annotation type.\r\n\r\nExample1: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be sorted into groups of assays using merge.\r\n \r\n 1a: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222 = %2 will sort the assays into two groups.\r\n\r\n One group were %2=1 (assays Assay_1_A and Assay_1_B)\r\n One group were %2=2  (assays Assay_2_A and Assay_2_B) \r\n\r\n 1b: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222 = %3 will sort the assays into two groups.\r\n\r\n One group were %3=A (assays Assay_1_A and Assay_2_A)\r\n One group were %3=B  (assays Assay_1_B and Assay_1_B) \r\n\r\nNew name - This text will be used in the name of the new merged assays. The name will be this string followed by the groupname.\r\n\r\nMerge method - Choose one of the methodes described above.\r\n\r\nRatio - If merge method "ratio of ratio" is chosen the form of the ratio must be specified. This is done either in the ratio parameter or in ratio annotation type and ratio annotation value. In the ratio parameter you can choose a  %-number followed by the two values it can take. The last character in the string must be the delimiter the user has choosen ot use. The other way a user can specify the ratio is by choosing an annotation type in the list and specify the values in the annotation values parameter. This is done by writing the values with the delimiter used last. \r\n\r\nex.\r\n\r\n%1|vr1|vr2|\r\n\r\nThis will take the values from %1 in the assayname and put the assay with value vr1 over the assay with values vr2. Notice that the final character is the delimiter (this can of course be any character).\r\n\r\nExample2: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be sorted into groups of assays using merge.\r\n\r\n 1a: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222  = %2 will sort the assays into two groups.\r\n\r\n One group were %2=1 (assays Assay_1_A and Assay_1_B)\r\n One group were %2=2  (assays Assay_2_A and Assay_2_B)\r\n\r\nBy setting parameter \221Ratio\222 = %3|A|B| ratios of ratios will be created as:\r\n        Assay_1_A / Assay_1_B\r\n        Assay_2_A / Assay_2_B\r\n \r\nArithmetic mean\r\nhttp://mathworld.wolfram.com/ArithmeticMean.html\r\nGeometric mean\r\nhttp://mathworld.wolfram.com/GeometricMean.html\r\n
  • plugins/base1/se.lu.onk.MergeBioAssay/trunk/doc/run

    r704 r776  
    22
    33progdir="`dirname \"$0\"`"
    4 java -cp "$CLASSPATH:$progdir/mergebioassay.jar" mergebioassay/MergeBioAssay stdin.txt
     4java -cp "$CLASSPATH:$progdir/BaseFile/BaseFile.jar:$progdir/mergebioassay.jar" mergebioassay/MergeBioAssay stdin.txt
  • plugins/base1/se.lu.onk/trunk/build.xml

    r758 r776  
    1717  <property name="lib" location="lib" />
    1818  <property name="virtualarray.lib" location="VirtualArray/lib" />
    19   <property name="mergebioassay.doc" location="MergeBioAssay/doc" />
    2019  <property name="qpackage.lib" location="QPackage/lib" />
    2120  <property name="smooth.doc" location="smooth/doc" />
     
    2423  <property name="basefile.src" location="BaseFile/src" />
    2524  <property name="virtualarray.src" location="VirtualArray/src" />
    26   <property name="mergebioassay.src" location="MergeBioAssay/src" />
    2725  <property name="qpackage.src" location="QPackage/src" />
    2826  <property name="center.src" location="Center/src" />
     
    3836  <property name="basefile.bin" location="${bin}/BaseFile" />
    3937  <property name="virtualarray.bin" location="${bin}/VirtualArray" />
    40   <property name="mergebioassay.bin" location="${bin}/MergeBioAssay" />
    4138  <property name="qpackage.bin" location="${bin}/QPackage" />
    4239  <property name="center.bin" location="${bin}/Center" />
     
    5249 
    5350  <!-- package -->
    54   <property name="mergebioassay.pac" value="${dist}/mergebioassay"/>
    5551  <property name="smooth.pac" value="${dist}/smooth"/>
    5652
     
    6864  <target name="compile" description="--> Compiles all the packages">
    6965    <ant target="virtualarray.compile" />
    70     <ant target="mergebioassay.compile" />
    7166    <ant target="qpackage.compile" />
    7267    <ant target="center.compile" />
     
    105100 
    106101  <!-- - - - - - - - - - - - - - - - - -
    107       target: mergebioassay.compile
    108      - - - - - - - - - - - - - - - - - -->
    109     <target name="mergebioassay.compile" depends="basefile.compile">
    110       <mkdir dir="${mergebioassay.bin}"/>
    111       <javac
    112         srcdir="${mergebioassay.src}"
    113         destdir="${mergebioassay.bin}"
    114         classpath="${basefile.bin}"
    115         debug="true"
    116         deprecation="true"
    117         encoding="ISO-8859-1"
    118       />
    119     </target>
    120  
    121   <!-- - - - - - - - - - - - - - - - - -
    122102      target: qpackage.compile
    123103     - - - - - - - - - - - - - - - - - -->
     
    254234    ================================== -->
    255235  <target name="dist"
    256     depends="virtualarray.dist, mergebioassay.dist,
     236    depends="virtualarray.dist,
    257237      qpackage.dist, center.dist, lowess.dist, smooth.dist"
    258238    description="--> Creates a ditributable gzipfile for each package">
     
    277257 
    278258  <!-- - - - - - - - - - - - - - - - - -
    279       target: mergebioassay.dist                     
    280      - - - - - - - - - - - - - - - - - -->
    281   <target name="mergebioassay.dist" depends="mergebioassay.compile">
    282     <mkdir dir="${dist}" />
    283     <jar destfile="${dist}/mergebioassay.jar">
    284       <fileset dir="${basefile.src}" />
    285       <fileset dir="${basefile.bin}" />
    286       <fileset dir="${mergebioassay.bin}" />
    287       <fileset dir="${mergebioassay.src}" />
    288         <manifest>
    289           <attribute name="Built-By" value="${user.name}"/>
    290           <attribute name="Main-Class" value="mergebioassay.MergeBioAssay"/>
    291         </manifest>
    292     </jar>
    293   </target>
    294  
    295   <!-- - - - - - - - - - - - - - - - - -
    296259      target: qpackage.dist                     
    297260     - - - - - - - - - - - - - - - - - -->
     
    429392 
    430393 
    431   <!-- =================================
    432       target: mergebioassay.package             
    433      ================================= -->
    434   <target name="mergebioassay.package" depends="mergebioassay.dist" description="--> Create a zip file containting all files necessary for distribution.">
    435     <mkdir dir="${mergebioassay.pac}"/>
    436     <copy file="${dist}/mergebioassay.jar" todir="${mergebioassay.pac}" />
    437     <copy file="${doc}/gpl.txt" todir="${mergebioassay.pac}" />
    438     <copy file="${mergebioassay.doc}/INSTALL.txt" todir="${mergebioassay.pac}" />
    439     <copy file="${mergebioassay.doc}/mergebioassay.base" todir="${mergebioassay.pac}" />
    440     <copy file="${mergebioassay.doc}/run" todir="${mergebioassay.pac}" />
    441     <zip destfile="mergebioassay.zip" basedir="${mergebioassay.pac}" />
    442   </target>
    443 
    444394  <!-- =================================
    445395      target: smooth.package             
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