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CHANGELOG.md

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GobyWeb2 Plugins Change log

Towards release 2.2.2 (future)

  1. ENSEMBL_ANNOTATIONS resource: Biomart.groovy script now restarts dropped connections up to three times. Advance version number to 2.1.2.
  2. DIFF_EXP_GOBY and DIFF_EXP_GOBY_ARTIFACT: Require at least two groups for a Goby DiffExp. The code will not work with a single group and no group comparison.

Release 2.2.1 (Aug 9 2013)

  1. Fix VEP plugin for new version of Variant Effect Predictor (v72). Upgrade links for ensembl API distribution. Fetch and decompress ensembl-tools archive because VEP is now packaged in this file (would have been nice to see this listed as a change in the VEP/Ensembl API change log.
  2. ENSEMBL_ANNOTATIONS resource: Biomart.groovy script. Add filter by chromosome for new annotation kinds. This attribute forces download chromosome by chromosome, which is necessary with Biomart for large tables.
  3. ENSEMBL_ANNOTATIONS resource: Add pre-packed cache to speed up biomart annotation installs. The cached file is written and read from ~gobyweb/url-cache. Edit the plugin as needed to suit your particular local installation.
  4. upgrade GOBYWEB_SERVER_SIDE/global_goby.jar to Goby 2.3.2 pre-release
  5. Expose BWA aln options in BWA_GOBY_ARTIFACT plugin.
  6. PLAST (parallel last) plugin: Extend PLAST to support paired end reads. New version of Goby that supports --paired argument in run-parallel.