ENSEMBL_ANNOTATIONS resource: Biomart.groovy script now restarts dropped connections up to three times. Advance version number to 2.1.2.
Merge branch 'master' of bitbucket.org:campagnelaboratory/gobyweb2-plugins
Describe changes in log.
Require at least two groups for a Goby DiffExp. The code will not work with a single group and no group comparison.
Fix GRCh37 ensemble build name in ENSEMBLE_GENOMES artifact script.
Use 1000g assembly also for 1000GENOMES in ENSEMBLE_GENOMES artifact script.
Ignoring warnings and errors from the shell when decompressing a top level genome in FAI_INDEXED_GENOMES. The script checks by itself afterwards if the genome was decompressed successfully.
Testing bitbucket # of users prevents commits
Fix GOBY_CCP_API artifact. The release is compressed in a single archive on chagall while the artifact was expecting to find the release in a dedicated folder.
Fix typos in option IDs. Make DB output optional.
Fix GSNAP with artifact aligner.
Source PROTOBUF_CPP and GOBY_CPP setups when installing BWA_WITH_GOBY_ARTIFACT artifacts. This is needed because BWA is executed during the installation.
Source PROTOBUF_CPP and GOBY_CPP setups when executing BWA_GOBY_ARTIFACT artifacts.
Merge branch 'master' of ssh://bitbucket.org/campagnelaboratory/gobyweb2-plugins
Always run annotations for methylation analysis at base level.
Update ENSEMBL_API to version 73.
Merge remote-tracking branch 'origin/master'
Update VARIANT_EFFECT_PREDICTOR to version 73.
Adding goby 2.3.3 preview.
Include Goby commit 3817c4c (Remove filter on (germlineCount > failedCountGermline))