Deprecation

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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 after being added to this page.

Core Applications

2021-07-14
  • snpeff - 4.3p
  • java - java/1.7.0_02, java/1.6.0_31
  • clusterfinder - 313, 718
  • prokka - 1.10, 1.11
  • R - 3.0.2
  • detonate - 1.9
  • vcflib - 201503013
  • switchseq - 20140907
  • freebayes - 0.9.15, 1.0.1-20151115, 1.0.2-20160217, 1.2.0-20180409
  • python - 2.7.8, 2.7.13
  • intel/2013.sp1.3.174 metacv - 2.3.0
  • gcc/5.2.0 multiqc - 1.1, 1.5
  • cutadapt - 1.1, 1.8.1, 2.1, 2.4, 2.5, 2.6, 2.7, 3.2, 3.3
  • gcc/5.2.0 cutadapt - 1.10, 1.15, 1.16, 1.17
  • gcc/5.2.0 opencv - 2.4.13, 2.4.8
2021-02-16
  • R - 3.5.1
  • arcgis - 10.3.1, 1.5.1
  • busco - 3.01
  • edta - 1.8.3, 1.9.0, 1.9.4
  • virsorder - 1.0.3
  • ncbi_blast - 2.4.0, 2.5.0, 2.2.27, 2.2.27, 2.2.30
  • rstudio - 0.99.903-1, 0.99.903, 1.0.136, 1.0.143, 1.1.419
  • qiime2 - 2.0.6, 2017.9, 2017.10, 2017.11, 2017.12, 2018.4
  • atram - 2.0, 2.1, 2.1.2
  • snpeff - 3.3, 3.6, 4.0e, 4.1, 4.2
  • picard - 1.69, 1.72, 1.80, 1.113, 1.137, 2.0.1
  • cmake - 2.8.12.1, 2.8.8, 3.1.0, 3.6.3, 3.12.3, 3.14.5
  • mageck - 0.5.7
  • nanovar - 1.0.1

gcc/5.2.0

  • cpat - 1.2.2
  • blasr - 20160518
  • mpest - 1.5
  • mirena - 2.0
  • statsmodels - 0.8.0
  • tracer - 0.5.1
  • nextgenmap - 0.5.3
  • hisat2 - 2.0.4, 2.0.5
  • quota-alignment - 220170905
  • raxml - 8.2.8
  • masurca - 3.1.3, 3.2.1, 3.2.4, 3.3.0
  • bayescenv - 1.1
  • pipipes - 1.5.0
  • bcbio-nextgen - 0.9.9
  • pyfasta - 0.5.2
  • pirs - 2.0.2
  • graphmap - 0.4.0
  • rcorrector - 1.0.2
  • cute - 20160116
  • pyscaf - 0.12a
  • r2r - 1.0.4
  • parsimonator - 1.0.2
  • kim - 1.8.0
  • pecaller - 1.0.0
  • finestructure - 2.0.7, 2.1.3
  • amptk - 0.8.0, 0.8.5
  • htseq - 0.9.1, 0.10.0, 0.11.0
  • dnaml - 1.0
  • skesa - 2.3.0
  • cube - 4.3.4
  • regtools - 0.4.0
  • gambit - 15.1.0, 16.0.0
  • midas - 20160830
  • metaphinder - 20161215
  • fusioninspector - 1.1.0
  • obitools - 1.2.11
  • wevote - 1.5.0, 1.8.0
  • majiq - 1.0.5
  • cgal - 4.9
  • recycler - 0.62
  • microbecensus - 1.0.7
  • racon - 20161013
  • bcftools - 1.4, 1.8
  • detonenate - 1.11
  • snappy - 1.1.7
  • neat-genreads - 20171102, 20190331
  • ngsutils - 20160507
  • hlahd - 1.1.1
  • kinfin - 1.0.1
  • pauvre - 0.1.86
  • hgtfinder - 20160720
  • icallsv - 0.0.6
  • admxtools - 20160513
  • potion - 1.1.2
  • sexcmd - 20170823
  • cnvkit - 0.9.0
  • ufits - 0.7.2
  • freec - 9.6, 11.0
  • hybphylomaker - 1.5
  • opera - 2.0.6
  • batvi - 1.00
  • paraview - 5.3.
  • graphlan - 0.9.7
  • cryptsplice - 20180111
  • discosnp - 2.2.10
  • agouti - 0.3.3
  • angel - 2.3
  • arcs - 1.0.0, 1.0.1, 1.0.5
  • busco - 3.02
  • augustus - 3.3
  • bali-phy - 2.3.8
  • bamm - 2.5.0
  • bashdb - 4.4-0.94
  • bcftools - 1.4, 1.5, 1.6, 1.8, 1.9
  • bcl2fastq - 2.17.1.14, 2.19.1.403
  • boost - 1.49.0 1.54.0
  • cellprofiler - 2.2.0
2021-01-01
  • angsd - 20150306, 20150909
  • get_homologues - 20150529
2020-07-01

gcc/5.2.0 python/3.5 cleanup

  • cvxopt - 1.1.8
  • ponytools - 0.1
  • irep - 20161025
  • lace - 0.99
  • smcpp - 1.8.0
  • amas - 0.98, 0.99
  • pyani - 0.2.1
  • cvxopt - 1.1.8
  • smcpp - 1.8.0
  • gubbins - 20150519, 20150902, 20160421

gcc/5.2.0 python/3.6 cleanup

  • whatshap - 0.14.1
  • circlator - 1.5.1
  • nanoplot - 1.0.0
  • spades - 3.7.1, 3.10.1
  • kat - 2.3.4
  • epic - 0.2.9
  • illumina-utils - 2.0.2, 2.3
  • albacore - 2.1.10
  • samtools - 1.4.1
  • anvio - 2.0.2, 2.1.0, 2.3.2, 2.4.0
  • nanofilt - 20180408
  • pvactools - 1.0.4
  • porechop - 0.2.3, 0.2.4
  • getorganelle - 1.6.2e
  • chewbbaca - 0.2.5
  • minipolish - 0.1.2
  • bigsi - 0.3.8
  • ariba - 2.13.1
  • biscot - 1.0
  • click-demultiplex - 0.1.0
  • amp - 0.6.1
  • dcm2bids - 2.1.4
  • krocus - 1.0.1
  • nanopack - 1.0.0
  • metasub_utils - 3.0.0
  • taiyaki - 3.0.1, 4.1.0
  • hg-color - 1.1.1

python/2.7.14 cleanup

  • norgal - 1.0.0
  • ploidyngs - 3.1.2
  • maftools - 0.1
  • multigeneblast - 1.1.13
  • crisprcasfinder - 4.2.17
  • alphagenes - 1.0
  • platypus - 0.8.1
  • target - 2.10
  • phylophlan - 0.99
  • hecil - 20180926
  • kmer - 1934
  • mace - 1.2
  • distruct - 2.2
  • dadi - 1.7.0
  • ete - 2.1.539
  • nucdiff - 2.0.2
2020-06-01

gcc/5.2.0 python/2.7.10 cleanup

  • last - 801
  • vcf-kit - 0.1.2
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
  • nipype - 0.12.1 - gcc/5.2.0
  • 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
  • frealign - 9.11
  • khmer - 1.1, 2.0
  • idp-fusion - 1.1.1
  • homblocks - 1.0
  • cobrapy - 0.3.2
  • astrid - 20150807
  • macs - 1.3.7.1-py27, 1.3.7.1, 1.4.2-gx, 1.4.2, 1.4.3
  • garm - 0.7.4
  • strelka - 1.0.15 2.9.2
  • phonopy - 1.9.2
  • sga - 0.10.14
  • markerminer - 20150429, 20150511
  • manta - 1.2.2
  • gkno - 1.30.18
  • falcon - 20130305
  • sepp - 1.0, 3.0
  • pacbio - 3.1.1, 4.0.0
  • iep - 3.6
  • wgs - 8.1, 8.2, 8.3rc1
  • dbg2olc - 0.6
  • oncotator - 1.5.1.0, 1.5.2.0, 1.5.3.0, 1.8.0.0
  • mapsplice - 2.1.5, 2.1.7
  • vtk - 6.1.0
  • nextallele - 20140718
  • plumist - 1.1
  • tomopy - 0.0.3, 0.0.3.1
  • cutadapt - 1.7.1
  • ghmm - 0.9rc3
  • rpy - 2.6.2
  • crossmap - 0.2.3
  • eigenmt - 20160228
  • libgdata - 2.0.18
  • pbjelly - 14.7.14, 14.9.9, 15.2.20
  • rseqc - 2.3.7, 2.6.2
  • eman2 - 2.11, 2.12
  • mycc - 20150710
  • gemini - 0.6.6a, 0.13.1, 0.18.0
  • biom - 1.3.1
  • velvet - 1.2.10-gx
  • weblogo - 3.3-gx
  • screen - 4.6.2
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

2020-06-11
  • openmpi/1.10.2
  • openmpi/2.0.3
  • openmpi/2.1.2

Singularity

Singularity /data images directory was renamed to images.REMOVE to be removed in the future: /data/apps/singularity/images.REMOVE/