Permalink
Browse files

release 1.4.0

  • Loading branch information...
1 parent ab88290 commit 8756f74529d19013cdfaf978d03056ad2873a268 Johannes Goll committed Dec 1, 2012
Showing 989 changed files with 6,059 additions and 1,182 deletions.
View
0 LICENSE.txt 100755 → 100644
No changes.
View
91 README 100755 → 100644
@@ -1,80 +1,37 @@
-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
+EXAMPLE DATA
-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
+/data/tab
+/data/xml
-VIDEO DOCUMENTATION
-5 min overview
-http://www.youtube.com/watch?v=DJNjM7LMVWU
+DeLong et al. Vertical Ocean Depth Profile datasets (7 libraries)
+http://www.scienceonline.org/cgi/content/full/311/5760/496
+JCVI's Prokaryotic Metagenomics Annotation Pipeline (JPMAP) was used to
+annotate the reads
-web tutorial
-http://www.youtube.com/watch?v=7FPJaPyLjMk&feature=relmfu
+https://github.com/jcvi/JCVI_HMP_metagenomic_pipeline
+http://standardsingenomics.org/index.php/sigen/article/view/sigs.651139
-implementation details
-http://www.youtube.com/watch?v=j0rlTIkvfvI
-RELEASE NOTES
-JCVI Metagenomics Reports - Version 1.3.2 (bug fix release)
+/data/humann
-Bug Fixes:
+NIH HMP Metabolic Reconstruction datasets (7 libraries)
+HMP Unifed Metabolic Analysis Network (HUMAnN) pipeline was used to annotate
+the reads
-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.
---
+http://huttenhower.sph.harvard.edu/humann
-JCVI Metagenomics Reports - Version 1.3.1
+See also
+http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0029044
-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
+/data/jpmap
-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
+NIH HMP Pretty-Good-Assembly datasets (2 libraries)
+JCVI's Prokaryotic Metagenomics Annotation Pipeline (JPMAP) has been used to
+annotate the contigs
-Bug Fixes:
-METAREP-408 fix compare panel misalignment
---
+https://github.com/jcvi/JCVI_HMP_metagenomic_pipeline
+http://standardsingenomics.org/index.php/sigen/article/view/sigs.651139
-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
-
-New Feature
-METAREP-215 - Search all datasets option; generate meta-information summaries
-METAREP-217 - Allow users to test METAREP without creating an account
-METAREP-218 - Allow distance matrix export for hierarchical clustering, heatmap, mds plots
-METAREP-219 - Added color legend to heatmap
-METAREP-220 - Fixed search example links in search help dialog
-METAREP-221 - Use new radio buttons in compare page to limit selection to project datasets
-METAREP-223 - Compare datasets using Wilcoxon Rank Sum Test
-METAREP-224 - Ajax support for search dataset pages
---
+See also
+http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.002904
View
21 app/config/constants.php 100755 → 100644
@@ -13,7 +13,7 @@
*
* @link http://www.jcvi.org/metarep METAREP Project
* @package metarep
-* @version METAREP v 1.3.0
+* @version METAREP v 1.4.0
* @author Johannes Goll
* @lastmodified 2010-07-09
* @license http://www.opensource.org/licenses/mit-license.php The MIT License
@@ -31,9 +31,9 @@
define('HEATMAP_COLOR_YELLOW_BLUE', 2);
define('HEATMAP_COLOR_BLUE', 3);
define('HEATMAP_COLOR_GREEN', 4);
+define('HEATMAP_COLOR_RED_BLUE', 5);
//define compare options
-define('FISHER', 0);
define('ABSOLUTE_COUNTS', 1);
define('RELATIVE_COUNTS', 2);
define('HEATMAP_COUNTS', 3);
@@ -44,6 +44,8 @@
define('MDS_PLOT', 8);
define('HEATMAP_PLOT', 9);
define('MOSAIC_PLOT', 10);
+define('FISHER', 11);
+define('PROPORTION_TEST', 12);
//define compare dataset mode
define('SHOW_ALL_DATASETS',0);
@@ -57,7 +59,11 @@
define('PVALUE_BONFERONI_HIGH_SIGNIFICANCE',4);
define('PVALUE_BONFERONI_MEDIUM_SIGNIFICANCE',5);
define('PVALUE_BONFERONI_LOW_SIGNIFICANCE',6);
-define('PVALUE_ALL',7);
+define('PVALUE_FDR_HIGH_SIGNIFICANCE',7);
+define('PVALUE_FDR_MEDIUM_SIGNIFICANCE',8);
+define('PVALUE_FDR_LOW_SIGNIFICANCE',9);
+
+define('PVALUE_ALL',10);
//define distance matrices
define('DISTANCE_HORN','horn');
@@ -97,6 +103,13 @@
define('HEATMAP_GREEN_START', '31A354');
define('HEATMAP_GREEN_END', 'E5F5E0');
+define('HEATMAP_RED_BLUE_START', '7FBF7B');
+define('HEATMAP_RED_BLUE_END', 'F99D31');
+
define('PHP_HTTP_TRANSPORT_CURL_REUSE', 'CURL_NO_REUSE');
define('PHP_HTTP_TRANSPORT_CURL_NOREUSE', 'CURL_NO_REUSE');
-define('PHP_HTTP_TRANSPORT_FILE_GET_CONTENTS', 'FILE_GET_CONTENTS');
+define('PHP_HTTP_TRANSPORT_FILE_GET_CONTENTS', 'FILE_GET_CONTENTS');
+
+define('SOLR_RESULT_FACETS_UNWEIGHTED', 1);
+define('SOLR_RESULT_FACETS_WEIGHTED', 2);
+define('SOLR_RESULT_SINGLE_WEIGHTED', 3);
View
@@ -206,6 +206,22 @@
'lock' => false, //[optional] use file locking
'serialize' => true,
));
+
+/**
+ *
+ * Model Cache Engine Configuration
+ * Default settings provided below
+ *
+ * File storage engine.
+ */
+ Cache::config('_cake_model_', array(
+ 'engine' => 'File', //[required]
+ 'duration'=> '+999 days', //[optional]
+ 'path' => METAREP_TMP_DIR, //[optional] use system tmp directory - remember to use absolute path
+ 'prefix' => 'phylo_metarep_cake_model_', //[optional] prefix every cache file with this string
+ 'lock' => false, //[optional] use file locking
+ 'serialize' => true,
+ ));
/**
*
View
@@ -1,7 +1,7 @@
<?php
/***********************************************************
-* File: database.php
-* Description: configuration file for METAREP datasources
+* File: database.php
+* Description: configuration file for cakephp datasources
*
* PHP versions 4 and 5
*
@@ -13,23 +13,22 @@
*
* @link http://www.jcvi.org/metarep METAREP Project
* @package metarep
-* @version METAREP v 1.3.4
+* @version METAREP v 1.4.0
* @author Johannes Goll
-* @lastmodified 2011-10-12
+* @lastmodified 2010-07-09
* @license http://www.opensource.org/licenses/mit-license.php The MIT License
**/
class DATABASE_CONFIG {
- //METAREP MySQL database connection parameters
var $default = array(
'driver' => 'mysqli',
'persistent' => true,
- 'host' => 'localhost',
- 'login' => '<your-login>',
- 'password' => '<your-password>',
- 'database' => 'metarep',
- );
+ 'host' => 'mysql51-dmz-pro',
+ 'login' => 'repneomgx',
+ 'password' => 'g+k2_p*LPn',
+ 'database' => 'ifx_metagenomics_reports',
+ );
//METAREP Blog connection parameters
var $blog = array(
View
0 app/config/htaccess/htaccess_app 100755 → 100644
No changes.
View
0 app/config/htaccess/htaccess_root 100755 → 100644
No changes.
View
No changes.
Oops, something went wrong.

0 comments on commit 8756f74

Please sign in to comment.