@chienchi chienchi released this Aug 29, 2018 · 73 commits to v1.5 since this release

Assets 2

EDGE version 2.3.1

  • fix bug: blank SRA accesion variable
  • Add comma separated single reads support for batch submit
  • Add script to update existing projects status, runtime, submission time
  • Add contig taxonomy classification info (species) into JBrowse annotation gff track
  • Update samtools from 1.6 to 1.9

EDGE GUI 2.3.1

  • fix bug: corrupted gz file using Upload function

@chienchi chienchi released this Jul 24, 2018 · 73 commits to v1.5 since this release

Assets 2

EDGE version 2.3.0

  • Update Kraken version from 0.10.4 beta to 1.0
  • Update Metaphlan from 1.7.7 to 2.7.7
  • Add global numCPU option for runReadsToGenome and runReadsToContig scripts
  • Add Qiime taxonomy plot bar chart and alpha diversity analysis for only one sample
  • fix bug: fasta header correction for consensus pipeline
  • fix bug: project rerun in docker container. remove some system call
  • update PyPiRt version from 0.3 to 0.3.2. ID to SampleID.

EDGE-UI version 2.3.0

  • Add Take Notes Button in result page
  • Update userManagement API to return all fields of project page in json to speed up page loading
  • Update Metaphlan to Metaphlan2
  • Multiple SRA number input with comma separated
  • Add Phred Quality Offset for QC module
  • fix bug: project report selection

@chienchi chienchi released this Jun 27, 2018 · 73 commits to v1.5 since this release

Assets 2

New features
• Report generation
• Pathogen analysis and characterization
• Presence/absence of targeted amplicons
• Differential gene expression (RNA-Seq)
• Tools for analysis of Nanopore MinIon data
More updates

May 3, 2018
Apr 26, 2018
v2.1.0-rc
Pre-release
Pre-release

@chienchi chienchi released this Dec 6, 2016 · 34 commits to v1.5 since this release

Assets 2

Updates:

  • One of the MetaComp requirements udpated its version (cowplot) broken the EDGE installation: update R version from 3.2.2 to 3.3.2 and MetaComp from v1.1 to v1.2
  • Separate auto-run feature from edge_info into a cronjob.
  • Fix bugs: max_num_jobs, path of rig run, module tests
  • Override cpu usage from config
  • Add select all checkbox for the project page
  • NCBI is moving from http to https for security and privacy improvement which caused SRA download feature failed. We have updated our script to accommondate the change. In addition, if it failed to download from NCBI-SRA, it will try EBI-ENA and DDBJ.
  • The thirdparty tools now include R3.3.2 and Blast+2.5.0.
    • ftp://ftp.lanl.gov/public/genome/EDGE/1.5/edge_v1.5_thirdParty_softwares.tgz

@chienchi chienchi released this Oct 4, 2016 · 52 commits to v1.5 since this release

Assets 2

New modules:

  1. Specialty Gene Profiling
  2. Qiime pipeline for amplicon data analysis

Updates:

  1. R version 2.15.3 to 3.2.2,
  2. KronaTools version 2.4 to 2.6,
  3. Bowtie2 2.1.0 to 2.2.6,
  4. gridExtra version 0.9.1 to 2.0.0
  5. Upgrade sratoolkit version from 2.4.4 to 2.5.4 which support proxy setup and make sra2fastq.pl work on pacbio and solid platform.
  6. SPAdes from 3.5.0 to 3.7.1 (with meta flag for metagenome)
  7. Update project dir by using secure code instead of project id
  8. Add email functions when job complete or shared to others
  9. Separate [system] configruation from edge_config.tmpl into sys.properties.
  10. MEGAHIT metagenome assembler.
  11. Sample metadata Input
  12. Many GUI features improvements
  13. Add MetaComp package installation.(https://github.com/seninp-bioinfo/MetaComp.).

Database update:

  1. GOTTCHA db version v20150825

Virtual Machine:

  1. VMware .ova file: ftp://ftp.lanl.gov/public/genome/EDGE/1.5/VirtualMachine/
  2. Docker: https://hub.docker.com/r/chienchilo/edge_v1.5/

Bugs fixes: batch submit bugs, tree view cutting issue, upload function fail when user management system is off, overly running taxonomy profiling tools in parallel... etc.

We are actively updating the documentation for the release. Please see http://edge.readthedocs.io/en/v1.5/

@chienchi chienchi released this Jun 15, 2016 · 26 commits to master since this release

Assets 2
  • fix no accession number genbank to gff conversion bug
  • fix bug: limiting jobs by available processors
  • add a hash table on host file to avoid duplication
  • remove session info from the log
  • chmod on the EDGE_output directory
  • add .php into cgi scripts. fix bug with http port for non 80
  • make the example apache configuration file ready for copy with EDGE installation
  • fix bug on install user management system: error_msg:Fatal Exception unknown column "spassword" in field list.
  • add email_notification switch for user management system
  • remove unsupport taxanomy profiling tool in the example config file
  • tolower on $annotateProgram assignment
  • fix bug: run the EDGE through command line with absoulte path
  • fix bugs: batch submit point to wrong path. Escape symbol characters of the description field
  • use -noColorLog for the test example run which fix the output html no value issue
  • check permisson before adding symlink to edge_ui/JBrowse/data
Oct 15, 2015

v1.1

Version 1.1. This corresponds to the codebase / live site (bioedge.la…
…nl.gov) for manuscript.