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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| README.txt | 2009-11-09 | 2.9 kB | |
| pathogen_data.tgz | 2009-11-06 | 3.3 GB | |
| gff3_validator_v.2.50.tgz | 2009-11-06 | 67.8 kB | |
| pathogen_portal_final_release_jcvi.tar.gz | 2009-11-06 | 116.1 MB | |
| pathogen_portal_mt4.sql.gz | 2009-11-03 | 74.7 MB | |
| Totals: 5 Items | 3.5 GB | 0 |
Pathogen Portal README Summary of the Pathogen Portal All of the files are available on SourceForge at https://sourceforge.net/projects/pathogenportal/files/ # ------------------------------------------------------------------------------ # Install Movable Type 4.x # ------------------------------------------------------------------------------ a. Follow the instructions to install Movable Type http://www.movabletype.org/documentation/installation/ # ------------------------------------------------------------------------------ # MySQL database (pathogen_portal_mt4.sql.gz) # ------------------------------------------------------------------------------ a. Create your mysql database http://www.movabletype.org/documentation/installation/detailed-instructions.html Its not necessary, but assuming you use the same database name (pathogen_portal_cms) mysqladmin create pathogen_portal_cms -u [username] -p b. Decompress and Restore the database from the backup gzip -d pathogen_portal_mt4.sql.gz mysql -h localhost -u [username] -p [password] pathogen_portal_cms < pathogen_portal_mt4.sql # ------------------------------------------------------------------------------ # Portal code (pathogen_portal_final_release_jcvi.tar.gz) # ------------------------------------------------------------------------------ a. cgi-bin Contains all of the portal scripts and libraries for managing the site and data release process. See code for the details. b. doc See doc/HOWTO.txt for instructions on how to run the data processing pipeline. c. gb Contains GBrowse 1.x installation currently in use. d. html The html directory is the DOCUMENT_ROOT for the Apache server. It is also the "Site Root" for Movable Type. After installing Movable Type, you can set this parameter by logging into the MT administration panel, and under Preferences -> Publishing, you can set the Site Root to this directory. Movable Type will publish the index files to the Site Root directory, and the categories are published in a directory structure underneath the Site Root. The current version of www.pathogenportal.org requires both the files stored in our SourceForge repository under the html directory plus the files that will be published by Movable Type based on the backup we are providing you of the MT database. # ------------------------------------------------------------------------------ # Portal Portal data directory (pathogen_data.tgz) # ------------------------------------------------------------------------------ gff3, specialty_genes and xml directories These directories contain the data (generally unmodified) provided by the various BRCs. lucene, lookup directories These directories are produced and the content is auto-generated by the data processing pipeline. See the doc/HOWTO for details.