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/