Difference between revisions of "Deprecation"

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* most - 20160721
 
* most - 20160721
 
* rnaquast - 1.2.0
 
* rnaquast - 1.2.0
*  
+
* sdt - 1.2
 +
* marygold - 0.2
 +
* kmergenie - 1.6741
 +
* haptree - 1.0
 +
* hmmsplicer - 0.9.5
 +
* mocat - 1.3r2, 2.0
 +
* metamos - 1.5.0rc4-20140827
 +
* iclipro - 0.1.1
 +
* bamreadcount - 20150216
 +
* spark - 2.1.0
 +
* falcon_unzip - 20160623
 +
* pbcommand - 20151203
 +
* stacks 1.05, 1.18, 1.21, 1.24, 1.35, 1.45, 1.48
 +
* poretools - 0.5.0
 +
* transabyss - 1.5.4
 +
* orthofinder - 0.2.5, 0.6.0, 2.1.2, 2.2.1, 2.2.3, 2.2.6, 2.2.7, 2.3.3, 2.3.8
 +
* snappy - 1.2.1
 +
* reago - 1.1
 +
* srst2 - 0.2.0
 +
* spades - 3.0.0, 3.1.0, 3.5.0, 3.6.0, 3.6.2, 3.9.0, 3.10.0
  
 
;2020-04-01:
 
;2020-04-01:

Revision as of 22:30, 23 April 2020

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.

Core Applications

2020-05-01
  • opencv - 2.4.8 - gcc/4.7.2
  • rnaskim - .20140625 - gcc/4.7.2
  • syzygy - 1.2.7 - gcc/4.7.2
  • cgat - 0.2.3
  • pyrad - 3.0.63
  • ddocent - 20160425
  • ceas - 1.0.2
  • metassembler - 1.5
  • dapars - 0.9.0
  • miso - 0.5.2
  • anvio - 2.0.0
  • phyluce - 20140427, 20151103, 20160715
  • conifer - 0.2.2
  • bsmap - 2.74
  • seqmagick - 20150923
  • clipper 1.0
  • fast-iclip - 0.9.1
  • bedops - 2.4.2
  • mats - 2.1.0, 3.2.1.beta
  • arc - 20140305, 20140312
  • cellprofiler - 2.0, 2.2.0
  • peer - 20120508
  • busco - 2.0b
  • agalm - 0.3.5
  • pbsmrtpipe - 20151202
  • afni - 2016_0_19-openmpi, 2016_2_09
  • gsutil - 4.15
  • agalma - 0.5.0
  • meme - 4.8.1
  • binsanity - 0.1.3, 0.2.5.9
  • exomcnv - 1.4
  • last - 193, 247, 531
  • sweep - 20160211
  • shannon - 20160211
  • shorah - 20130830, 20131204
  • treecorr - 3.2.3
  • ngscat - 0.1
  • cufflinks - 2.2.0
  • ectools - 20140311, 20141201
  • concoct - 0.3.1
  • bcbio-nextgen - 0.8.7
  • ale - 20150507
  • cerulean - 0.1
  • most - 20160721
  • rnaquast - 1.2.0
  • sdt - 1.2
  • marygold - 0.2
  • kmergenie - 1.6741
  • haptree - 1.0
  • hmmsplicer - 0.9.5
  • mocat - 1.3r2, 2.0
  • metamos - 1.5.0rc4-20140827
  • iclipro - 0.1.1
  • bamreadcount - 20150216
  • spark - 2.1.0
  • falcon_unzip - 20160623
  • pbcommand - 20151203
  • stacks 1.05, 1.18, 1.21, 1.24, 1.35, 1.45, 1.48
  • poretools - 0.5.0
  • transabyss - 1.5.4
  • orthofinder - 0.2.5, 0.6.0, 2.1.2, 2.2.1, 2.2.3, 2.2.6, 2.2.7, 2.3.3, 2.3.8
  • snappy - 1.2.1
  • reago - 1.1
  • srst2 - 0.2.0
  • spades - 3.0.0, 3.1.0, 3.5.0, 3.6.0, 3.6.2, 3.9.0, 3.10.0
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
2020-03-26
  • python/2.6.8
  • python/2.7.3
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

CUDA 9 Applications

2020-04-01
  • Guppy - 2.3.5, 2.3.7, 3.1.5, 3.2.1, 3.2.2
  • beagle - 3.0.2.20181009, 3.0.1.20180607

MPI Applications