https://sourceforge.net/p/altanalyze/wiki/DBaseInstallationError/Recent changes to DBaseInstallationErrorenSat, 01 Feb 2014 01:06:52 -0000https://sourceforge.net/p/altanalyze/wiki/DBaseInstallationError/<div class="markdown_content"><h3 id="why-does-altanalyze-crash-when-trying-to-download-the-database-when-first-run"><em>Why Does <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a> crash when trying to download the database when first run?</em></h3> <p><em><strong>Answer:</strong></em>: The first time <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a> is opened, the user will be prompted to allow <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a> to establish an internet connection to download a species database. Since some locations have restricted proxy settings, an error may appear here, preventing an internet connection (note: this error is properly reported in version 1.16 of <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a>, but still prevents proper download). </p> <p>Although to properly fix this issue, <a href="http://www.altanalyze.org" rel="nofollow">http://www.altanalyze.org</a> will need to be allowed proxy access, the species databases can also be downloaded manually using the following steps: </p> <p><em>Note: the following steps are for human exon array analysis. If this is not the case, see the "Alternative Species/Array Instruction" first.</em></p> <h4 id="download-and-extract-following-zip-files">Download and extract following zip files:</h4> <ol> <li>Download the alternative exon database for your species <a class="" href="http://altanalyze.org/archiveDBs/AltDatabase/updated" rel="nofollow">here</a> (e.g., <a class="" href="../EnsMart55">EnsMart55</a>/Hs.zip for the latest human Exon 1.0 and Gene 1.0 database) to "<a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a>_v2release/<a class="" href="../AltDatabase">AltDatabase</a>". If not analyzing human, mouse or rat, download the species archive with the extension "RNASeq.zip". </li> <li>Download the GO-Elite database for your species <a class="" href="http://altanalyze.org/archiveDBs/Databases/" rel="nofollow">here</a> (e.g., <a class="" href="../EnsMart55">EnsMart55</a>/Hs.zip for the latest human annotations) to the folder "<a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a>_v1release/<a class="" href="../AltDatabase">AltDatabase</a>/<a class="" href="../EnsMart55">EnsMart55</a>/goelite" (<a class="" href="../EnsMart55">EnsMart55</a> is used as an example). </li> <li>Download the GO-Elite OBO.zip file from <a class="" href="http://altanalyze.org/archiveDBs/Databases/" rel="nofollow">here</a> to the same goelite folder as in #2 and extract. </li> <li>Download the configuration files "species_all.txt", "array_versions.txt" and "source_data.txt" from <a class="" href="http://www.altanalyze.org/archiveDBs/Config/" rel="nofollow">here</a> to the folder "Config". Although these files are already present, they are over-written as blank files when trying to connect online. </li> </ol> <h4 id="optional"><em>OPTIONAL</em></h4> <h4 id="download-and-extract-affymetrix-library-files-to-altanalyze_v1releaseaffymetrixlibraryfiles">Download and extract Affymetrix library files to "<a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a>_v1release/affymetrix/<a class="" href="../LibraryFiles">LibraryFiles</a>":</h4> <p>1) Download the .pgf, .clf and .bgp zip gzip files for your array from <a class="" href="http://altanalyze.org/archiveDBs/LibraryFiles" rel="nofollow">here</a>. Human arrays have the prefix "Hu", mouse "Mo" and rat "Ra". Exon arrays .contain "Ex" in the filename, whereas gene arrays have "Gene". </p> <p>Once completed, you should be ready to run <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a> and will not be prompted to download any files. For assistance, <a class="" href="/p/altanalyze/wiki/ContactUs/">ContactUs</a>. </p></div>AnonymousSat, 01 Feb 2014 01:06:52 -0000https://sourceforge.net2dce5d4c50d78438233290151c2ff9d230f36f7e