add installation instructions and remove HowToRun

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documentation/source/installation.rst

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+Installation & Run instructions
+==============
+
+Reference files
+^^^^^^^^^^^^^^^^
+To get all necessary reference files run the script $PATH_TO_PLUGIN_DIRECTORY/installation/downloadReferences.sh from the destination path for all files.
+Please convert the bigwig file in databases/UCSC to a BedGraph (https://genome.ucsc.edu/goldenpath/help/bigWig.html) and save it under wgEncodeCrgMapabilityAlign100mer_chr.bedGraph, 
+compress it with bgzip and index with tabix.
+The variable baseDirectoryReference in the project.xml  needs to be set to the path from which the downloader script was run.
+
+Software
+^^^^^^^^^
+All software required to run ACEseq is stored in Bioconda and can be downloaded to set up a conda environment. Specifications about the packages are given in `$PATH_TO_PLUGIN_DIRECTORY/resources/configurationFiles/analysisCopyNumberEstimation.xml`.
+
+The workflow contains a description of a [Conda](https://conda.io/docs/) environment. A number of Conda packages from [BioConda](https://bioconda.github.io/index.html) are required. You should set up the Conda environment at a centralized position available from all compute hosts. 
+
+First install the BioConda channels:
+
+::
+
+    conda config --add channels r
+
+::
+
+    conda config --add channels defaults
+
+::
+
+    conda config --add channels conda-forge
+
+::
+
+    conda config --add channels bioconda
+
+
+Then install the environment
+
+::
+
+	conda env create -n ACEseqWorkflow -f $PATH_TO_PLUGIN_DIRECTORY/resources/copyNumberEstimationWorkflow/environments/conda.yml
+
+
+Roddy-based version
+^^^^^^^^^^^^^^^^^^^^^
+The Roddy-based version can be downloaded from XYZ. The output directory can be specified within configurations/projectsACEseqTest.xml. Here the variables "baseDirectoryReference", "inputBaseDirectory", "outputBaseDirectory", "outputAnalysisBaseDirectory" need to be set. Additionally the SV=no and runWithSv=false needs to be set if SV breakpoints should not be included. Otherwise "svOutputDirectory" and the SV bedpe filename in the filenames section needs to be set.
+
+Technical specifications need to be set within the file configurations/applicationProperties.ini. The path to the project.xml and the path to the plugins ($PATH_TO_PLUGIN_DIRECTORY/Roddy/dist/plugins/ needs to be set under configurationDirectories and pluginDirectories. Finally the job manager and execution host need to be set.
+
+The execution can be Please have a look at the following default application properties ini
+file:
+
+.. code-block:: ini
+
+    [COMMON]
+    useRoddyVersion=current                     # Use the most current version for tests
+
+    [DIRECTORIES]
+    configurationDirectories=[FOLDER_WITH_CONFIGURATION_FILES]
+    pluginDirectories=[FOLDER_WITH_PLUGINS]
+
+    [COMMANDS]
+    jobManagerClass=de.dkfz.roddy.execution.jobs.direct.synchronousexecution.DirectSynchronousExecutionJobManager
+    #jobManagerClass=de.dkfz.roddy.execution.jobs.cluster.pbs.PBSJobManager
+    #jobManagerClass=de.dkfz.roddy.execution.jobs.cluster.sge.SGEJobManager
+    #jobManagerClass=de.dkfz.roddy.execution.jobs.cluster.slurm.SlurmJobManager
+    #jobManagerClass=de.dkfz.roddy.execution.jobs.cluster.lsf.rest.LSFRestJobManager
+    commandFactoryUpdateInterval=300
+    commandLogTruncate=80                       # Truncate logged commands to this length. If <= 0, then no truncation.
+
+    [COMMANDLINE]
+    CLI.executionServiceUser=USERNAME
+    CLI.executionServiceClass=de.dkfz.roddy.execution.io.LocalExecutionService
+    #CLI.executionServiceClass=de.dkfz.roddy.execution.io.SSHExecutionService
+    CLI.executionServiceHost=[YOURHOST]
+    CLI.executionServiceAuth=keyfile
+    #CLI.executionServiceAuth=password
+    CLI.executionServicePasswd=
+    CLI.executionServiceStorePassword=false
+    CLI.executionServiceUseCompression=false
+    CLI.fileSystemInfoProviderClass=de.dkfz.roddy.execution.io.fs.FileSystemInfoProvider
+
+
+::
+
+    sh $PATH_TO_PLUGIN_DIRECTORY/Roddy/roddy.sh rerun ACEseq@copyNumberEstimation $pid \
+    --useconfig=$PATH_TO_PLUGIN_DIRECTORY/applicationProperties.ini \
+    --cvalues="bamfile_list:$pathToControlBamFile;$pathToTumorBamFile,sample_list:control;tumor,possibleControlSampleNamePrefixes:control,possibleTumorSampleNamePrefixes:tumor"
+
+
+More information on Roddy can be found `here <https://roddy-documentation.readthedocs.io/>`_.
+
+Docker version
+^^^^^^^^^^^^^^^
+The Docker-based version can be downloaded form XYZ.