1.7.1

Release 1.7.1 includes a plugin for methylation estimation over annotated regions of the genome and bug fixes for problems found after 1.7 was deployed. This is the first public release of GobyWeb with the plugin infrastructure.

1.7

GobyWeb 1.7 is a major release with lots of new features (released Jan 9 2012 to our CTSC community). We have added a brand new plugin mechanism to make it easier to integrate new aligners and analysis tools with GobyWeb. New plugins can be added at run-time and the user interface adapts as needed.

  • We parallelized count calculations for Goby and DESeq statistics. You should see major speed improvements for exon analysis.
  • Add a mechanism for resource plugins. Alignment and analysis plugins can require resources (by id and version). Only plugins for which all resources are available in the instance of GobyWeb install. The files that a resource plugin are copied to the job directory of alignment/analysis plugins that use the resource. The latest version of a resource is configured it if matches the minimal version number requested by the client plugin. By convention, resource plugins should be described under the plugins/resources directory, and named with ID_VERSION (all uppercase).
  • Added support for plugins for alignment and aligment analyses (e.g., diff exp, seqvar)
  • New methylation plugin. We introduce the ability to reuse plugin scripts from other plugins. In this case, the methylation plugin imports the SEQ_VAR_GOBY script.sh file as its script. The feature also makes it possible to name plugin scripts something other than script.sh, and to import other files as needed from different plugins.

1.6.2

This version supports single end and paired-end files uploaded in the .fastq.gz.tar format. This format is being delivered by the WMC epigenomic core facility and consists of tar files containing .fastq.gz files. GobyWeb will automatically recognize files that end in the extension .fastq.gz.tar and convert such files to the compact-reads format for further processing. The upload supports paired-end input when the fastq.gz file match the pattern *R0_???* *R1_???* where ? is a digit. For instance, if a tar file contains a_R0_000.fastq.gz and a_R1_000.fastq.gz, the two fastq files are assembled to reconstitute the pairs. Please note that since the epigenomics core provides both reads passing filters and reading not passing filters, we remove all reads not passing quality filters (to this end we assume the reads are produced by the Illumina 1.8+ pipeline and follow the procedure described at http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/, keeping reads without :Y: in the FASTQ read-id line).

1.6.1

This version was slightly modified from version 1.6 to facilitate distribution and installation of a binary distribution. It has been packaged on November 9th 2011 (release tag 20111109).

1.6

Version released on Oct 29 1011 to our CTSC investigators. New features and bug fixes include:

  • Performs read pre-processing on the grid. This provides much better throughput when importing several read files for projects with billions of reads.
  • Convert tab delimited or VCF format to SQLLite tables on the grid. Group comparison now only show the job completed status when the data is readily available and viewable in table format. Several imports can also proceed in parallel, as supported by compute grid capacity.
  • Read import now provides status updates in a way similar to alignment and group comparison jobs.
  • Multi-download was broken in version 1.5 when we migrated the application to a new application server. Multi-download creation is fixed.
  • The type of columns in TSV files is now determined automatically and this type is used when importing the table. This enables to search columns for differential expression results in the Table viewer more efficiently.

1.5

Version released in Sept 2011 to our CTSC investigators. Version 1.5 is a major upgrade that supports many additional features including
  • Spliced alignment with GSNAP for RNA-Seq data
  • Calling differential allelic expression in RNA-Seq data (with Goby)
  • Calling CNVs with significant coverage differences between groups of samples in DNA-Seq data
  • Calling genotypes in DNA-Seq (and download VCF files, which can be viewed in IGV)
  • Comparing genotypes across groups of samples (e.g., allelic tests at sites covered with reads, or discovery or new variations or mutations)
  • Estimating methylation rates in bisulfite converted samples in Methyl-Seq or RRBS data and finding sites differentially methylated between groups of samples (methylation rates are written to VCF and can be viewed natively in IGV).

1.1

This version was released to our CTSC investigators in the Spring 2011 and added these features:

- Ability to directly upload FASTQ, csfasta, and fasta to GobyWeb, without prior conversion to compact-reads. You no longer need to use Goby on the command line before you start an analysis with the web tool. Please upload compressed files to minimize transfer time.
-  Ability to upload files of any size (we removed the 2GB limit of the first version)
- Easy way to find any element of information by tag (use the search box on the top right)
- Sharing now supports starting new differential expression analyses with alignments shared with the user.

1.0

This first semi-public release of GobyWeb was made available to investigators of our CTSC at WMC, MSKCC, HSS and Hunter College in January 2011. The version focused on RNA-Seq data analysis and had support for the BWA and Last aligners.