Changeset 629


Ignore:
Timestamp:
Mar 13, 2008, 12:01:09 PM (13 years ago)
Author:
Nicklas Nordborg
Message:

References #89: Installation program and documentation

Preparing for release. Added some more information to README_SNP.

Location:
plugins/base2/net.sf.basedb.illumina/trunk
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • plugins/base2/net.sf.basedb.illumina/trunk/INSTALL

    r624 r629  
    3636 1. Unpack the tar.gz file to a directory of your choice.
    3737 2. Stop your Tomcat server that is running BASE and all job agents, if any.
    38  3. Copy the illumina-plugins-xxx.jar (where xxx depends on the version number)
    39     to your BASE plug-ins directory. This directory is specified by the
    40     'plugins.dir' option in your base.config file and defaults to
    41     <basedir>/plugins.[[BR]]   
    42     If you have job agents that are running from another location, copy
    43     the jar file to a location the job agents has access to.   
     38 3. Copy the illumina-plugins.jar to your BASE plug-ins directory. This directory
     39    is specified by the 'plugins.dir' option in your base.config file and defaults
     40    to <basedir>/plugins.[[BR]]   
     41    If you have job agents that are running from another location, you must also
     42    copy the jar file to a location the job agents has access to.   
    4443 4. From the ''config'' directory, copy:
    4544     * ''illumina-extended-properties.xml'' to <basedir>''/www/WEB-INF/classes/extended-properties/''
     
    7069    agents as well.
    7170   
    72 Make sure that the job agents have access to the illumina-plugins-xxx.jar file,
     71Make sure that the job agents have access to the illumina-plugins.jar file,
    7372and to the same raw data types and extended property configurations files as
    7473the Tomcat web server. If the job agents are not running from the same BASE
    7574installation directory, you may need to copy the files to a proper location.
    76 We recommend that you always put the illumina-plugins-xxx.jar inside the
     75We recommend that you always put the illumina-plugins.jar inside the
    7776plugins.dir directory. If you do, BASE will automatically find the JAR file
    7877in job agents. Otherwise, you may have to configure the JAR path manually
  • plugins/base2/net.sf.basedb.illumina/trunk/README_SNP

    r628 r629  
    3232== Illumina SNP raw data files files ==
    3333
    34 TODO
     34The SNP raw data files are created from BeadStudio and may contain multiple
     35samples. The file should be saved as a tab-separated text file. The first
     36line is the header line which contains the column names. Some of the columns
     37are specific for each sample, some are common columns valid for all samples.
     38Sample specific columns are prefixed with the sample name, followed by a dot
     39that is followed by a generic column name. For example, UC199_B.GType, where
     40UC199_B is the sample name and GType is the generic column name. The following
     41table lists the columns that are required by the plug-ins in this package.
     42
     43|| '''Column'''   || '''Column type''' || '''Example value''' ||
     44|| Address        || Common            || 830575              ||     
     45|| GenTrain Score || Common            || 0,8607027           ||
     46|| GType          || Sample            || BB                  ||
     47|| Log R Ratio    || Sample            || 0,1801754           ||
     48|| B Allele Freq  || Sample            || 1                   ||
     49
     50If any of those columns are missing, the plug-ins may not function correctly.
     51Additional columns, both common and sample-specific, may be present in the data
     52file. When the import plug-in parses the input file it will split the file into
     53one file for each sample. The new files will include all common columns, and
     54all sample columns for a specific sample. The column headers in the new files
     55only includes the generic column name, without the sample name prefix.
     56
    3557
    3658== Illumina SNP manifest files ==
     
    124146in step 3 are shared to the appropriate users, for example, the Everyone group.
    125147
     148== Analyzing SNP data ==
     149
     150The first step is to create a root bioassayset. To do this:
     151
     152 1. Goto the "Bioassay sets" tab of your experiment.
     153 2. Click on the "New root bioassayset" button.
     154 3. This should start the "Illumina SNP root biassayset creator" plug-in.
     155 4. You must tell it which raw data sets to use.
     156 5. You may also have to specify character set and/or which decimal separator
     157    that is used in your data files.
     158 6. Finish the job registration and wait for the plug-in to complete.
     159 
     160The above procedure creates a root bioassayset which means that data from the files
     161are imported into the database. BASE can only store data as numeric values in a
     162predetermined number of "channels". The number of channels for SNP data is 3, which
     163means that 3 data columns can be imported. Besides this, the Address column is
     164imported as the 'position' value. This means that plug-ins that are used later in
     165the analysis have the possibility to extract other columns directly from the data
     166files, simply by finding the row which has the same Address value as the position.
     167
     168Note! This position->Address relation is guaranteed to be correct only for
     169bioassay sets living in the same "data cube" as the root bioassay set.
     170During the analysis, other plug-ins may decide to create a new "data cube",
     171re-arrange the position numbers and break the mapping.
     172
     173The table below shows how data from the file are imported into the database.
     174
     175|| '''Column'''   || '''Imported to'''                                 ||
     176|| Address        || position                                          ||
     177|| GType          || ch(1): AA=1.0, AB=0.0, BB=-1.0, Other values=null ||
     178|| Log R Ratio    || ch(2)                                             ||
     179|| B Allele Freq  || ch(3)                                             ||
     180
     181Tip! The installation program has created 3 formulas: GType=ch(1),
     182Log R Ratio=ch(2) and B Allele Freq=ch(3). The formulas can be used when
     183displaying or plotting data instead of the channel numbers. It means no
     184real difference, except that the formula names will be used in column
     185headers, etc. instead of the generic channel numbers.
  • plugins/base2/net.sf.basedb.illumina/trunk/build.xml

    r585 r629  
    77  <!-- variables used -->
    88  <property name="name" value="illumina-plugins" />
    9   <property name="version" value="1.0pre" />
     9  <property name="version" value="1.0" />
    1010  <property name="src" location="src" description="Location of source files" />
    1111  <property name="build" location="build" description="Location of compiled files" />
     
    3939  <target
    4040    name="dist"
    41     depends="build"
     41    depends="clean,build"
    4242    >
    4343    <copy todir="${dist}">
    44       <fileset dir="." includes="README,LICENSE,INSTALL" />
     44      <fileset dir="." includes="README*,LICENSE,INSTALL" />
    4545      <fileset dir="." includes="config/*" />
    4646    </copy>
     
    4949  <target
    5050    name="package"
    51     depends="clean,dist"
     51    depends="dist"
    5252    description="Create binary distribution package"
    5353    >
     
    8282    description="Compiles the plugin and put in jar"
    8383    >
    84     <property name="jar" value="${name}-${version}.jar" />
     84    <property name="jar" value="${name}.jar" />
    8585    <mkdir dir="${build}" />
    8686    <javac
     
    9999    </copy>
    100100    <replace token="%%plugins.jar%%" value="${jar}" file="${build}/META-INF/base-plugins.xml" />
    101 
    102 
    103101    <jar
    104102      jarfile="${dist}/${jar}"
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