Offline Support for AltAnalyze
When starting AltAnalyze 2.0 and greater, it will require the download of multiple zipped database files. If you do not have an internet connection on that machine or AltAnalyze is unable to download the necessary files due to a proxy, firewall or other issue, follow the below directions.
On a machine with support for downloading files through http, download the following files from http://altanalyze.org/archiveDBs/. This example assumes the user is working with human or Hs data.
Base Download Files
Primary Gene Database
.../AltDatabase/updated/EnsMart65/Hs.zip (save to AltDatabase folder and extract)
Lineage Profiler Database
.../AltDatabase/updated/EnsMart65/Hs_LineageProfiler.zip (save to AltDatabase/EnsMart65/ensembl and extract)
GO-Elite Annotation Database
.../Databases/EnsMart65Plus/Hs.zip (save to AltDatabase/EnsMart65/goelite and extract
GO-Elite Ontology Database
.../Databases/EnsMart65Plus/OBO.zip (save to AltDatabase/EnsMart65/goelite and extract)
Support for Junction Arrays and RNA-Seq
If you want to perform a Affymetrix junction array or an RNA-Seq analysis, additionally download the following to the folder AltDatabase and extract:
.../AltDatabase/updated/EnsMart65/Hs_junction_Glue.zip (Glue array)
Microarray Library Files
Affymetrix arrays require library files to be downloaded. These can be obtained from the manufacturer or obtained from here.
Download ALL of the files for your array to AltAnalyze/AltDatabase/affymetrix/LibraryFiles and extract.
When running the python source-code directly, other Python specific dependencies will be need to be installed to support data visualization, clustering and QC analyses. See here for more details.