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 ===
=== 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.