ChangeLog.txt

-- Version 1.1
2015/08/19
1. Add size limit to contig for annotation ( default 700bp)
2. Display heatmap at community profiling section
3. Add script to 1. convert newick tree to phyloxml 2. midpoint reroot 3. add annotation for url and descriptions
4. Updated JBrowse to 1.11.6. 
5. Improved tree and tooltip visulization.
6. Testing/documentate installation on CentOS 6, CentOS 7 and Ubuntu 14.04
7. Support fastq.gz input
8. Added project managment functions/widget, resource monitor widget
9. Added queuing function, auto start queued projects
10. Update GOTTCHA module to 1.0b
11. Update host removal script to output host fastq file and using similarity cutoff instead alignment score.
12. Add selectmenu for choosing host, reference genomes ( Support multiple selection )
13. Update Virus Database of GOTTCHA
14. Add paired reads check. If failed, will use them as single end reads
15. Add buttons to add paired-end/single-end fasta input field in Advanced option
16. Add Batch submit 
17. Reorganized output directory structure.
18. Add RAxML tree builder
19. Remove 0% coverd contigs
20. Add Select (ref)  genomes, SRA input function for SNP phylogeny
21. Add input from NCBI SRA function and sratoolkit
22. Add Contig classifictaion function by BWA. Remove Blast section of EDGE Gui
23. Add LCA function to contig classifier
24. Check duplicate input error
25. Add rank switch to the summary of taxonomy classification.
26. Add User Management System
27. Replace GOTTCHA databases to xHUMAN3x databases.
28. Update bwa version from 0.7.9 to 0.7.12. 
29. Add RATT annotation option on EDGE GUI
30. Allow user to add other genomes in Phylogenomic analysis
31. Correct INDEL count number in contigMapToRef
32. Add all NCBI RefSeq to reference selecting menu.
33. Server-side session implemented. Session expiration detection and deletion.
34. Reference selection includes annotations. (NCBI_genomes.tar.gz)
35. Add social network login function (Facebook, google, windows live, Linkedin)
36. Add SPAdes 3.5 assembler (can input Pacbio/Nanoport for gap closure) and user provided contigs options to skip asssmebly
37. Update prokka to 1.11
38. Add tooltip and Mission popup
39. Add NextSeq platform check and automatically adjust opt_q to 15 if opt_q < 15 for QC module
40. Add Upload Files Function. Max file size is '5gb'. Allowed File types are fastq, fasta and genbank and can be in gzip format. Files will be kept for 7 days.
41. GOTTCHA with plasmid and read count
42. Remove metaphyler-srv 
43. Multiple improvements and bugfixes

-- Version 1.0
2014/08/26
1. * Jquery edge_ui implementation for input and output html
2. Allow multiple host removal
3. Several bugs fixs.
4. Add SNP phylogeny 
5. Add primer Tm and length range to primer design
6. Add lazyload to improve result page loading performance
7. Manual created online at edge.rtfd.org
8. Add Contig Blast result
9. Remove Perl Tk GUI and package
10. Bugs fixed.

-- Version 0.5
2014/04/10
1. Add GOTTCHA profiling to
2. Add JBrowse
3. Add function to generate radar chart
4. Add a python script for starting a local web host
5. Update main script and gui to start the http localhost when job processed.
   and Auto lauch result html page when job finishd.
6. Add script generating JBrowse tracks.
7. Add "debug" option to microbial_profiling.pl. 
8. Allow most of modules to on/off switch
9. Update bwa from 0.7.5a to 0.7.9
10. Update parallel version
11. Update prokka from 1.7 to 1.9
12. Add barrnap for rRNA prediction
13. Add adapter trimming and phiX filtering options for QC step
14. Remove File::Tee dependency and fix program call path issue
15. Update INSTALL script to more control options
16. add Metascope, FastTree and RAxML tools
17. add output HTML munger in runPipeline

-- Version 0.4
2014/2/10
1. Update bwa from 0.7.5a to 0.7.7
2. Add Version into process log and bug fix on annotation flag
3. Fix a major bug on gui when output directory is not existed3.
4. Comment out MEGAN 
5. Remove redundant ktImportBWA script 

-- Version 0.32
2013/12/18
1. Replace MEGAN tree plot script with custom Perl scrips/modules.
2. Add krona_portable.pl script to generate portable krona html and fix runReadsToGenome.pl when input non-alphanumeric reference name
3. Add process log and error log into project output directory
4. Fix bugs on phageFinder and pdf cat when there is no protein annotation result.
5. Add annotation check box and function
6. Add bwa mapping reads id to Taxonomy lookup text file (.classification)
7. Add contig id to Taxonomy lookup text file (.classification)

-- Version 0.31
2013/12/11
1. Improve primer Adjudication module with Tm calculation and sorting.
2. Add kraken-0.10.2-beta thirdParty software for taxonomy classification
3. Update the Perl GUI interface
4. Add Annotation stats output
5. Add existing output directory detection and warning.
6. Add README.pdf documentation
7. use bitbucket (git) for version control


-- Version 0.3 --
2013/11/10
1.Improve primer Adjudication module for Novel pathgen
2.Improve primer Validation module to allow checking multiple primer pairs in fasta 
  and IUPAC degenerate base check 
3. Update the Perl GUI interface

-- Version 0.2 --  
2013/09/10
For EDGE use case 2:  Extreme Symptom
Adding modules
1. Annotation: Prokka or RATT
2. Phage finder
3. Taxonomy analysis
4. novel contigs/regions Analysis
5. SNP/INDEL analysis

-- Version 0.1 --   
2013/06/01
For EDGE use case I: Assay Failure detection
Have modules:
1. Data QC
2. Host Removal QC 
3. IDBA Assembling
4. Map Reads To Contig
5. Map Reads To Reference Genomes
6. Map Contigs To Reference Genomes 
7. PCR Assay Validation and Adjudication