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ConstellationMap

A downstream visualization and analysis tool for gene set enrichment results with interactive web visualizer.

Language:
R;Java
Operating System:
any
Original Author:
Felix Wu;Broad Institute
Uploaded by:
flwu on January 14, 2016 11:20
Version Comment:
Initial production release.

Private server installation instructions for ConstellationMap

Posted by flwu on January 25, 2016 12:54

A kind user recently alerted us to the fact that private installations of ConstellationMap are failing due to a faulty manifest file, which prevents required R packages from automatically loading during installation of the module. We aim to fix the manifest file in a future version of ConstellationMap. For now, please either use the public GenePattern server's instance of ConstellationMap (http://genepattern.broadinstitute.org) or follow the instructions below to install ConstellationMap on a private server. 1. Install ConstellationMap v1.2 from GParc on your private GenePattern server (requires module author privileges) 2. Download the following source archives to some local directory (e.g., ~/Downloads). https://cran.r-project.org/src/contrib/Archive/CvM2SL2Test/CvM2SL2Test_2.0-1.tar.gz https://cran.r-project.org/src/contrib/Archive/MASS/MASS_7.3-33.tar.gz https://cran.r-project.org/src/contrib/calibrate_1.7.2.tar.gz https://cran.r-project.org/src/contrib/getopt_1.20.0.tar.gz https://cran.r-project.org/src/contrib/Archive/gmodels/gmodels_2.15.4.1.tar.gz https://cran.r-project.org/src/contrib/Archive/gtools/gtools_3.4.1.tar.gz https://cran.r-project.org/src/contrib/Archive/maptools/maptools_0.8-30.tar.gz https://cran.r-project.org/src/contrib/Archive/optparse/optparse_1.2.0.tar.gz https://cran.r-project.org/src/contrib/parmigene_1.0.2.tar.gz https://cran.r-project.org/src/contrib/Archive/plotrix/plotrix_3.5-7.tar.gz https://cran.r-project.org/src/contrib/Archive/rgl/rgl_0.93.996.tar.gz https://cran.r-project.org/src/contrib/Archive/smacof/smacof_1.5-0.tar.gz https://cran.r-project.org/src/contrib/Archive/verification/verification_1.40.tar.gz https://cran.r-project.org/src/contrib/Archive/sp/sp_1.0-17.tar.gz https://cran.r-project.org/src/contrib/Archive/fields/fields_8.2-1.tar.gz https://cran.r-project.org/src/contrib/Archive/boot/boot_1.3-16.tar.gz https://cran.r-project.org/src/contrib/CircStats_0.2-4.tar.gz https://cran.r-project.org/src/contrib/Archive/dtw/dtw_1.17-1.tar.gz 3. Start an R session (make sure it's R-3.0) and install the packages with the following command: > install.packages("/path/to/package/archive.tar.gz", lib="$GP_HOME/patches/rlib/3.0/site-library", repos=NULL, type="source") where "/path/to/package/archive.tar.gz" is the path to a downloaded source archive and "$GP_HOME" is the home directory of your GenePattern server. The install.packages(...) command should be executed for each package archive. 4. Run a ConstellationMap job. If there are no package-related errors, then package installation was done successfully. Please contact gp-help@broadinstitute.org if you have further questions or issues. -Felix

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