CNV Workshop 2.0.10 released

2010-05-13
2013-04-26
  • Kevin Murphy
    Kevin Murphy
    2010-05-13

    CNV Workshop 2.0.10 is available for download; all users should upgrade to this version. This release fixes several bugs that effectively rendered 2.0.9 unusable for most installations. A CentOS VM image containing this release will be posted shortly.

    Look for CNV Workshop 2.1 possibly by the end of the summer.

    Relevant excerpt from docs/CHANGES.txt:

    === 2.0.10 Upgrading instructions (2.0.9 to 2.0.10) ===

    * 2.0.10 should be used instead of 2.0.9.

    * See upgrading instructions for 2.0.9 below if you haven't already.

    === 2.0.10 Enhancements ===

    NA

    === 2.0.10 Bug fixes ===

    Fixed broken normals queries for non-CHOP installations in CNV Workshop 2.0.9.
    cnvCaller.pl no longer fails on case-sensitive filesystems (MySQL issue).
    GBrowse image map no longer gets "out of sync" (is not reloaded on pans/zooms) when synchronize is off.
    Documentation files in docs directory are now in the most portable text format (DOS/Windows).

    === 2.0.9 Upgrading instructions (2.0.8 to 2.0.9) ===

    * DO NOT USE 2.0.9.  Use 2.0.10 instead.

    * Apply the most recent CHOP normals data (http://cnv.chop.edu/cnvdata/cnv2_hg18.mysqldump.sql.bz2 or
    http://cnv.chop.edu/cnvdata/cnv2_hg18.mysqldump.sql.zip) to get the latest annotation and the new gender table.
    After expanding the compressed data file, do the following:

        {{{
        mysql -e "drop database cnv2_hg18"
        mysql -e "create database cnv2_hg18"
        mysql cnv2_hg18 < cnv2_hg18.mysqldump.sql
        perl src/main/backend/annotateNormalsDatabase.pl cnv2_hg18
        }}}

    * Update your cnvCalls annotation by running 'perl src/main/backend/cnvReannotator.pl' - but before that, please
    read the relevant section in ADMIN.txt first.

    * See all previous relevant upgrading instructions in docs/CHANGES.txt in the main distribution.