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CHANGELOG
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### 1.1.0 (2018-11-01)
##### New Features
* Setting of development status for integrated tools. tool_status = ["Coming soon", "Active", "Disabled", "Testing"]
* Implementation of user "Projects" that allow to have n workspaces per user and group files/folders under user criteria.
* New way of launching tools starting from tool discovery instead of input files selection.
* New log reporting system for running jobs - more visual and interactive
* Library for a better automation and homogenization on building the custom tool web forms
* Creation of automatic documentation for input requirements and arguments from tool definition
* Tool skeleton with PHP, JS and HTML templates for easing the integration of new tools
* Automatic data loading for new registered users from their previous anomymous account
* New helpdesk operations: request for extra space; become tool developer; integrate a new tool
* Implementation of tool integration methods - online generation of test files
* Implementation of tool integration methods - online tool submission
* Tool usage pannel for statistics for admins and tool developers
* User's job managment panel
* New 'Rerun job' feature
* Jbrowse updated to 1.12.3
* Integration of BigNASim trajetories
* Openstack login via tokens
* Addition of file system related operations: renaming, moving, etc.
* New panel for tool developers with their tool statistics and logs
##### Bug Fixes
* Reset password via keycloak
* Bug PMES status 'In limbo'
* Dynamic dimensioning of VMs using OCCI available template resources
* Any many others...
##### New Tools
* MACS2: identifies statistically significantly enriched genomic regions in ChIP- and DNase-seq data (Mark McDowall)
* Bowtie2: Align FASTQ data using Bowtie2 (Mark McDowall)
* Process WGBS: Align WGBS data, uses BS Seeker2 and Bowtie2 (Mark McDowall)
##### Tools Upgraded
* TADbit bin: TADbit Hi-C binning. (Francois Serra)
* TADbit map parse and filter: TADbit Hi-C mapping, parsing mapped reads and filtering of artifactual reads. Francois Serra & David Castillo)
* TADbit model: TADbit 3D modeling. (Francois Serra)
* TADbit normalize: TADbit Hi-C normalize. (Francois Serra)
* TADbit segment: TADbit Hi-C segment - TADs and compartments. (Francois Serra)
* Nucleosome Dynamics Nucleosome Dynamics Tools for performing nucleosome-related analysis based on MNase-seq experimental data Illa Ricard, Buitrago Diana, Brun Isabelle
--------------------------------
##### MuGVRE Tools (in production)
* 3DConsensus: Analyse a protein-DNA complex 3D structure to identify interactions by integrating experimental data on the protein's DNA specificity (Marco Pasi)
* Chromatin Dynamics: With the Chromatin Dynamics tool you can create your own 'beads-on-a-string' representation of a chromatin fiber. (Jürgen Walther)
* MC-DNA: is a coarse-grained DNA model in which the internal dynamics are described with helical parameters. (Jürgen Walther)
* MD Energy Refinement: Molecular Dynamics workflow to energetically minimize a structure. MD Setup + 100ps free MD. (Pau Andrio)
* NAFlex: analyses Set of analyses to extract Nucleic Acids flexibility properties from Molecular Dynamics trajectories (Adam Hospital)
* Nucleosome Dynamics: Tools for performing nucleosome-related analysis based on MNase-seq experimental data (Illa Ricard, Buitrago Diana, Brun Isabelle)
* pyDock: PyDock is a tool for the structural prediction of protein-protein interactions (Brian Jiménez-García)
* pyDockDNA: PyDockDNA is a tool for the structural prediction of protein-DNA interactions (Brian Jiménez-García)
* Process Genomes: Generates BWA, Bowtie2 and GEM indexes for a given genome (Mark McDowall)
##### MuGVRE Visualizers (in production)
* Jbrowse: A next-generation genome browser built with JavaScript and HTML5. (MMB IRB)
* NGL: Viewer for molecular visualization. WebGL is employed to display molecules like proteins and DNA/RNA with a variety of representations. (MMB IRB)
* TADkit: 3D genome browser and TADbit front-end (CNAG)
--------------------------------
##### Dev Tools
* BWA MEM: Align FASTQ data using BWA mem (Mark McDowall)
* Process ChIP-seq: Align ChIP-seq data, filtering with BioBamBam and Peak Calling using MACS2. (Mark McDowall)
* Process RNA-seq: Align RNA-seq data, gene expression calling with Kallisto (Mark McDowall)
* Chromatin Assortativity (Centre de Recherches en Cancérologie de Toulouse)
* CHiCAGO pipeline (Pablo Acera)
* Process DamID-seq Data (Mark McDowall)
* BioBamBam2 Filtering (Mark McDowall)
* TrimGalore (Mark McDowall)
* BWA ALN (Mark McDowall)
* Analyse FASTQ Files (Mark McDowall)
* BS Seeker2 Methylation Peak Caller (Mark McDowall)
* BS Seeker2 Aligner (Mark McDowall)
* BS Seeker2 Filter (Mark McDowall)
* WGBS BS Seeker 2 Indexer (Mark McDowall)
* Sleuth
##### Dev Visualizers
* CytoScape (Centre de Recherches en Cancérologie de Toulouse)
### neat (2010-03-23)
##### Code rearrangement
* Current tree directory structure created
* Template creation for tools, configuration files and PHP pages.
* Easier installation with better documentation, more configurable parameters, database skeleton, sample tools and datasets, etc.
* Neat composer project for better managing 3th party dependencies
* Cleanest building of tool's help pages
* No direct link to user's files/