# Supported software in EasyBuild 5.0

Due to cleaning up easyconfigs using a deprecated toolchain (cfr. https://docs.easybuild.io/policies/toolchains), the number of supported software is going to decrease significantly in EaysBuild 5.0 compared to the latest EasyBuild 4.x

To limit the "damage" a bit, this document provides a list of software that is currently no longer supported in the `5.0.x` branch of the easyconfigs repository, so we can figure out whether or not we want to salvage the support for these, or not.

The idea is to go through this list, and figure out i) why the software is no longer supported (not relevant anymore, collapsed into a bundle, etc.), ii) whether we should try and preserve the support for that software, or not.

Legend:

- BUNDLE: this software has been collapsed into a bundle in recent easyconfig generation, and so is actually still supported
- KEEP: this software is still relevant, we should try and retain support for it
- RIP: this software is no longer relevant, so there's no need to still supported it
- PR: there are open PRs for this software with a recent toolchain, which we should try and get merged

## Status 2023-11-08

Software for which easyconfigs are available in EasyBuild v4.8.2, but no more in `5.0.x` branch of easyconfigs repository.

### 0-9

- 3d-dna: KEEP?
- 3to2: RIP
- ~~4ti2 (https://github.com/easybuilders/easybuild-easyconfigs/pull/19192)~~

### A

- ada
- ADDA
- ADMIXTURE
- AFNI
- AGFusion
- ALADIN
- Albacore
- ALFA
- Allinea
- ALLPATHS-LG
- Alpha
- ALPS
- Amara
- amask
- AMPL-MP
- amplimap
- AmrPlusPlus
- aNCI
- andi
- ANGEL
- Annif
- ANSYS_CFD
- anvio
- APBS
- arcasHLA
- ARCH
- Arlequin
- ARPACK++
- ArrayFire
- ART
- ARTS
- ARWEN
- ASHS
- Assimulo
- ASTRID
- ATLAS
- atomate
- AtomPAW
- atropos
- ATSAS
- attrdict
- augur
- AutoDockSuite
- AutoGrid
- AutoMap
- autopep8

### B

- BAMSurgeon
- BamUtil
- Bash
- bat
- BatMeth2
- BayesAss
- BayeScan
- BayeScEnv
- bbcp
- bc
- BCALM
- bcgTree
- behave
- BFAST
- BFC
- bgen-reader
- bibtexparser
- BiG-SCAPE
- BinSanity
- Bio-EUtilities
- Bio-SamTools
- biomart-perl
- BirdNET
- biscuit
- bitarray
- BLACS
- BLASR
- blasr_libcpp
- BlobTools
- bnpy
- BOINC
- BoltzTraP
- Bonmin
- Bpipe
- BreakDancer
- BSMAPz
- BSseeker2
- Bullet
- bwakit
- BWISE
- BXH_XCEDE_TOOLS
- byacc
- byobu

### C

- cadaver
- Caffe
- cairomm
- Calcam
- Calendrical
- CAP3
- Cargo
- Carma
- CaSpER
- CastXML
- CaVEMan
- CAVIAR
- cctools
- cdbfasta
- cddlib
- CellMix
- CFDEMcoupling
- cftime
- cget
- CGmapTools
- CGNS
- CHASE
- Cheetah
- chi2comb
- ChimPipe
- Chromaprint
- CIF2Cell
- CIRCexplorer
- CIRI
- cisTEM
- CITE-seq-Count
- CLAPACK
- ClonalFrameML
- CLooG
- ClusterShell
- CNT-ILP
- CNVnator
- Co-phylog
- CoCoALib
- CODEX2
- Commet
- Con3F
- configparser
- CPB
- cram
- cramtools
- CRF++
- CrossMap
- CrossTalkZ
- CryptoMiniSat
- CrystFEL
- CSBLAST
- Cube
- CuCLARK
- custodian
- CVXPY
- cysignals
- cytoolz
- cytosim
- cyvcf2

### D

- dadi
- dagitty
- damageproto
- dammit
- DANPOS2
- davix
- deap
- decona
- deconf
- DeconICA
- DeepSurv
- DeMixT
- destiny
- detonate
- DFT-D4
- DIAL
- DicomBrowser
- Diffutils
- dijitso
- distributed
- DL_POLY_Classic
- DMCfun
- DOLFIN
- Doris
- dropEst
- DSA
- DSRC
- dtcwt

### E

- E-ANTIC
- ea-utils
- earthengine-api
- EasyQC
- ED2
- EggLib
- elastix
- ELPH
- EMU
- enchant
- EnsEMBLCoreAPI
- entrypoints
- EPD
- EPIC
- EricScript
- ESMValTool
- Essentia
- ETSF_IO
- eudev
- evmix
- ExaBayes
- eXpress

### F

- f90cache
- Faber
- faceswap
- FALCON
- FANN
- FastaIndex
- fastPHASE
- fastq-pair
- fastqsplitter
- fastqz
- FastRFS
- fastStructure
- FastViromeExplorer
- fatslim
- fbm
- FCM
- fdstools
- feh
- FEniCS
- Ferret
- FFC
- FFLAS-FFPACK
- ffnet
- FGSL
- FIAT
- FigureGen
- findhap
- findutils
- find_circ
- fineRADstructure
- fineSTRUCTURE
- Firefox
- FireWorks
- FIt-SNE
- FIX
- fixesproto
- FLAIR
- FLEUR
- Flexbar
- FlexiDot
- FMILibrary
- FMRIprep
- FoldX
- fontsproto
- fqtrim
- fqzcomp
- FRANz
- FreeFEM
- FreeFem++
- FreeSASA
- freetype-py
- FRUIT
- FRUIT_processor
- FSLeyes
- fullrmc
- FUNWAVE-TVD
- FuSeq
- FusionCatcher
- future
- fxtract

### G

- G-PhoCS
- g2log
- Gaia
- GAMESS-US
- gap
- GapCloser
- GARLI
- GAT
- Gblocks
- gbs2ploidy
- gdbgui
- GDCHART
- gdist
- gearshifft
- GEM-library
- gencore_variant_detection
- GenomeMapper
- GenomeTester4
- Genome_Profiler
- GenotypeHarmonizer
- Gerris
- GETORB
- GFOLD
- GIMIC
- gimkl
- gimpi
- gimpic: RIP (just CUDA dep nowdays)
- GIMPS
- giolf
- giolfc: RIP (just CUDA dep nowdays)
- git-extras
- Givaro
- Giza
- Glade
- glibc: How was ever a thing?
- GLIMMER
- GlobusConnectPersonal
- glproto
- gmpich
- gmpolf
- gmvapich2
- gmvolf
- GNU
- GP2C
- gradunwarp
- graph-tool
- GraPhlAn
- GraphMap
- GraphMap2
- GRASP
- Grep
- gretl
- grib_api
- GRIT
- GRNBoost
- GroIMP
- GromacsWrapper
- gsettings-desktop-schemas
- gSOAP
- gsport
- GTOOL
- guenomu

### H

- H5hut
- hanythingondemand
- HAPGEN2
- HBase
- HDDM
- hdf5storage
- HDFView
- HEALPix
- heaptrack
- Hello
- HiC-Pro
- HIPS
- hl7apy
- HLAminer
- HOME
- HPCX
- hub
- hyperspy
- HyPo

### I

- i-cisTarget
- i-PI
- I-TASSER
- ICA-AROMA
- icmake
- iCount
- igv-reports
- IMa2
- IMa2p
- Imlib2
- IMPUTE2
- Inelastica
- Infomap
- inputproto
- IntaRNA
- INTEGRATE
- INTEGRATE-Neo
- ioapi
- IOzone
- io_lib
- Ipopt
- ipp
- IPy
- ipyparallel
- ipyrad
- IronPython
- itpp

### J

- JAXFrontCE
- jhbuild
- JiTCODE
- jModelTest
- JWM

### K

- Kaiju
- KAT
- kbproto
- khmer
- KmerGenie
- kpcalg
- Kratos
- kwant
- KWIML
- kWIP
- KyotoCabinet

### L

- lancet
- LASTZ
- LCov
- LeadIT
- LEMON
- less
- libav
- libbitmask
- libcmaes
- libcpuset
- libdivsufsort
- libfontenc
- libglade
- libgtextutils
- libibmad
- libibumad
- libICE: BUNDLE (X11)
- LiBis
- libmo_unpack
- libosmium
- libpsortb
- libpthread-stubs: BUNDLE (X11)
- librosa
- libsamplerate
- libSM: BUNDLE (X11)
- libssh
- libtar
- libutempter
- LibUUID
- libuv
- libX11: BUNDLE (X11)
- libXau: BUNDLE (X11)
- libxcb: BUNDLE (X11)E
- libXcursor: BUNDLE (X11)
- libXdamage: BUNDLE (X11)
- libXdmcp: BUNDLE (X11)
- libXext: BUNDLE (X11)
- libXfixes: BUNDLE (X11)
- libXfont: BUNDLE (X11)
- libXft: BUNDLE (X11)
- libXi: BUNDLE (X11)
- libXinerama: BUNDLE (X11)
- libxkbcommon: BUNDLE (X11)
- libXmu: BUNDLE (X11)
- libXp: BUNDLE (X11)
- libXpm: BUNDLE (X11)
- libXrandr: BUNDLE (X11)
- libXrender: BUNDLE (X11)
- libXt: BUNDLE (X11)
- libXxf86vm: BUNDLE (X11)
- libzeep
- lie_learn
- liknorm
- limix
- LinBox
- Lmod
- LoFreq
- Log-Log4perl
- logaddexp
- LOHHLA
- Loki
- lrslib
- LSMS
- LtrDetector
- Lucene-Geo-Gazetteer
- LUSCUS
- lynx

### M

- MACH
- magick
- MagresPython
- MAJIQ
- makedepf90
- MapSplice
- Maq
- MARS
- MathGL
- mawk
- mc
- mdtest
- medImgProc
- MEGACC
- Meld
- memkind
- memory-profiler
- meRanTK
- MERCKX
- MESS
- MetaboAnalystR
- metaerg
- MetaGeneAnnotator
- Metaxa2
- mhcflurry
- MINC
- MinCED
- minieigen
- Minimac4
- miRDeep2
- MitoZ
- mkl-dnn
- mkl_fft
- MLC
- MMSEQ
- MOABS
- MOB-suite
- modred
- Molekel
- Molpro
- MOOSE
- mordecai
- MoreRONN
- Mothur
- motionSegmentation
- MPICH2
- mpiP
- MPJ-Express
- MSM
- MTL4
- MultiNest
- Multiwfn
- MuPeXI
- MuSiC
- MuTect
- mutil
- MVAPICH2
- mxml
- MyCC
- MyMediaLite
- mympingpong
- mypy
- MySQL
- MySQL-python
- mysqlclient

### N

- nanonet
- nauty
- NCBI-Toolkit
- ncompress
- nd2reader
- ne
- NEdit
- Nek5000
- neon
- netCDF-C++
- netloc
- netMHCIIpan
- netMHCpan
- NeuroKit
- NEXUS-CL
- NGS-Python
- NGSadmix
- NIfTI
- nifti2dicom
- NIMBLE
- NLMpy
- Node-RED
- Normaliz
- nose-parameterized
- novoalign
- NOVOPlasty
- npstat
- NRGLjubljana
- ntEdit
- ntHits
- numpy: BUNDLE (SciPy-bundle)
- NxTrim

### O

- Oases
- OBITools
- OCaml
- OCNet
- OMA
- OOMPA
- OpenColorIO
- OpenFOAM-Extend
- OpenKIM-API
- OpenMS
- OpenNLP
- OpenPIV
- OPERA
- OptiType
- OR-Tools
- OrfM
- OrthoMCL
- ownCloud
- oxford_asl

### P

- p4-phylogenetics
- p4vasp
- pandas-datareader
- PANDAseq
- PARI-GP
- pasta
- PaStiX
- path.py
- pbbam
- pbcopper
- pbdagcon
- pbmm2
- PBSuite
- pbs_python
- PCAngsd
- PCC
- PCL
- PCMSolver
- PCRaster
- PennCNV
- Percolator
- perl-app-cpanminus
- Perl4-CoreLibs
- PGDSpider
- PGI
- PHANOTATE
- PHASE
- PHAST
- PheWAS
- PheWeb
- PhiPack
- PHLAT
- phono3py
- PhyloBayes-MPI
- phylokit
- phylonaut
- PIL
- PileOMeth
- PIMS
- Pingouin
- pip: : BUNDLE (Python)
- pIRS
- Pisces
- piSvM
- piSvM-JSC
- pizzly
- PlaScope
- PLAST
- Platanus
- Platypus
- plc
- PLINKSEQ
- Ploticus
- plotly: plotly.py exists
- PLplot
- pomkl
- pompi
- poretools
- Portcullis
- Postgres-XL
- PPfold
- ppl
- pplpy
- PRC
- printproto: BUNDLE (X11)
- ProjectQ
- prompt-toolkit
- proovread
- propy
- ProtHint
- protozero
- pscom
- PSI
- PSIPRED
- psmc
- psmpi
- psmpi2
- PSORTb
- psrecord
- pstoedit
- ptemcee
- PTESFinder
- pubtcrs
- py
- pyABC
- PyAPS3
- Pychopper
- PyCifRW
- pycma
- pycodestyle
- PyCogent
- PyDatastream
- pydlpoly
- pyenchant
- PyFFmpeg
- pyfits
- PyFMI
- PyFR
- pygccxml
- pyGIMLi
- Pygments
- pygrib
- PyGTK
- PyGTS
- PyGWAS
- pyhdf
- Pyke3
- pymatgen-db
- pymemcache
- PyNAST
- pyplusplus
- PyQt: RIP (PyQt5, PyQt6)
- PyRe
- pyringe
- Pyro4
- PyRosetta
- pyScaf
- pysndfx
- Pysolar
- pysqlite
- pystran
- python-hl7
- python-weka-wrapper3
- pythran
- PyVCF

### Q

- Q6
- qcint
- QDD
- QEMU
- QIIME
- QML
- qpth
- Qt: RIP (Qt5, Qt6 instead)
- qtop
- QuaZIP
- Quip
- Quorum
- QuTiP

### R

- RaGOO
- randfold
- randrproto
- rapidtide
- Rascaf
- Ray-assembler
- RBFOpt
- Rcorrector
- rCUDA
- Reads2snp
- Reapr
- Red
- Redundans
- RELION
- ReMatCh
- REMORA
- renderproto
- RepastHPC
- requests
- RERconverge
- rhdf5
- RheoTool
- rickflow
- RNAclust
- RNAcode
- RNAIndel
- RNAmmer
- RNAz
- ROI_PAC
- ROME
- rootpy
- root_numpy
- Rosetta
- rpmrebuild
- RQGIS3
- RStan
- rstanarm
- Ruby-Tk

### S

- S-Lang
- S4
- SAGE
- Sailfish
- SALib
- SALMON-TDDFT
- Samcef
- SAS
- savvy
- SCALCE
- sciClone
- ScientificPython
- scikit-cuda
- scikit-multilearn
- SCIPhI
- scipy
- SCnorm
- SCOOP
- scp
- Scrappie
- SDCC
- SDL
- SDL_image
- SDSL
- SearchGUI
- SECAPR
- Seeder
- segmentation-models
- SeisSol
- SelEstim
- sep
- Seq-Gen
- seq2HLA
- Seqmagick
- SeqPrep
- Shannon
- shapAAR
- sharutils
- shift
- SHORE
- sickle
- SimpleElastix
- simpy
- SimVascular
- SingleM
- SIP
- sketchmap
- skewer
- SLATEC
- sleuth
- slidingwindow
- smafa
- smallgenomeutilities
- SMARTdenovo
- Smoldyn
- SNAPE-pooled
- snaphu
- SNPhylo
- SOAPaligner
- SOAPdenovo-Trans
- SOAPdenovo2
- SOAPfuse
- socat
- SolexaQA++
- spectral.methods
- Sphinx
- SpiceyPy
- SPLASH
- SpliceMap
- split-seq
- splitRef
- SPRNG
- SSAHA2
- SSN
- STAMP
- StaMPS
- Stampy
- STAR-Fusion
- STIR
- stpipeline
- strelka
- suds
- SUMACLUST
- SUMATRA
- SunPy
- supermagic
- supernova
- SVDetect
- SVDquest
- swarm
- SWASH
- swissknife
- SYMPHONY

### T

- taco
- TagLib
- Taiyaki
- TCC
- tecplot360ex
- Telescope
- terastructure
- Tesla-Deployment-Kit
- testpath
- TEToolkit
- Text-CSV
- THetA
- thurstonianIRT
- TiCCutils
- Tika
- TiMBL
- TinyDB
- Tombo
- TotalView
- Tracer
- Transrate
- travis
- TreeShrink
- TRUST
- tsne
- TVB
- tvb-data
- TVB-deps
- tvb-framework
- tvb-library

### U

- UCLUST
- udocker
- UFL
- umis
- UNAFold
- units
- UQTk
- USPEX

### V

- Vampir
- VarDict
- VariantMetaCaller
- variant_tools
- vartools
- VAtools
- VCF-kit
- vcfnp
- VEGAS
- verifyBamID
- VERSE
- VirSorter
- VMTK
- vsc-base
- vsc-install
- vsc-mympirun-scoop
- vsc-processcontrol
- VV
- VXL

### W

- wcwidth
- WebSocket++
- WEKA
- wheel: BUNDLE (Python)
- Winnowmap
- WISExome
- wkhtmltopdf
- WRF-Fire
- wrf-python
- wxPropertyGrid

### X

- XALT
- xbitmaps: BUNDLE (X11)
- xcb-proto: BUNDLE (X11)
- xcb-util: BUNDLE (X11)
- xcb-util-image: BUNDLE (X11)
- xcb-util-keysyms: BUNDLE (X11)
- xcb-util-renderutil: BUNDLE (X11)
- xcb-util-wm: BUNDLE (X11)
- xCell
- xextproto
- xf86vidmodeproto
- xineramaproto
- XKeyboardConfig: BUNDLE (X11)
- XMDS2
- XMLSec
- XMLStarlet
- xonsh
- XSD
- XTandem

### Y

- Yade
- YAPS

### Z

- zingeR
- zlibbioc
- ZPAQ