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 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

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/