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| ##################################################### | |
| ## ## | |
| ## 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 | |
| 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-6.10.0-0 | |
| al | |
| gacutil | |
| mcs | |
| mono | |
| 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 | |
| node-20.13.1-0 | |
| node-22.14.0=node-22.14.0-0 | |
| node-22=node-22.14.0 | |
| node-22 | |
| node22=node | |
| npm22=npm | |
| npx22=npx | |
| node=node-22 | |
| 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 | |
| visualstudiocode | |
| jdk-7u80-1 | |
| jdk-7u80=jdk-7u80-1 | |
| jdk-7=jdk-7u80 | |
| java-7=jdk-7 | |
| java-7 | |
| java7=java | |
| jdk-8u181-0 | |
| jdk-8u181=jdk-8u181-0 | |
| jdk-8=jdk-8u181 | |
| java-8=jdk-8 | |
| java-8 | |
| java8=java | |
| javac8=javac | |
| 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 | |
| jar | |
| java | |
| javac | |
| javadoc | |
| 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-1.3.2-0 | |
| inkscape-1.3=inkscape | |
| inkview-1.3=inkview | |
| inkscape=inkscape-1.4-0 | |
| 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=python-3.11.7-1 | |
| python3.11 | |
| python3.11-config | |
| pip3.11 | |
| pydoc3.11 | |
| napari.rc7=napari | |
| tfpython=python3 | |
| python3.11=python-3.11 | |
| python-3.12=python-3.12.8-0 | |
| python3.12 | |
| python3.12-config | |
| pip3.12 | |
| pydoc3.12 | |
| python3.12=python-3.12 | |
| python-3.13=python-3.13.2-0 | |
| python3.13 | |
| python3.13-config | |
| pip3.13 | |
| pydoc3.13 | |
| python3.13=python-3.13 | |
| # b) default python, see PEP 0394 too | |
| python-3=python-3.12 | |
| 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 | |
| html2text | |
| htseq-count | |
| htseq-qa | |
| idr | |
| ipython | |
| jupyter | |
| jupyter-lab | |
| macs3 | |
| meson | |
| multiBamSummary | |
| multiBigwigSummary | |
| multiqc | |
| napari | |
| nbshow | |
| pairtools | |
| pip | |
| plotCorrelation | |
| plotCoverage | |
| plotEnrichment | |
| plotFingerprint | |
| plotHeatmap | |
| plotPCA | |
| plotProfile | |
| snakemake | |
| 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 | |
| rstudio-server-2024.09.0-375-1 | |
| rstudio-server | |
| # R-devel=R-devel-2017-02-02-1 | |
| chromium=chromium-116.0.5845.179-0 | |
| chrome | |
| chromium | |
| codium=codium-1.96.4.25017-0 | |
| 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-1.84.1-0 | |
| rustc | |
| cargo | |
| cargo-clippy | |
| 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-7.37.0-0 | |
| 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-open-source-2.5.0-0 | |
| pymol25=pymol | |
| pymol=pymol-open-source-3.1.0-0 | |
| 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 | |
| nextflow23=nextflow | |
| nextflow-24.10.5-0 | |
| 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 | |
| # initial/devel installation | |
| fragpipe | |
| fragpipe | |
| # 'production' installation | |
| fragpipe-22.0-0 | |
| fragpipe22=mxfragpipe | |
| octave-9.4.0-0 | |
| mkoctfile | |
| octave | |
| octave-cli | |
| octave-config | |
| gradle-8.13-0 | |
| gradle | |
| ##################################################### | |
| ## ## | |
| ## DO NOT EDIT outside of the mxtools repository ! ## | |
| ## ## | |
| ##################################################### |