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
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- 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
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- 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
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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
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- 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
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- 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/