From 70a112c27c573b79d8d5f25f0116767c36231bb3 Mon Sep 17 00:00:00 2001 From: kleinhei Date: Wed, 30 Aug 2017 21:18:49 +0200 Subject: [PATCH] add installation instructions and remove HowToRun --- documentation/source/HowToRun.rst | 12 --- documentation/source/_static/default.css | 3 + documentation/source/installation.rst | 94 ++++++++++++++++++++++++ 3 files changed, 97 insertions(+), 12 deletions(-) delete mode 100644 documentation/source/HowToRun.rst create mode 100644 documentation/source/_static/default.css create mode 100644 documentation/source/installation.rst diff --git a/documentation/source/HowToRun.rst b/documentation/source/HowToRun.rst deleted file mode 100644 index 267dc71..0000000 --- a/documentation/source/HowToRun.rst +++ /dev/null @@ -1,12 +0,0 @@ -How to Run -=========== - - - - -noControl -=== - - -rescueControl -==== diff --git a/documentation/source/_static/default.css b/documentation/source/_static/default.css new file mode 100644 index 0000000..b07bdb1 --- /dev/null +++ b/documentation/source/_static/default.css @@ -0,0 +1,3 @@ +.wy-nav-content { + max-width: none; +} diff --git a/documentation/source/installation.rst b/documentation/source/installation.rst new file mode 100644 index 0000000..68a7b77 --- /dev/null +++ b/documentation/source/installation.rst @@ -0,0 +1,94 @@ +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 `_. + +Docker version +^^^^^^^^^^^^^^^ +The Docker-based version can be downloaded form XYZ.