config

#####################################################
##                                                 ##
## DO NOT EDIT outside of the mxtools repository ! ##
##                                                 ##
#####################################################

# file format:
#
# package [command] [command...]
#	[command] [command...]
#
#
# makebin recreates ../bin, ../lib from this configuration file.
# each manually created package requires also an profile (./lib/$PKG.profile), which sets
# the environment for the package. the packages path should be prepended to the original
# path for wrappers to work.
#
# makebin will create ../bin/prun - a wrapper for any command in any package.
# (eg. prun staden $SHELL) and ../bin/$COMMAND for each command defined in this
# file.
#
# only commands, which are to be pubslished to the general environment should
# go here. no package internal stuff.
#
#
# some examples following:
#
# this one is really short (/usr/local/package/lib/mariux64ant.profile, without #! !!!)
#
#   export PATH=/package/mariux64/ant/bin:${PATH}
#
# mind the mode '644' and/or your umask
#
# to distribute w. cleanup do:
#   pdist push --delete --files=/usr/local/package my_devel_host
#   pdist push --delete --files=/usr/local/package --para=100 ALL
#
# no real application yet.


# Software from Sanger Center related to sequencing processing
# Alfred Beck
# this and more in /package/assembly
#

newbadger	phrap2gap

#
# Alfred Beck...
#
dotter dotter

phrap
	phrap phrap.longreads phrap.manyreads
	gcphrap
	cross_match cross_match.manyreads

phred	phred

# Donald Buczek

ddbtools
	iview
	dircmp
	vncviewer

# who uses yaml2json? pandoc is now part of haskell
# but this one is still under ddbtools/pandoc
pandoc
	yaml2json

# repeatmasker RepeatMasker

trnascan
	tRNAscan-SE

# PM & AB
emboss
	EMBOSS

orpheus dps

#
# MPI (message passing interface) - libraries and executables
lam
	hboot
	hcc
	hcp
	hf77
	lamboot
	lamclean
	lamd
	lamexec
	lamgrow
	lamhalt
	laminfo
	lamnodes
	lamshrink
	lamtrace
	mpiCC
	mpiCC_lam
	mpicc
	mpicc_lam
	mpif77
	mpif77_lam
	mpimsg
	mpirun
	mpirun_lam
	mpitask
	mpiexec
	recon
	tkill
	tping
	wipe
	mpic++

#
#  tree-puzzle
#  ML phylogenetic reconstruction package
#  www.tree-puzzle.de
#
#tree_puzzle
#	puzzle
#	ppuzzle
#	puzzle51
#	ppuzzle51

#
# R statistic package
#r	R2.15.2
#	R2.15.1
#	R2.14.1
#	R2.12.1


#
#  molphy
#  MOLPHY () by Jun Adachi & Masami Hasegawa
#  http://www.ism.ac.jp/software/ismlib/softother.e.html#molphy
#  ftp://ftp.ism.ac.jp/pub/ISMLIB/MOLPHY/
#
molphy
	njdist
	nucml
	nucst
	protml
	protst
	ali2mol
	clus2mol
	degene4
	degene4l
	disjoint
	dna2ami
	eali2mol
	egetcds
	getcds
	ggetcds
	inf2mol
	infocode
	infocode2
	int2mol
	mc2mol
	mega2mol
	mol2inf
	mol2int
	mol2mol
	mol2phy
	mol2seq
	molcat
	molcodon
	molcons
	molcut
	molinfo
	mollist
	molmerge
	molrev
	molsplit
	must2mol
	njt2tpl
	nuc2NUC
	nuc2code
	nuc2ptn
	phy2mol
	rmid3
	rminsdel
	rmleu
	rmsyno
	seq2mol
	seqwrap

#
#  treeview
#  the TreeView program by Rod Page
#  http://taxonomy.zoology.gla.ac.uk/rod/treeviewx/.
#

treeviewx
	tvx

#
# MATLAB ABT Vin & andere
#
matlab
	matlab
#	matlabr2013a
#	matlabr2011b
#	mex
	mcc
	mbuild


#jexpress
#        Jexpress


# vokabel, ocaml, dict alles (alt-) package/has
#
# vokabel
# 	vokabel
# 	itvokabel
# 	frvokabel
# 	spvokabel
#
# ocaml
#         ocamlrun
#         ocamlc
#         ocaml
#         ocamllex
#         ocamlyacc
#         ocamldep
#         ocamlprof
#         ocamlcp
#         ocamlmktop
#         labltk
#         ocamlbrowser
#         ocamldebug
#
# dict
# 	dict
# 	dictd
# 	dictzip

# Peters Image-Gallery-Datenbank
imgdb	igal

# mfold
mfold
	add-dHdSTm
	filter-sort
	nafold2
	quikfold
	ss-count
	add-dHdSTm2
	ct_boxplot_ng
	genss
	naview
	sav2p-num
	tgd
	auto_ct2ps
	ct_compare
	h-num
	naview.exe
	sav2p-num2
	auxgen
	distance
	h-num.exe
	newtemp
	sav2plot
	batgen
	efn
	mfold
	plt22gif
	sav2plot2
	boxplot_ng
	efn2
	nafold
	plt22ps
	scorer
#ct2rnaml -nur noch im Package unafold

unafold
	ITC-plot.pl
	UNAFold.pl
	concentration
	concentration-same
	concentrations-same.pl
	concentrations.pl
	ct-energy
	ct-energy-det.pl
	ct-ext
	ct-prob
	ct-uniq
	ct2rnaml
	dG2Cp
	dG2dH
	dG2dS
	ensemble-dg
	ensemble-dg-same
	ensemble-ext
	ensemble-ext-same
	h-num.pl
	hybrid
	hybrid-2s.pl
	hybrid-min
	hybrid-plot
	hybrid-plot-ng
	hybrid-select.pl
	hybrid-ss
	hybrid-ss-2s.pl
	hybrid-ss-min
	hybrid-ss-noml
	hybrid-ss-simple
	hybrid2-2s-x.pl
	hybrid2-2s.pl
	hybrid2-min-x.pl
	hybrid2-min.pl
	hybrid2-x.pl
	hybrid2.pl
	melt.pl
	plot2ann.pl
	sbs
	ss-count.pl

# ab
reputer	repfind repselect repvis

compass
	mk_compass_db
	compass_vs_db
	compass

primer3
	primer3

cytoscape-3.9.1-0
	cytoscape

# admintools
admin
        mtime.pl
        archiver.pl
        fdu
        findd
        multitar
        eierlegendewollmilchsau.pl
        eier
        ovi
        diskcheck
        tw_replace.pl
        scd
        sousage.pl
        kvm
        ddrescue
        ddrescuelog
        ddrutility
        ddru_ntfsbitmap
        ddru_ntfsfindbad
        ddru_diskutility
        ddru_findbad.sh
        growisofs
        tagdelete
        delete_tagged.sh
        sw_cli
        ssh_tag.pl
        sas_error_check.pl
        nufo
        meson-options.py

# tex/bibtex tool
jabref
	jabref

#SplitsTree: Analyzing and Visualizing Evolutionary Data
splitstree
	SplitsTree

mathematica
	mathematica

possum
	mkvtree
	possumdist
	possumdist-mt
	possumfreqs
	possumsearch
	possumsearch-mt
	prints2gen
	transfac2gen

ssaha
	ssaha2
	ssaha

blastz
	blastz

# Kent's blat not blast
blat
	blat
	faToNib
	faToTwoBit
	gfClient
	gfServer
	nibFrag
	pslPretty
	pslReps
	pslSort
	twoBitInfo
	twoBitToFa

psipred
	pfilt
	psipass2
	psipred
	seq2mtx

viennarna
	AnalyseDists
	AnalyseSeqs
	Kinfold
	RNALfold
	RNAalifold
	RNAcofold
	RNAdistance
	RNAduplex
	RNAeval
	RNAfold
	RNAforester
	RNAheat
	RNAinverse
	RNApaln
	RNApdist
	RNAplfold
	RNAplot
	RNAsubop

jruby
	jgem
	jirb
	jirb_swing
	jruby
	jrubyc

jalview
	Jalview

octave
	mkoctfile
	octave
	octave-cli
	octave-config

radius	radadm

infernal
	cmalign   cmbuild   cmemit    cmscore   cmsearch

spatt
	cpspatt
	gspatt
	ldspatt
	oldxspatt
	sspatt
	xspatt

pdfsam
	pdfsam_console
	pdfsam

mcl
	clm
	clmformat
	mcl
	mclcm
	mclblastline
	mclpipeline
	mcx
	mcxarray
	mcxassemble
	mcxdeblast
	mcxdump
	mcxi
	mcxload
	mcxmap
	mcxrand
	mcxsubs

eagleview
	EagleIndexFasta
	EagleIndexSff
	EagleIndexSffM
	EagleView

allegro
	allegro

mummer
#        annotate
        combineMUMs
        delta-filter
        dnadiff
        exact-tandems
        gaps
        mapview
        mgaps
        mummer
        mummerplot
        nucmer
        nucmer2xfig
        postnuc
        postpro
        prenuc
        prepro
        promer
        repeat-match
        run-mummer1
        run-mummer3
        show-aligns
        show-coords
        show-diff
        show-snps
        show-tiling

trawler
	verrepresentation.pl
	pipeline_trawler_01_som.pl
	pipeline_trawler_01_som_single_strand.pl
	pipeline_trawler_02.pl
	pipeline_trawler_02_no_orthologs.pl
	pipeline_trawler_02_no_orthologs_single_strand.pl
	pipeline_trawler_02_single_strand.pl
	pipeline_trawler_03.pl
	trawler.pl

ANNOTATE
	ANNOTATE_v3.04

trimal
	trimal
	readal

gblocks
	Gblocks

phylobayes
	ancestral
	bf
	bpcomp
	brpo
	cvrep
	pb
	ppred
	readcv
	readdiv
	readpb
	stopafter
	stoppb
	subsample
	sumcv
	tracecomp
	tree2ps

python-2.7=python-2.7.16-0
	python2.7
	python2.7-config
	pip2.7

python-2=python-2.7
	python2			# PEP 0394 https://www.python.org/dev/peps/pep-0394/
	python2-config		# PEP 0394
	idle2=idle		# PEP 0394
	pydoc2=pydoc		# PEP 0394
	pip2
	ipython2
	virtualenv2=virtualenv

python2=python-2	# this has been published

R_ddbtools
	R-3.2.3
	Rscript-3.2.3

mariux64python27
#        python-2.7
#        python-2.7-config
#        python-2.7-2to3
#        python-2.7-idle
#        python-2.7-pydoc


mariux64R
	R-3.3.2
	R-3.3.1
	R-3.2.0
	R-3.1.2
	R-3.1.1
        R-3.1.0
        R-3.0.2
        R-3.0.0
        Rscript-3.3.2
        Rscript-3.3.1
        Rscript-3.2.0
        Rscript-3.1.2
        Rscript-3.1.1
        Rscript-3.1.0
        Rscript-3.0.2
        Rscript-3.0.0
#       R-2.15.3
#       R-2
#       R2
        Rscript-2.15.3
        Rscript-2
        Rscript2

mariux64ant
  ant-1.9=ant

mariux64

texlive2012

texlive2015

texlive2020

texlive2022
	a2ping
	a5toa4
	adhocfilelist
	afm2afm
	afm2pl
	afm2tfm
	aleph
	allcm
	allec
	allneeded
	amstex
	arara
	arlatex
	authorindex
	autoinst
	autosp
	axohelp
	bbl2bib
	bbox
	bg5+latex
	bg5+pdflatex
	bg5conv
	bg5latex
	bg5pdflatex
	bib2gls
	bibdoiadd
	bibexport
	bibmradd
	bibtex
	bibtex8
	bibtexu
	biburl2doi
	bibzbladd
	bundledoc
	cachepic
	cef5conv
	cef5latex
	cef5pdflatex
	cefconv
	ceflatex
	cefpdflatex
	cefsconv
	cefslatex
	cefspdflatex
	cfftot1
	checkcites
	checklistings
	chkdvifont
	chklref
	chktex
	chkweb
	cjk-gs-integrate
	cllualatex
	cluttex
	clxelatex
	context
	contextjit
	convbkmk
	convertgls2bib
	cslatex
	csplain
	ctan-o-mat
	ctanbib
	ctangle
	ctanify
	ctanupload
	ctie
	ctwill
	ctwill-refsort
	ctwill-twinx
	cweave
	de-macro
	depythontex
	detex
	devnag
	deweb
	diadia
	disdvi
	dosepsbin
	dt2dv
	dtxgen
	dv2dt
	dvi2fax
	dvi2tty
	dviasm
	dvibook
	dviconcat
	dvicopy
	dvidvi
	dvigif
	dvihp
	dviinfox
	dvilj
	dvilj2p
	dvilj4
	dvilj4l
	dvilj6
	dvilualatex
	dvilualatex-dev
	dviluatex
	dvipdfm
	dvipdfmx
	dvipdft
	dvipng
	dvipos
	dvips
	dvired
	dviselect
	dvispc
	dvisvgm
	dvitodvi
	dvitomp
	dvitype
	e2pall
	ebb
	ebong
	eplain
	epsffit
	epspdf
	epspdftk
	epstopdf
	eptex
	etex
	euptex
	exceltex
	extconv
	extractbb
	extractres
	fig4latex
	findhyph
	fmtutil
	fmtutil-sys
	fmtutil-user
	fontinst
	fragmaster
	gbklatex
	gbkpdflatex
	getmapdl
	gftodvi
	gftopk
	gftype
	gregorio
	gsftopk
	hbf2gf
	ht
	htcontext
	htlatex
	htmex
	httex
	httexi
	htxelatex
	htxetex
	includeres
	inimf
	initex
	installfont-tl
	jadetex
	jamo-normalize
	jfmutil
	kanji-config-updmap
	kanji-config-updmap-sys
	kanji-config-updmap-user
	kanji-fontmap-creator
	ketcindy
	komkindex
	kpseaccess
	kpsepath
	kpsereadlink
	kpsestat
	kpsetool
	kpsewhere
	kpsewhich
	kpsexpand
	l3build
	lacheck
	lamed
	latex
	latex-dev
	latex-git-log
	latex-papersize
	latex2man
	latex2nemeth
	latexdef
	latexdiff
	latexdiff-vc
	latexfileversion
	latexindent
	latexmk
	latexpand
	latexrevise
	lily-glyph-commands
	lily-image-commands
	lily-rebuild-pdfs
	listbib
	listings-ext.sh
	lollipop
	ltx2crossrefxml
	ltxfileinfo
	ltximg
	luacsplain
	luahbtex
	luajithbtex
	luajittex
	lualatex
	lualatex-dev
	luaotfload-tool
	luatex
	luatools
	lwarpmk
	m-tx
	mag
	make4ht
	makedtx
	makeglossaries
	makeglossaries-lite
	makeindex
	makejvf
	match_parens
	mathspic
	mendex
	mex
	mf
	mf-nowin
	mf2pt1
	mflua
	mflua-nowin
	mfluajit
	mfluajit-nowin
	mfplain
	mft
	mk4ht
	mkgrkindex
	mkindex
	mkjobtexmf
	mkocp
	mkofm
	mkpic
	mkt1font
	mktexfmt
	mktexlsr
	mktexmf
	mktexpk
	mktextfm
	mllatex
	mltex
	mmafm
	mmpfb
	mpost
	mptopdf
	msxlint
	mtxrun
	mtxrunjit
	multibibliography
	musixflx
	musixtex
	odvicopy
	odvitype
	ofm2opl
	omfonts
	opl2ofm
	optex
	ot2kpx
	otangle
	otfinfo
	otftotfm
	otp2ocp
	outocp
	ovf2ovp
	ovp2ovf
	pamphletangler
	patgen
	pbibtex
	pdfannotextractor
	pdfatfi
	pdfbook2
	pdfclose
	pdfcrop
	pdfcslatex
	pdfcsplain
	pdfetex
	pdfjadetex
	pdfjam
	pdflatex
	pdflatex-dev
	pdflatexpicscale
	pdfmex
	pdfopen
	pdftex
	pdftex-quiet
	pdftosrc
	pdfxmltex
	pdfxup
	pdvitomp
	pdvitype
	pedigree
	perltex
	pfarrei
	pfb2pfa
	pk2bm
	pkfix
	pkfix-helper
	pktogf
	pktype
	platex
	platex-dev
	pltotf
	pmpost
	pmxab
	pmxchords
	pn2pdf
	pooltype
	ppltotf
	prepmx
	ps2eps
	ps2frag
	ps2pk
	ps4pdf
	psbook
	psjoin
	pslatex
	psnup
	psresize
	psselect
	pst2pdf
	pstops
	ptex
	ptex2pdf
	ptftopl
	purifyeps
	pygmentex
	pythontex
	r-mpost
	r-pmpost
	r-upmpost
	repstopdf
	rpdfcrop
	rubibtex
	rubikrotation
	rumakeindex
	rungs
	scor2prt
	simpdftex
	sjisconv
	sjislatex
	sjispdflatex
	splitindex
	srcredact
	sty2dtx
	svn-multi
	synctex
	t1ascii
	t1asm
	t1binary
	t1disasm
	t1dotlessj
	t1lint
	t1mac
	t1rawafm
	t1reencode
	t1testpage
	t1unmac
	t4ht
	tangle
	teckit_compile
	tex
	tex2aspc
	tex4ebook
	tex4ht
	texconfig
	texconfig-dialog
	texconfig-sys
	texcount
	texdef
	texdiff
	texdirflatten
	texdoc
	texdoctk
	texexec
	texfot
	texhash
	texlinks
	texliveonfly
	texloganalyser
	texlua
	texluac
	texluajit
	texluajitc
	texmfstart
	texosquery
	texosquery-jre5
	texosquery-jre8
	texplate
	texsis
	tftopl
	thumbpdf
	tie
	tlcockpit
	tlmgr
	tlshell
	tpic2pdftex
	ttf2afm
	ttf2kotexfont
	ttf2pk
	ttf2tfm
	ttfdump
	ttftotype42
	typeoutfileinfo
	ulqda
	upbibtex
	updmap
	updmap-sys
	updmap-user
	updvitomp
	updvitype
	uplatex
	uplatex-dev
	upmendex
	upmpost
	uppltotf
	uptex
	uptftopl
	urlbst
	utf8mex
	vftovp
	vlna
	vpe
	vpl2ovp
	vpl2vpl
	vptovf
	weave
	webquiz
	wofm2opl
	wopl2ofm
	wordcount
	wovf2ovp
	wovp2ovf
	x86_64-pc-linux-gnu
	xdvi
	xdvi-xaw
	xdvipdfmx
	xelatex
	xelatex-dev
	xetex
	xhlatex
	xindex
	xmltex
	yplan

mx_tools
        vacation-admin

icepdf
	icepdfview

samba
	smbstatus smbclient smbcontrol net

pbackup
	pbackup

cyrus
	sieveshell

archive		robot

mono	mono
	mcs
	gacutil
	al

mono6=mono-6.10.0-0
  mono6=mono

node-8.11.4-0
node-8.11.4=node-8.11.4-0
node-8=node-8.11.4
node-8
	node8=node
	npm8=npm


node-10.16.0-0
node-10.16.0=node-10.16.0-0
node-10=node-10.16.0
node-10
	node10
	npm10
	npx10

node-12.4.0-0
node-12.4.0=node-12.4.0-0
node-12=node-12.4.0
node-12
	node12=node
	npm12=npm
	npx12=npx

node-16.17.0-0
node-16.17.0=node-16.17.0-0
node-16=node-16.17.0
node-16
	node16=node
	npm16=npm
	npx16=npx

node-18.16.0-0
node-18.16.0=node-18.16.0-0
node-18=node-18.16.0
node-18
	node18=node
	npm18=npm
	npx18=npx

node-20.13.1-0
node-20.13.1=node-20.13.1-0
node-20=node-20.13.1
node-20
	node20=node
	npm20=npm
	npx20=npx

node=node-20
	node
	npm
	npx

gephi
  gephi

### sra-tools: following ones are no longer in the package
# align-cache
# ccextract
# check-corrupt
# general-loader
# md5cp
# pacbio-loadxml
# pileup-stats
# read-filter-redact
# vdb-diff

sra-tools=sra-tools-3.0.0-0
	abi-dump
	abi-load
	align-info
	bam-load
	cache-mgr
	cg-load
	copycat
	fasterq-dump
	fastq-dump
	fastq-load
	helicos-load
	illumina-dump
	illumina-load
	kar
	kdbmeta
	kget
	latf-load
	pacbio-load
	prefetch
	rcexplain
	remote-fuser
	sam-dump
	sff-dump
	sff-load
	sra-pileup
	sra-sort
	sra-stat
	srapath
	srf-load
	test-sra
	vdb-config
	vdb-copy
	vdb-decrypt
	vdb-dump
	vdb-encrypt
	vdb-lock
	vdb-passwd
	vdb-unlock
	vdb-validate

flightgear
  fgfs
  osgviewer

# prep fuer david, openal-info dann weghauen (thomas)
OpenRA
  openra

obs-studio
  obs

vscode-1.92.0-0
  code

jdk-7u80-1
jdk-7u80=jdk-7u80-1
jdk-7=jdk-7u80
java-7=jdk-7
java-7
	java7=java

jdk-8u141-0
jdk-8u141=jdk-8u141-0
jdk-8=jdk-8u141
java-8=jdk-8
java-8
	java8=java

jdk-9.0.1-0
jdk-9.0.1=jdk-9.0.1-0
jdk-9=jdk-9.0.1
java-9=jdk-9
java-9
	java9=java

openjdk-11.0.3.2-0
jdk-11=openjdk-11.0.3.2-0
  java11=java
  javac11=javac

openjdk-14.0.2.12-0
jdk-14=openjdk-14.0.2.12-0
  java14=java
  javac14=javac

openjdk-17.0.2.8-0
jdk-17=openjdk-17.0.2.8-0
  java17=java
  javac17=javac

openjdk-21.0.0.35-0
jdk-21=openjdk-21.0.0.35-0
  java21=java
  javac21=javac

inkscape-0.92.4-0
	inkscape-0.92=inkscape
	inkview-0.92=inkview

inkscape-1.0-1
	inkscape-1.0=inkscape
	inkview-1.0=inkview

inkscape-1.1.2-0
	inkscape-1.1=inkscape
	inkview-1.1=inkview

inkscape-1.2.2-1
	inkscape-1.2=inkscape
	inkview-1.2=inkview

inkscape=inkscape-1.3.2-0
	inkscape
	inkview

perl-5.12.1-0
	perl5.12.1
perl-5.18.2-0
	perl5.18.2
perl-5.24.1-2
	perl5.24.1
perl-5.26.1-5
	perl5.26.1
perl-5.26.2-1
	perl5.26.2
perl-5.28.1-0
	perl5.28.1
perl-5.34.0-0
	perl5.34.0
perl=perl-5.34.0-0

R-3.3.3-2
	R-3.3.3=R
	Rscript-3.3.3=Rscript

R-3.4.0-0
	R-3.4.0=R
	Rscript-3.4.0=Rscript

R-3.4.3-0
        R-3.4.3=R
        Rscript-3.4.3=Rscript

R-3.4.4-0
        R-3.4.4=R
        Rscript-3.4.4=Rscript

R-3.5.1-1
        R-3.5.1=R
        Rscript-3.5.1=Rscript

R-3.5.1-2
        R-3.5.2=R
        Rscript-3.5.2=Rscript

R-3.5.3-0
        R-3.5.3=R
        Rscript-3.5.3=Rscript

R-3.6.0-0
        R-3.6.0=R
        Rscript-3.6.0=Rscript

R-3.6.1-1
        R-3.6.1=R
        Rscript-3.6.1=Rscript

R-3.6.3-0
        R-3.6.3=R
        Rscript-3.6.3=Rscript

R-4.0.1-0
        R-4.0.1=R
        Rscript-4.0.1=Rscript

R-4.0.5-0
        R-4.0.5=R
        Rscript-4.0.5=Rscript

R-4.1.0-0
        R-4.1.0=R
        Rscript-4.1.0=Rscript

R-4.2.1-0
        R-4.2.1=R
        Rscript-4.2.1=Rscript

R-4.2.2-0
        R-4.2.2=R
        Rscript-4.2.2=Rscript

R-4.4.0-0
        R-4.4.0=R
        Rscript-4.4.0=Rscript

R3=R-3.6.3-0
  R3=R
  R-3=R
  Rscript3=Rscript
  Rscript-3=Rscript

R-4.2.2-0
  R4.2=R
  R-4.2=R
  Rscript4.2=Rscript
  Rscript-4.2=Rscript

R-4.3.0-0
  R4.3=R
  R-4.3=R
  Rscript4.3=Rscript
  Rscript-4.3=Rscript

R4=R-4.4.1-0
  R4=R
  R-4=R
  Rscript4=Rscript
  Rscript-4=Rscript

R=R4
  R
  Rscript

# a) manage python versions

python-3.6=python-3.6.6-1
	python3.6
	python3.6-config
	pip3.6
	pydoc3.6

python3.6=python-3.6

python-3.7=python-3.7.7-0
	python3.7
	python3.7-config
	pip3.7
	pydoc3.7
	cooltools-0.3.0=cooltools

python3.7=python-3.7

python-3.8.8-0
	cooltools-0.3.2=cooltools

python-3.8=python-3.8.9-1
	python3.8
	python3.8-config
	pip3.8
	pydoc3.8

python3.8=python-3.8

python-3.9.6-0
  cooltools-0.4.0=cooltools
  cooltools

python-3.9.7-0
  cooltools-0.4.1=cooltools

python-3.9=python-3.9.12-0
	python3.9
	python3.9-config
	pip3.9
	pydoc3.9
	macs2

python3.9=python-3.9

python-3.10.8-0
  cooltools-0.5.1=cooltools

python-3.10=python-3.10.12-0
	python3.10
	python3.10-config
	pip3.10
	pydoc3.10

python3.10=python-3.10

python-3.11.7-0
	napari
	snakemake

python-3.11=python-3.11.7-1
	python3.11
	python3.11-config
	pip3.11
	pydoc3.11
	napari.rc7=napari

python3.11=python-3.11


# b) default python, see PEP 0394 too

python-3=python-3.11
	python3
	python3-config
	idle3=idle
	pydoc3=pydoc
	pip3
	ipython3

python3=python-3

# c) manage python based tools (meson, snakemake, ...)
# Check existence! And mind python3-wrapper.be0 too

python=python-3
  asciidoc
  bamCompare
  bamCoverage
  bwameth.py
  cola
  computeMatrix
  computeMatrixOperations
  cooler
  cutadapt
  czi2tif
  czifile
  deeptools
  git-cola
  git-dag
  hic2cool
  htseq-count
  htseq-qa
  idr
  ipython
  jupyter
  jupyter-lab
  macs3
  meson
  multiBamSummary
  multiBigwigSummary
  multiqc
  nbshow
  pairtools
  pip
  plotCorrelation
  plotCoverage
  plotEnrichment
  plotFingerprint
  plotHeatmap
  plotPCA
  plotProfile
  spyder
  stg
  tadtool
  truvari
  umi_tools
  virtualenv
  virtualenv3=virtualenv
  whatshap

imagej=imagej-1.54f-0
	imagej

pypy=pypy-3.10-v7.3.13-0
	pypy
	pypy3
	pypy3.10
	pypypip=pip

rstudio-1.1.383-0
  rstudio-1.1=rstudio

rstudio-1.2.5019-1
  rstudio-1.2=rstudio
  rsession-1.2=rsession

rstudio-1.4.1103-0
  rstudio-1.4=rstudio
  rsession-1.4=rsession

rstudio-debpkg-1.4.1717-0
  rstudio-debpkg=rstudio
  rstudio-debpkg-nv=rstudio-nv

rstudio-2022.02.3-492-0
  rstudio-2022.02=rstudio
  rstudio-nv-2022.02=rstudio-nv
  rssession-2022.02=rsession

rstudio-2023.12.1-402-0
  rstudio-2023.12=rstudio
  rstudio-nv-2023.12=rstudio-nv
  rssession-2023.12=rsession
	rstudio
  rsession



R-devel=R-devel-2017-02-02-1

Anaconda=Anaconda3
Anaconda3=Anaconda3-5.0.1-0

chromium=chromium-116.0.5845.179-0
        chrome
        chromium

codium=codium-1.94.2.24286-0
	codium
	code

cuda-9.0=cuda-9.0.176-0
cuda-9.1=cuda-9.1.85-0
cuda-9.2=cuda-9.2.148-0
cuda-9=cuda-9.0          # keep default 9.0 because of tensorflow

cuda-10.0=cuda-10.0.130-0
cuda-10.1=cuda-10.1.105-0
cuda-10.2=cuda-10.2.89-1
cuda-10=cuda-10.0        # keep default 10.0 because of tensorflow ...

cuda-11.0=cuda-11.0.3-0
cuda-11.1=cuda-11.1.1-0
cuda-11.3=cuda-11.3.1-0
cuda-11.5=cuda-11.5.2-0
cuda-11.7=cuda-11.7.1-0
cuda-11.8=cuda-11.8.0-0
cuda-11=cuda-11.8
cuda-12.1=cuda-12.1.0-0

cuda=cuda-11
	bin2c
	computeprof
	cu++filt
	cuda-gdb
	cuda-gdbserver
	cuda-memcheck
	cudafe
	cudafe++
	cuobjdump
	fatbinary
	nvcc
	nvdisasm
	nvlink
	nvprof
	nvprune
	ptxas
	trtexec


gcc-5=gcc-5.5.0-1
  ecj
  gappletviewer
  g++5=g++
  gcc5=gcc
  gccgo
  gcj
  gfortran5=gfortran

gcc-8=gcc-8.4.0-0
  g++8=g++
  gcc8=gcc
  gfortran8=gfortran

gcc-9=gcc-9.3.0-0
  g++9=g++
  gcc9=gcc
  gfortran9=gfortran

gcc-10=gcc-10.3.0-0
  g++10=g++
  gcc10=gcc
  gfortran10=gfortran

gcc-11=gcc-11.1.0-0
  g++11=g++
  gcc11=gcc
  gfortran11=gfortran

gcc-12=gcc-12.2.0-0
  g++12=g++
  gcc12=gcc
  gfortran12=gfortran

gcc-13=gcc-13.2.0-0
  g++13=g++
  gcc13=gcc
  gfortran13=gfortran

gcc-14=gcc-14.1.0-0
  g++14=g++
  gcc14=gcc
  gfortran14=gfortran

palemoon-27.7.2-0
  palemoon

tcl=tcl-8.6.8-0

stellarium-0.22.2-0
  stellarium

tulip-5.6.3-0
  tulip

igv-2.4.14-0
  igv24=igv

igv-2.5.2-0
  igv25=igv

igv-2.8.0-0
  igv28=igv

igv-2.9.2-0
  igv29=igv

igv-2.15.2-0
  igv
  igvxmem
  igv_hidpi
  igvxmem_hidpi

igv-2.17.1-0
  igv217=igv

julia-0.6.4-0
  julia-0.6.4
  julia-debug-0.6.4

julia-1.0.0-0
  julia-1.0.0
  julia-debug-1.0.0

julia-1.1.0-0
  julia-1.1.0
  julia-debug-1.1.0

julia=julia-1.6.1-0
  julia=julia-1.6.1

mysql-workbench
  mysql-workbench

CellProfiler-2.2.0-0
  cellprofiler2=cellprofiler

CellProfiler-3.1.5-0
  cellprofiler

CellProfiler-4.2.1-0
  cellprofiler4=cellprofiler

rust=rustc-1.73.0-0
  rustc
  cargo
  cbindgens
  rustdoc
  rustfmt

apache-maven-3.8.4-0
  mvn mvnDebug

concorde-03.12.19-1
  linkern

avidemux-2.8.0-0
  avidemux3_cli
  avidemux3_jobs_qt5
  avidemux3_qt5
  avidemux=avidemux3_qt5

LibreCAD-2.2.0.rc1-0
  librecad
  ttf2lff

brlcad-7.28.0-0
  brlcad=mged

tcc-0.9.27-0
  tcc

paraview
  paraview

visit
  visit

brave=brave-browser-1.43.89-0
    brave

blender
	blender

cistem
	cisTEM

relion-3.0.5-0
	relion

signal-desktop=signal-desktop-7.16.0-0
  signal-desktop

meld-3.20.1-0
  meld3=meld
  meld

gis
  qgis
  proj

claws-mail-3.17.4-0
  claws-mail

ocaml-4.08.1-0
  ocaml
  ocamlc ocamlcp ocamldep ocamllex
  ocamlmklib ocamlmktop ocamlobjinfo
  ocamlopt ocamloptp
  ocamlprof ocamlrun ocamlyacc
  ocamldoc ocamlfind

xfig-3.2.7-1
  xfig
  pic2tpic fig2ps2tex fig2dev transfig
  pnmtopng pnmtojpeg ppmtogif ppmtobmp pamtotiff
  pamscale pnmflip pnmgamma pnmnlfilt pamcut pbmtext
  pbmtopgm pamtopnm
  giftopnm pngtopam bmptopnm jpegtopnm tifftopnm

orca-1.3.1-0
  orca

libheif-1.6.0-0
  heif-convert
  heif-info

instagraal
  instagraal

cufflinks-2.2.1-2
  compress_gtf
  cuffcompare
  cuffdiff
  cufflinks
  cuffmerge
  cuffnorm
  cuffquant
  gffread
  gtf_to_sam

voreen
  voreen

bazel=bazel-5.4.1-0
  bazel

bazel-6.2.1-0
  bazel-6.2.1=bazel


meme=meme-5.1.1-0
  ame
  centrimo
  dreme
  dust
  fimo
  glam2
  glam2scan
  gomo
  mast
  mcast
  meme
  meme-chip
  momo
  meme-purge=purge
  spamo
  tgene
  tomtom

qemu3=qemu-3.1.1-0
  qemu3-img=qemu-img
  qemu3-system-aarch64=qemu-system-aarch64
  qemu3-system-ppc64=qemu-system-ppc64
  qemu3-system-x86_64=qemu-system-x86_64
  qemu3-x86_64=qemu-x86_64
  qemu3-keymap=qemu-keymap

qemu4=qemu-4.2.1-0
  qemu4-img=qemu-img
  qemu4-system-aarch64=qemu-system-aarch64
  qemu4-system-ppc64=qemu-system-ppc64
  qemu4-system-x86_64=qemu-system-x86_64
  qemu4-x86_64=qemu-x86_64
  qemu4-keymap=qemu-keymap

qemu5=qemu-5.1.0-0
  qemu5-img=qemu-img
  qemu5-system-aarch64=qemu-system-aarch64
  qemu5-system-ppc64=qemu-system-ppc64
  qemu5-system-x86_64=qemu-system-x86_64
  qemu5-x86_64=qemu-x86_64
  qemu5-keymap=qemu-keymap

qemu6=qemu-6.2.0-0
  qemu6-img=qemu-img
  qemu6-system-aarch64=qemu-system-aarch64
  qemu6-system-ppc64=qemu-system-ppc64
  qemu6-system-x86_64=qemu-system-x86_64
  qemu6-x86_64=qemu-x86_64
  qemu6-keymap=qemu-keymap

qemu7=qemu-7.2.0-1
  qemu7-img=qemu-img
  qemu7-system-aarch64=qemu-system-aarch64
  qemu7-system-ppc64=qemu-system-ppc64
  qemu7-system-x86_64=qemu-system-x86_64
  qemu7-x86_64=qemu-x86_64
  qemu7-keymap=qemu-keymap

qemu=qemu5

fontforge=fontforge-20200314-0
  fontforge
  fontimage
  fontlint

ugene=ugene-36.0-0
  ugene

haskell=haskell-9.2.2-0
  ghcup cabal ghc ghc-pkg ghci haddock
  haskell-language-server-wrapper hp2ps
  hpc hsc2hs runghc runhaskell
  pandoc

audacity=audacity-2.4.2-0
  audacity

pymol=pymol-open-source-2.5.0-0
  pymol

pdftk=pdftk-3.3.2-0
  pdftk

ant=apache-ant-1.10.12-0
  ant

atom=atom-1.60.0-1
  atom

pulsar=pulsar-1.113.0-0
  pulsar

llvm-12=llvm-12.0.1-0
  lld-12=lld
  clang-12=clang

llvm-13=llvm-13.0.1-0
  lld-13=lld
  clang-13=clang

llvm-15=llvm-15.0.4-0
  lld-15=lld
  clang-15=clang

llvm-16=llvm-16.0.1-0
  lld-16=lld
  clang-16=clang

llvm-17=llvm-17.0.6-0
  lld-17=lld
  clang-17=clang

llvm=llvm-15
lld=llvm
clang=llvm

freecad=freecad-0.20-0
  FreeCAD
  FreeCADCmd

ghidra-10.1.5-0
  ghidra=ghidraRun
  ghidraRun

ilastik
  ilastik

charliecloud-0.34-0
  ch-checkns
  ch-convert
  ch-fromhost
  ch-image
  ch-run
  ch-run-oci
  ch-ssh
  nvidia-container-cli

nextflow-22.10.0-0
  nextflow22=nextflow

nextflow-23.10.0-1
  nextflow

bmake-20230522-0
  bmake

apptainer-1.2.4-0
  apptainer
  singularity
  run-singularity

slurm
  mxslurmctrl
  sbatch
  sbcast
  scancel
  scontrol
  sdiag
  sh5util
  sinfo
  squeue
  srun
  sstat
  sview

zig=zig-0.11.0-1
  zig

nedit-ng=nedit-ng-2020.1.75800b6bd-0
  nc-ng
  nedit-import
  nedit-ng

github-cli=github-cli-2.48.0-0
  gh

wine=wine-9.10-0
  wine
  winecfg
  wineconsole
  winefile
  winemine
  winepath
  winetricks

proot=proot-5.4.0-0
  care
  proot

# Good Old Games
gog
  doom
  xpenguins

#####################################################
##                                                 ##
## DO NOT EDIT outside of the mxtools repository ! ##
##                                                 ##
#####################################################