README
December 5, 2012 ยท View on GitHub
METAREP DIRECTORIES
/app web application files
/cake cake framework files
/data example datasets
/scripts perl and R scripts
/doc documentation
/db relational databases
/solr solr/lucene configuration files
/vendors 3rd-party php tools
INSTALLATION AND ADDTIONAL INFORMATION Please visit the project's wiki page at http://wiki.github.com/jcvi/METAREP for additional information. The 1.3.2 installation guide can be found at https://github.com/jcvi/METAREP/wiki/Installation-Guide-v-1.3.2
VIDEO DOCUMENTATION 5 min overview http://www.youtube.com/watch?v=DJNjM7LMVWU
web tutorial http://www.youtube.com/watch?v=7FPJaPyLjMk&feature=relmfu
implementation details http://www.youtube.com/watch?v=j0rlTIkvfvI
RELEASE NOTES JCVI Metagenomics Reports - Version 1.4.0
New Feature: METAREP-461 Import dataset option for Admin via project page
METAREP-206 New Blast Page to find homologous sequences in selected datasets, display and export results
METAREP-460 New Search Page option to search datasets using user defined sequences at three homology cut-off levels (1E-5, 1E-20 and 1E-50)
METAREP-461 Deprecate common name field in Compare Page (will be replaced with a high level summary, similar to the View Page Summary tab in the next release)
METAREP-462 Adjust Compare Page Layout for new versions of Chrome/Firefox
METAREP-435 New project link shortcut from user dashboard page project listings
METAREP-434 Select datasets for population creation by filtering datasets based on descriptions
METAREP-437 Updated download file header
METAREP-421 Fisher's Exact Test to compare two datasets (exact test)
METAREP-422 Equality of Proportions Test to compare two datasets (large sample approximation)
METAREP-432 False Discovery Rate calculation and filtering for multiple testing correction
METAREP-424 Compare two pathway maps with log odds ratio and significance color coding (available for 'Statistical tests (2 datasets)' option on the KEGG pathway level; click on image in the last column)
JCVI Metagenomics Reports - Version 1.3.2 (bug fix release)
Bug Fixes:
METAREP-477 Mosaic Plot option was missing in scripts/r/plots.r METAREP-478 Population creation process expected core organization by project ID; the process was fixed to work with a root level core organization as generated by the metarep_loader.pl script.
JCVI Metagenomics Reports - Version 1.3.1
New Feature: METAREP-391 update viral evidence summary for view page METAREP-409 update NCBI taxonomy, KEGG, GO, and enzymes:
NCBI taxonomy version 09/30/2011: 280,602 new taxa KEGG version 09/01/2011: 21 new KEGG KO pathways; 1 new KEGG EC pathway Gene Ontology version 09/05/2011
METAREP-407 implement GO slim support for compare page METAREP-406 implement mosaic plot option for compare page METAREP-205 sequence export option for search page
Bug Fixes: METAREP-408 fix compare panel misalignment
JCVI Metagenomics Reports - Version 1.2.0
Improvement METAREP-244 - Increased speed of web page build-up METAREP-247 - Integrate new METAREP logo into web layout
New Feature METAREP-228 - Added unresolved taxonomy fractions to Browse APIS pages METAREP-243 - Search datasets using name based searches for Taxonomy, HMM, Enzymes, GO and KEGG pathway names METAREP-245 - Added search option to filter Browse Taxonomy/GO/Pathway/EC pages METAREP-248 - Implemented PHP based load balancing option
Bug Fixes METAREP-246 - Fix View Download Cache Issue
JCVI Metagenomics Reports - Version 1.1.0