Posted on Monday, December 06, 2021 at 01:15PM by Barbara Hill
As of GenePattern 3.9_21.12_b373 the GenePattern "patch mechanism" for installing support libraries for modules has been deprecated, in favor of the current best practice of creating or providing Docker containers for modules to run in.
This meant that a number of older, no longer supported modules have officially been deprecated and will no longer be available on our servers or from our module repositories. Their archives can be found in our Github organization, should you wish to revive them for your own purposes.
The impacted modules are as follows:
ABSOLUTE
ABSOLUTE.review
ABSOLUTE.summarize
Bowtie.aligner
Bowtie.indexer
CBS
Cuffcompare
Cuffdiff
Cufflinks
CufflinksCuffmergePipeline
Cuffmerge
Cuffnorm
Cuffquant
HAPSEG
HierarchicalClustering.MATLAB
HierarchicalClusteringImage.MATLABLu.Getz.Miska.Nature.June.2005.clustering.ep.mRNA.pipeline
Lu.Getz.Miska.Nature.June.2005.clustering.ep.miRNA.pipeline
Lu.Getz.Miska.Nature.June.2005.clustering.ALL.pipeline
Lu.Getz.Miska.Nature.June.2005.clustering.miGCM218.pipeline
Lu.Getz.Miska.Nature.June.2005.PDT.miRNA.pipeline
Lu.Getz.Miska.Nature.June.2005.PDT.mRNA.pipeline
ParallelCBS
PNN
PNNXValidationOptimization
RankNormalize
SAMTools.FastaIndex
SraToFastQ
TopHat