Deprecation

Apps and Databases to Remove

A list of software and the databases that are going to be deprecated. The modules are removed and the software is put into the REMOVE directories to be removed 6 months from being added to this page.

2020-04-01

• tophat - 2.0.8b, 2.0.1, 2.0.13, 2.0.11, 1.4.1, 1.3.3b, 1.3.0
• MATS - 3.0.4.beta, 3.0.6.beta, 3.0.8
• afni - 2011_12_21_1014, 2013_05_31, 2013_11_24-openmp
• agalma - 0.2.1
• amuse - 6.0
• arc - 20130715
• bayesrate - 1.3.43
• beta - 1.0.5
• cgat - 0.2.3
• cufflinks - 1.3.0, 2.0.0, 2.0.2
• emirge - 20130727
• eval - 2.2.8
• htseq - 0.5.3p3, 0.6.1p1
• libsvm - 3.12
• lsc - 0.3.1, 0.3, 1alpha, 1beta, 2.0
• maker - 2.10, 2.25b
• metamos - 1.3.1
• miso - 0.4.4, 0.4.9
• modeller - 9.11, 9.13
• msmbuilder - 2.5.1
• nexuscl - 2.1.18
• ngsutils - 20130722, 20150206
• partitionfinder - 1.0.1, 2.0.0-pre8, 2.0.0-pre10, 2.0.0-pre11
• phycas - 1.2.0
• scons - 2.3.0
• spades - 2.5.0, 2.5.1 - More will be removed in the future some are loaded as dependencies
• spanki - 0.4.1, 0.4.3, 0.5.0
• sparcc - 201402
• spimap - 1.1, .1.1.git20120501
• treefix - 1.1.10, 1.1.7
• vcflib - 20121207, 20141119
• velvet - 1.2.06, 1.2.07
• wgs - 7.0.1.23-pacbio, 7.0.1.23, 8.0.r4443-pacbio, 8.0.r4443
• idba-ud - 1.0.9, 1.1.0
• freebayes - 0.9.13, 0.9.14, 0.9.6, 0.9.7, 0.9.9.2

2020-03-01

• homer - 20130529, 4.5, 4.6, 4.7, databases
• fgenesb - 2012, databases
• picrust - 1.0.0-gx
• qiime - 1.5.0, 1.6.0, 1.8.0, 1.9.0
• iprscan - 4.8, 5.0rc6, 5.19-58.0, 5.24-63.0, 5.25-64.0, 5.26-65.0, 5.29-68.0.bak, database