[Blends-commit] [Git][blends-team/med][master] 2 commits: Render with blends-dev 0.6.102
Andreas Tille
gitlab at salsa.debian.org
Mon Apr 9 20:41:09 UTC 2018
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
a9a8844f by Andreas Tille at 2018-04-09T22:36:08+02:00
Render with blends-dev 0.6.102
- - - - -
98bc56e0 by Andreas Tille at 2018-04-09T22:40:26+02:00
Render with blends-dev 0.6.103
- - - - -
3 changed files:
- debian-med-tasks.desc
- debian/control
- dependency_data/debian-med_3.1.json
Changes:
=====================================
debian-med-tasks.desc
=====================================
--- a/debian-med-tasks.desc
+++ b/debian-med-tasks.desc
@@ -11,7 +11,7 @@ Description: Debian Med bioinformatics packages
This metapackage will install Debian packages for use in molecular biology,
structural biology and other biological sciences.
Test-new-install: mark show
-Key:
+Key:
med-bio
Task: med-bio-dev
@@ -21,7 +21,7 @@ Description: Debian Med packages for development of bioinformatics applications
This metapackage will install Debian packages which might be helpful
for development of applications for biological research.
Test-new-install: mark show
-Key:
+Key:
med-bio-dev
Task: med-cloud
@@ -32,7 +32,7 @@ Description: Debian Med bioinformatics applications usable in cloud computing
structural biology and bioinformatics for use in life sciences, that do not
depend on graphical toolkits and therefore can fit on system images for use
in cloud computing clusters, where space can be limited.
-Key:
+Key:
med-cloud
Task: med-data
@@ -42,7 +42,7 @@ Description: Debian Med drug databases
This metapackage will install free drug databases and related
applications. The database can be accessed by any EMR using
the application.
-Key:
+Key:
med-data
Task: med-dental
@@ -51,7 +51,7 @@ Section: debian-med
Description: Debian Med packages related to dental practice
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
-Key:
+Key:
med-dental
Task: med-epi
@@ -63,7 +63,7 @@ Description: Debian Med epidemiology related packages
statistical investigation. It might be a good idea to read the paper
"A short introduction to R for Epidemiology" at
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
-Key:
+Key:
med-epi
Task: med-his
@@ -75,7 +75,7 @@ Description: Debian Med suggestions for Hospital Information Systems
continuous work going on to package a ready to install system currently
only preconditions are finished but hopefully helpful in hospitals
anyway.
-Key:
+Key:
med-his
Task: med-imaging
@@ -92,7 +92,7 @@ Description: Debian Med image processing and visualization packages
software packages that can be used for visualization and for image processing
- either from a graphical user interface, the command line, or implemented in
workflows.
-Key:
+Key:
med-imaging
Task: med-imaging-dev
@@ -102,7 +102,7 @@ Description: Debian Med image processing and visualization packages development
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing and
visualization.
-Key:
+Key:
med-imaging-dev
Task: med-laboratory
@@ -111,7 +111,7 @@ Section: debian-med
Description: Debian Med suggestions for medical laboratories
This metapackage contains dependencies for software and that could
be useful ro run a medical laboratory.
-Key:
+Key:
med-laboratory
Task: med-oncology
@@ -120,7 +120,7 @@ Section: debian-med
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
oncology.
-Key:
+Key:
med-oncology
Task: med-pharmacy
@@ -130,7 +130,7 @@ Description: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
collection of software and documentation which is useful for
pharmaceutical research.
-Key:
+Key:
med-pharmacy
Task: med-physics
@@ -141,7 +141,7 @@ Description: Debian Med packages for medical physicists
collection of software and documentation which is useful for
medical physicists in radiation oncology, diagnostics imaging
and related fields.
-Key:
+Key:
med-physics
Task: med-practice
@@ -150,7 +150,7 @@ Section: debian-med
Description: Debian Med packages for practice management
This metapackage contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
-Key:
+Key:
med-practice
Task: med-psychology
@@ -159,7 +159,7 @@ Section: debian-med
Description: Debian Med packages for psychology
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
-Key:
+Key:
med-psychology
Task: med-rehabilitation
@@ -168,9 +168,18 @@ Section: debian-med
Description: Debian Med packages for rehabilitation technologies
This metapackage will install tools that are useful for
rehabilitation and therapy.
-Key:
+Key:
med-rehabilitation
+Task: med-research
+Parent: debian-med
+Section: debian-med
+Description: Debian Med packages for medical research
+ This metapackage will install tools that are useful for
+ medical research.
+Key:
+ med-research
+
Task: med-statistics
Parent: debian-med
Section: debian-med
@@ -178,7 +187,7 @@ Description: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
Test-new-install: mark show
-Key:
+Key:
med-statistics
Task: med-tools
@@ -187,7 +196,7 @@ Section: debian-med
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
-Key:
+Key:
med-tools
Task: med-typesetting
@@ -197,6 +206,6 @@ Description: Debian Med support for typesetting and publishing
This metapackage will install Debian packages that might be helpful
for typesetting and publishing in medical care and structural
biology.
-Key:
+Key:
med-typesetting
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -1,4 +1,4 @@
-# This file is autogenerated via make -f debian/rules dist. Do not edit!
+# This file is autogenerated. Do not edit!
Source: debian-med
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
@@ -56,25 +56,27 @@ Description: Debian Med general config package
Package: med-all
Section: metapackages
Architecture: all
+Depends: ${misc:Depends}
Recommends: med-bio,
- med-bio-dev,
- med-statistics
+ med-bio-dev,
+ med-statistics
Suggests: med-cloud,
- med-data,
- med-dental,
- med-epi,
- med-his,
- med-imaging,
- med-imaging-dev,
- med-laboratory,
- med-oncology,
- med-pharmacy,
- med-physics,
- med-practice,
- med-psychology,
- med-rehabilitation,
- med-tools,
- med-typesetting
+ med-data,
+ med-dental,
+ med-epi,
+ med-his,
+ med-imaging,
+ med-imaging-dev,
+ med-laboratory,
+ med-oncology,
+ med-pharmacy,
+ med-physics,
+ med-practice,
+ med-psychology,
+ med-rehabilitation,
+ med-research,
+ med-tools,
+ med-typesetting
Description: Default selection of tasks for Debian Med
This package is part of the Debian Med Pure Blend and installs all
tasks for a default installation of this blend.
@@ -82,683 +84,691 @@ Description: Default selection of tasks for Debian Med
Package: med-bio
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: abacas,
- abyss,
- acedb-other,
- adapterremoval,
- adun-core,
- aegean,
- aevol,
- alien-hunter,
- alter-sequence-alignment,
- altree,
- amap-align,
- ampliconnoise,
- andi,
- anfo,
- aragorn,
- arden,
- ariba,
- art-nextgen-simulation-tools,
- artemis,
- artfastqgenerator,
- assemblytics,
- atac,
- augustus,
- autodock,
- autodock-vina,
- autogrid,
- avogadro,
- axe-demultiplexer,
- baitfisher,
- ballview,
- bamtools,
- barrnap,
- bcftools,
- beads,
- beagle,
- beast-mcmc,
- beast2-mcmc,
- bedops,
- bedtools,
- belvu,
- berkeley-express,
- bio-eagle,
- bio-rainbow,
- bio-tradis,
- bitseq,
- blasr,
- blixem,
- bowtie,
- bowtie2,
- boxshade,
- bppphyview,
- bppsuite,
- brig,
- bwa,
- canu,
- cassiopee,
- cd-hit,
- cdbfasta,
- centrifuge,
- cgview,
- chimeraslayer,
- circlator,
- circos,
- clearcut,
- clonalframe,
- clonalframeml,
- clonalorigin,
- clustalo,
- clustalw,
- clustalx,
- codonw,
- concavity,
- conservation-code,
- crac,
- csb,
- cutadapt,
- daligner,
- datamash,
- dawg,
- dazzdb,
- deepnano,
- dialign,
- dialign-tx,
- diamond-aligner,
- dindel,
- discosnp,
- disulfinder,
- dnaclust,
- dotter,
- dssp,
- dwgsim,
- e-mem,
- ea-utils,
- ecopcr,
- edtsurf,
- eigensoft,
- embassy-domainatrix,
- embassy-domalign,
- embassy-domsearch,
- emboss,
- examl,
- exonerate,
- falcon,
- fastahack,
- fastaq,
- fastdnaml,
- fastlink,
- fastml,
- fastqc,
- fastqtl,
- fasttree,
- fastx-toolkit,
- ffindex,
- figtree,
- fitgcp,
- flexbar,
- fml-asm,
- freebayes,
- freecontact,
- fsa,
- fsm-lite,
- gamgi,
- garli,
- garlic,
- gasic,
- gbrowse,
- gdpc,
- genometools,
- gentle,
- gff2aplot,
- gff2ps,
- ghemical,
- giira,
- glam2,
- graphlan,
- grinder,
- gromacs,
- gubbins,
- gwama,
- harvest-tools,
- hhsuite,
- hilive,
- hinge,
- hisat2,
- hmmer,
- hmmer2,
- hyphy-mpi | hyphy-pt,
- hyphygui,
- idba,
- indelible,
- infernal,
- ipig,
- iqtree,
- iva,
- jaligner,
- jalview,
- jellyfish,
- jmodeltest,
- jmol,
- kalign,
- khmer,
- kineticstools,
- king-probe,
- kissplice,
- kmc,
- kmer,
- kraken,
- lamarc,
- lambda-align,
- last-align,
- leaff,
- lefse,
- librg-utils-perl,
- libvcflib-tools,
- logol-bin,
- loki,
- ltrsift,
- macs,
- macsyfinder,
- maffilter,
- mafft,
- mapdamage,
- mapsembler2,
- maq,
- maqview,
- mash,
- massxpert,
- mauve-aligner,
- melting,
- meryl,
- metaphlan2,
- metastudent,
- mhap,
- microbegps,
- microbiomeutil,
- minia,
- miniasm,
- minimap,
- mipe,
- mira-assembler,
- mlv-smile,
- mothur,
- mptp,
- mrbayes,
- mummer,
- murasaki,
- muscle,
- mustang,
- nanook,
- nanopolish,
- nast-ier,
- ncbi-blast+,
- ncbi-blast+-legacy,
- ncbi-entrez-direct,
- ncbi-epcr,
- ncbi-seg,
- ncbi-tools-bin,
- ncbi-tools-x11,
- ncl-tools,
- ncoils,
- neobio,
- njplot,
- norsnet,
- norsp,
- openms,
- paleomix,
- paml,
- paraclu,
- parsinsert,
- parsnp,
- patman,
- pbalign,
- pbbarcode,
- pbdagcon,
- pbgenomicconsensus,
- pbh5tools,
- pbhoney,
- pbjelly,
- pbsim,
- pbsuite,
- pdb2pqr,
- perlprimer,
- perm,
- pftools,
- phast,
- phipack,
- phybin,
- phylip,
- phyml,
- physamp,
- phyutility,
- picard-tools,
- piler,
- pirs,
- placnet,
- plasmidomics,
- plast,
- plink,
- plink1.9,
- plip,
- poa,
- populations,
- poretools,
- prank,
- predictnls,
- predictprotein,
- prime-phylo,
- primer3,
- proalign,
- probabel,
- probalign,
- probcons,
- proda,
- prodigal,
- profbval,
- profisis,
- profnet-bval,
- profnet-chop,
- profnet-con,
- profnet-isis,
- profnet-md,
- profnet-norsnet,
- profnet-prof,
- profnet-snapfun,
- profphd,
- profphd-net,
- profphd-utils,
- proftmb,
- progressivemauve,
- proteinortho,
- prottest,
- psortb,
- pycorrfit,
- pymol,
- pynast,
- pyscanfcs,
- python-cogent,
- python-treetime,
- python3-biomaj3,
- qcumber,
- qiime,
- qtltools,
- quorum,
- r-bioc-annotate,
- r-bioc-biostrings,
- r-bioc-cummerbund,
- r-bioc-deseq2,
- r-bioc-dnacopy,
- r-bioc-ebseq,
- r-bioc-genefilter,
- r-bioc-geneplotter,
- r-bioc-gviz,
- r-bioc-hilbertvis,
- r-bioc-impute,
- r-bioc-limma,
- r-bioc-mergeomics,
- r-bioc-metagenomeseq,
- r-bioc-phyloseq,
- r-bioc-rtracklayer,
- r-cran-adegenet,
- r-cran-adephylo,
- r-cran-ape,
- r-cran-bio3d,
- r-cran-distory,
- r-cran-genabel,
- r-cran-phangorn,
- r-cran-phytools,
- r-cran-pscbs,
- r-cran-qtl,
- r-cran-rotl,
- r-cran-seqinr,
- r-cran-treescape,
- r-cran-vegan,
- r-other-hms-dbmi-spp,
- r-other-mott-happy.hbrem,
- radiant,
- rambo-k,
- rapmap,
- rasmol,
- raster3d,
- rate4site,
- raxml,
- ray,
- rdp-alignment,
- rdp-classifier,
- rdp-readseq,
- readseq,
- reapr,
- relion-bin | relion-bin+mpi,
- relion-bin+gui | relion-bin+mpi+gui,
- repeatmasker-recon,
- reprof,
- rna-star,
- rnahybrid,
- roary,
- roguenarok,
- rsem,
- rtax,
- runcircos-gui,
- saint,
- salmon,
- sambamba,
- samtools,
- scrm,
- scythe,
- seaview,
- seer,
- seqan-apps,
- seqprep,
- seqsero,
- seqtk,
- sga,
- sibsim4,
- sickle,
- sigma-align,
- sim4,
- sim4db,
- smalr,
- smalt,
- smithwaterman,
- smrtanalysis,
- snap,
- snap-aligner,
- sniffles,
- snp-sites,
- snpomatic,
- soapdenovo,
- soapdenovo2,
- sortmerna,
- spaced,
- spades,
- sprai,
- spread-phy,
- squizz,
- sra-toolkit,
- srst2,
- ssake,
- sspace,
- ssw-align,
- stacks,
- staden,
- staden-io-lib-utils,
- subread,
- suitename,
- sumaclust,
- sumatra,
- sumtrees,
- surankco,
- swarm,
- t-coffee,
- tabix,
- tantan,
- theseus,
- tigr-glimmer,
- tm-align,
- tnseq-transit,
- tophat,
- topp,
- toppred,
- transdecoder,
- transrate-tools,
- transtermhp,
- tree-puzzle | tree-ppuzzle,
- treeview,
- treeviewx,
- trimmomatic,
- trinityrnaseq,
- uc-echo,
- varna,
- vcftools,
- velvet | velvet-long,
- velvetoptimiser,
- vsearch,
- wigeon,
- wise,
- zalign
+ abyss,
+ acedb-other,
+ adapterremoval,
+ adun-core,
+ aegean,
+ aevol,
+ alien-hunter,
+ alter-sequence-alignment,
+ altree,
+ amap-align,
+ ampliconnoise,
+ andi,
+ anfo,
+ aragorn,
+ arden,
+ ariba,
+ art-nextgen-simulation-tools,
+ artemis,
+ artfastqgenerator,
+ assemblytics,
+ atac,
+ augustus,
+ autodock,
+ autodock-vina,
+ autogrid,
+ avogadro,
+ axe-demultiplexer,
+ baitfisher,
+ bali-phy,
+ ballview,
+ bamtools,
+ barrnap,
+ bcftools,
+ beads,
+ beagle,
+ beast-mcmc,
+ beast2-mcmc,
+ bedops,
+ bedtools,
+ belvu,
+ berkeley-express,
+ bio-eagle,
+ bio-rainbow,
+ bio-tradis,
+ bitseq,
+ blasr,
+ blixem,
+ bowtie,
+ bowtie2,
+ boxshade,
+ bppphyview,
+ bppsuite,
+ brig,
+ bwa,
+ canu,
+ cassiopee,
+ cd-hit,
+ cdbfasta,
+ centrifuge,
+ cgview,
+ chimeraslayer,
+ circlator,
+ circos,
+ clearcut,
+ clonalframe,
+ clonalframeml,
+ clonalorigin,
+ clustalo,
+ clustalw,
+ clustalx,
+ codonw,
+ concavity,
+ conservation-code,
+ crac,
+ csb,
+ cutadapt,
+ daligner,
+ datamash,
+ dawg,
+ dazzdb,
+ deepnano,
+ dialign,
+ dialign-tx,
+ diamond-aligner,
+ dindel,
+ discosnp,
+ disulfinder,
+ dnaclust,
+ dotter,
+ dssp,
+ dwgsim,
+ e-mem,
+ ea-utils,
+ ecopcr,
+ edtsurf,
+ eigensoft,
+ embassy-domainatrix,
+ embassy-domalign,
+ embassy-domsearch,
+ emboss,
+ examl,
+ exonerate,
+ falcon,
+ fastahack,
+ fastaq,
+ fastdnaml,
+ fastlink,
+ fastml,
+ fastqc,
+ fastqtl,
+ fasttree,
+ fastx-toolkit,
+ ffindex,
+ figtree,
+ filo,
+ fitgcp,
+ flexbar,
+ fml-asm,
+ freebayes,
+ freecontact,
+ fsa,
+ fsm-lite,
+ gamgi,
+ garli,
+ garlic,
+ gasic,
+ gbrowse,
+ gdpc,
+ genometools,
+ gentle,
+ gff2aplot,
+ gff2ps,
+ ghemical,
+ giira,
+ glam2,
+ graphlan,
+ grinder,
+ gromacs,
+ gubbins,
+ gwama,
+ harvest-tools,
+ hhsuite,
+ hilive,
+ hinge,
+ hisat2,
+ hmmer,
+ hmmer2,
+ hyphy-mpi | hyphy-pt,
+ hyphygui,
+ idba,
+ indelible,
+ infernal,
+ ipig,
+ iqtree,
+ iva,
+ jaligner,
+ jalview,
+ jellyfish,
+ jmodeltest,
+ jmol,
+ kalign,
+ khmer,
+ kineticstools,
+ king-probe,
+ kissplice,
+ kmc,
+ kmer,
+ kraken,
+ lamarc,
+ lambda-align,
+ last-align,
+ leaff,
+ lefse,
+ librg-utils-perl,
+ libvcflib-tools,
+ logol-bin,
+ loki,
+ ltrsift,
+ macs,
+ macsyfinder,
+ maffilter,
+ mafft,
+ mapdamage,
+ mapsembler2,
+ maq,
+ maqview,
+ mash,
+ mauve-aligner,
+ melting,
+ meryl,
+ metaphlan2,
+ metastudent,
+ mhap,
+ microbegps,
+ microbiomeutil,
+ minia,
+ miniasm,
+ minimap,
+ mipe,
+ mira-assembler,
+ mlv-smile,
+ mothur,
+ mptp,
+ mrbayes,
+ msxpertsuite,
+ mummer,
+ murasaki,
+ muscle,
+ mustang,
+ nanook,
+ nanopolish,
+ nast-ier,
+ ncbi-blast+,
+ ncbi-blast+-legacy,
+ ncbi-entrez-direct,
+ ncbi-epcr,
+ ncbi-seg,
+ ncbi-tools-bin,
+ ncbi-tools-x11,
+ ncl-tools,
+ ncoils,
+ neobio,
+ njplot,
+ norsnet,
+ norsp,
+ openms,
+ paleomix,
+ paml,
+ paraclu,
+ parsinsert,
+ parsnp,
+ patman,
+ pbalign,
+ pbbarcode,
+ pbdagcon,
+ pbgenomicconsensus,
+ pbh5tools,
+ pbhoney,
+ pbjelly,
+ pbsim,
+ pbsuite,
+ pdb2pqr,
+ perlprimer,
+ perm,
+ pftools,
+ phast,
+ phipack,
+ phybin,
+ phylip,
+ phyml,
+ physamp,
+ phyutility,
+ picard-tools,
+ piler,
+ pirs,
+ placnet,
+ plasmidomics,
+ plast,
+ plink,
+ plink1.9,
+ plip,
+ poa,
+ populations,
+ poretools,
+ prank,
+ predictnls,
+ predictprotein,
+ prime-phylo,
+ primer3,
+ proalign,
+ probabel,
+ probalign,
+ probcons,
+ proda,
+ prodigal,
+ profbval,
+ profisis,
+ profnet-bval,
+ profnet-chop,
+ profnet-con,
+ profnet-isis,
+ profnet-md,
+ profnet-norsnet,
+ profnet-prof,
+ profnet-snapfun,
+ profphd,
+ profphd-net,
+ profphd-utils,
+ proftmb,
+ progressivemauve,
+ proteinortho,
+ prottest,
+ psortb,
+ pycorrfit,
+ pymol,
+ pynast,
+ pyscanfcs,
+ python-cogent,
+ python-treetime,
+ python3-biomaj3,
+ qcumber,
+ qiime,
+ qtltools,
+ quorum,
+ r-bioc-annotate,
+ r-bioc-biostrings,
+ r-bioc-cummerbund,
+ r-bioc-deseq2,
+ r-bioc-dnacopy,
+ r-bioc-ebseq,
+ r-bioc-genefilter,
+ r-bioc-geneplotter,
+ r-bioc-gviz,
+ r-bioc-hilbertvis,
+ r-bioc-impute,
+ r-bioc-limma,
+ r-bioc-mergeomics,
+ r-bioc-metagenomeseq,
+ r-bioc-pcamethods,
+ r-bioc-phyloseq,
+ r-bioc-rtracklayer,
+ r-cran-adegenet,
+ r-cran-adephylo,
+ r-cran-ape,
+ r-cran-bio3d,
+ r-cran-distory,
+ r-cran-genabel,
+ r-cran-phangorn,
+ r-cran-phytools,
+ r-cran-pscbs,
+ r-cran-qtl,
+ r-cran-rotl,
+ r-cran-seqinr,
+ r-cran-treescape,
+ r-cran-vegan,
+ r-other-hms-dbmi-spp,
+ r-other-mott-happy.hbrem,
+ radiant,
+ rambo-k,
+ rapmap,
+ rasmol,
+ raster3d,
+ rate4site,
+ raxml,
+ ray,
+ rdp-alignment,
+ rdp-classifier,
+ rdp-readseq,
+ readseq,
+ reapr,
+ relion-bin | relion-bin+mpi,
+ relion-bin+gui | relion-bin+mpi+gui,
+ repeatmasker-recon,
+ reprof,
+ rna-star,
+ rnahybrid,
+ roary,
+ roguenarok,
+ rsem,
+ rtax,
+ runcircos-gui,
+ saint,
+ salmon,
+ sambamba,
+ samtools,
+ scrm,
+ scythe,
+ seaview,
+ seer,
+ seqan-apps,
+ seqprep,
+ seqsero,
+ seqtk,
+ sga,
+ sibsim4,
+ sickle,
+ sigma-align,
+ sim4,
+ sim4db,
+ smalr,
+ smalt,
+ smithwaterman,
+ smrtanalysis,
+ snap,
+ snap-aligner,
+ sniffles,
+ snp-sites,
+ snpomatic,
+ soapdenovo,
+ soapdenovo2,
+ sortmerna,
+ spaced,
+ spades,
+ sprai,
+ spread-phy,
+ squizz,
+ sra-toolkit,
+ srst2,
+ ssake,
+ sspace,
+ ssw-align,
+ stacks,
+ staden,
+ staden-io-lib-utils,
+ subread,
+ suitename,
+ sumaclust,
+ sumatra,
+ sumtrees,
+ surankco,
+ swarm,
+ t-coffee,
+ tabix,
+ tantan,
+ theseus,
+ tigr-glimmer,
+ tm-align,
+ tnseq-transit,
+ tophat,
+ topp,
+ toppred,
+ transdecoder,
+ transrate-tools,
+ transtermhp,
+ tree-puzzle | tree-ppuzzle,
+ treeview,
+ treeviewx,
+ trimmomatic,
+ trinityrnaseq,
+ uc-echo,
+ varna,
+ vcftools,
+ velvet | velvet-long,
+ velvetoptimiser,
+ vsearch,
+ wigeon,
+ wise,
+ zalign
Suggests: acacia,
- adun.app,
- amos-assembler,
- amoscmp,
- annovar,
- apollo,
- arachne,
- arb,
- asap,
- autodocktools,
- axparafit,
- axpcoords,
- bagpipe,
- bambus,
- bandage,
- bcbio,
- biceps,
- big-blast,
- bigsdb,
- blat,
- blimps-utils,
- blobology,
- btk-core,
- cactus,
- caftools,
- cain,
- card-rgi,
- ccs,
- cdna-db,
- cellprofiler,
- cinema,
- cluster3,
- cmap,
- cnvkit,
- compclust,
- condetri,
- contrafold,
- contralign,
- coot,
- copycat,
- crossbow,
- crux-toolkit,
- cufflinks,
- cytoscape,
- das-proserver,
- dascrubber,
- dazzle,
- decipher,
- e-hive,
- ecell,
- elph,
- embassy-phylip,
- emboss-explorer,
- emmax,
- emperor,
- ensembl,
- est-db,
- estferret,
- estscan,
- euler-sr,
- euler2,
- exabayes,
- exalt,
- excavator,
- fasta,
- fasta3,
- ffp,
- figaro,
- filo,
- finex,
- forester,
- forge,
- galaxy,
- gassst,
- gatb-core,
- gatk,
- gbioseq,
- gbrowse-syn,
- genemark,
- genesplicer,
- genetrack,
- genezilla,
- genographer,
- getdata,
- glimmerhmm,
- gmap,
- gmv,
- grabix,
- haploview,
- hawkeye,
- hexamer,
- hilbertvisgui,
- htqc,
- igv,
- inspect,
- jbrowse,
- jigsaw,
- jstreeview,
- kempbasu,
- lagan,
- lofreq,
- lucy,
- mach-haplotyper,
- mage2tab,
- maker2,
- malt,
- manta,
- martj,
- maude,
- maxd,
- melting-gui,
- meme,
- mesquite,
- metabit,
- metarep,
- metastudent-data,
- metastudent-data-2,
- metastudent-data-3,
- mgltools-cadd,
- mgltools-pmv,
- mgltools-vision,
- migrate,
- minimus,
- mirbase,
- mobyle,
- mobyle-programs,
- mobyle-tutorials,
- modeller,
- molekel,
- mosaik-aligner,
- mpsqed,
- mrs,
- msatfinder,
- mugsy,
- mummergpu,
- mview,
- nanocall,
- nextsv,
- ngila,
- ngsqctoolkit,
- nw-align,
- oases,
- obitools,
- obo-edit,
- oligoarrayaux,
- omegamap,
- operondb,
- pal2nal,
- partigene,
- partitionfinder,
- patristic,
- pcma,
- pfaat,
- phagefinder,
- phpphylotree,
- phylographer,
- phylophlan,
- phyloviz-core,
- phylowin,
- pipasic,
- plato,
- porechop,
- profit,
- prokka,
- prot4est,
- pscan-tfbs,
- psipred,
- pssh2,
- pyrophosphate-tools,
- python-orange,
- python-reaper,
- qtlcart,
- qualimap,
- r-bioc-annotationhub,
- r-bioc-aroma.light,
- r-bioc-ensembldb,
- r-bioc-go.db,
- r-bioc-savr,
- r-cran-boolnet,
- r-cran-metamix,
- r-cran-pheatmap,
- r-cran-qqman,
- r-cran-rentrez,
- r-other-apmswapp,
- raccoon,
- raxml-ng,
- rbs-finder,
- repeatmasker,
- rmblast,
- roadtrips,
- roche454ace2caf,
- rose,
- rosetta,
- rsat,
- sap,
- science-workflow,
- scoary,
- segemehl,
- seq-gen,
- sequenceconverter.app,
- sift,
- sistr,
- situs,
- snpeff,
- soapaligner,
- soapsnp,
- solvate,
- sparta,
- spice,
- splitstree,
- ssaha,
- strap,
- strap-base,
- tab2mage,
- tacg,
- taverna,
- taxinspector,
- tetra,
- tide,
- tigr-glimmer-mg,
- tn-seqexplorer,
- toil,
- trace2dbest,
- tracetuner,
- treebuilder3d,
- treetime,
- tripal,
- trnascan-se,
- tvc,
- twain,
- ugene,
- umap,
- unc-fish,
- uniprime,
- varmatch,
- varscan,
- vienna-rna,
- vmd,
- x-tandem-pipeline,
- zodiac-zeden
+ adun.app,
+ amos-assembler,
+ amoscmp,
+ annovar,
+ apollo,
+ arachne,
+ arb,
+ asap,
+ autodocktools,
+ axparafit,
+ axpcoords,
+ bagpipe,
+ bambus,
+ bandage,
+ bcbio,
+ biceps,
+ big-blast,
+ bigsdb,
+ biosyntax-gedit,
+ blat,
+ blimps-utils,
+ blobology,
+ btk-core,
+ cactus,
+ caftools,
+ cain,
+ card-rgi,
+ ccs,
+ cdna-db,
+ cellprofiler,
+ chromhmm,
+ cinema,
+ cluster3,
+ cmap,
+ cnvkit,
+ compclust,
+ condetri,
+ contrafold,
+ contralign,
+ coot,
+ copycat,
+ crossbow,
+ crux-toolkit,
+ cufflinks,
+ cytoscape,
+ das-proserver,
+ dascrubber,
+ dazzle,
+ decipher,
+ e-hive,
+ ecell,
+ elph,
+ embassy-phylip,
+ emboss-explorer,
+ emmax,
+ emperor,
+ ensembl,
+ est-db,
+ estferret,
+ estscan,
+ euler-sr,
+ euler2,
+ exabayes,
+ exalt,
+ excavator,
+ fasta,
+ fasta3,
+ ffp,
+ figaro,
+ finex,
+ forester,
+ forge,
+ galaxy,
+ gassst,
+ gatb-core,
+ gatk,
+ gbioseq,
+ gbrowse-syn,
+ genemark,
+ genesplicer,
+ genetrack,
+ genezilla,
+ genographer,
+ getdata,
+ glimmerhmm,
+ gmap,
+ gmv,
+ grabix,
+ haploview,
+ hawkeye,
+ hexamer,
+ hilbertvisgui,
+ htqc,
+ igv,
+ inspect,
+ jbrowse,
+ jigsaw,
+ jstreeview,
+ kempbasu,
+ lagan,
+ lofreq,
+ lucy,
+ mach-haplotyper,
+ mage2tab,
+ maker2,
+ malt,
+ manta,
+ martj,
+ maude,
+ maxd,
+ melting-gui,
+ meme,
+ mesquite,
+ metabit,
+ metarep,
+ metastudent-data,
+ metastudent-data-2,
+ metastudent-data-3,
+ mgltools-cadd,
+ mgltools-pmv,
+ mgltools-vision,
+ migrate,
+ minimus,
+ mirbase,
+ mobyle,
+ mobyle-programs,
+ mobyle-tutorials,
+ modeller,
+ molekel,
+ mosaik-aligner,
+ mpsqed,
+ mrs,
+ msatfinder,
+ mugsy,
+ mummergpu,
+ mview,
+ nanocall,
+ nextsv,
+ ngila,
+ ngsqctoolkit,
+ nw-align,
+ oases,
+ obitools,
+ obo-edit,
+ oligoarrayaux,
+ omegamap,
+ operondb,
+ pal2nal,
+ partigene,
+ partitionfinder,
+ patristic,
+ pcma,
+ pfaat,
+ phagefinder,
+ phpphylotree,
+ phylographer,
+ phylophlan,
+ phyloviz-core,
+ phylowin,
+ pipasic,
+ plato,
+ porechop,
+ profit,
+ prokka,
+ prot4est,
+ pscan-tfbs,
+ psipred,
+ pssh2,
+ pyrophosphate-tools,
+ python-orange,
+ python-reaper,
+ qtlcart,
+ qualimap,
+ r-bioc-annotationhub,
+ r-bioc-aroma.light,
+ r-bioc-bitseq,
+ r-bioc-ensembldb,
+ r-bioc-go.db,
+ r-bioc-savr,
+ r-cran-boolnet,
+ r-cran-metamix,
+ r-cran-pheatmap,
+ r-cran-qqman,
+ r-cran-rentrez,
+ r-cran-samr,
+ r-other-apmswapp,
+ raccoon,
+ raxml-ng,
+ rbs-finder,
+ repeatmasker,
+ rmblast,
+ roadtrips,
+ roche454ace2caf,
+ rose,
+ rosetta,
+ rsat,
+ sap,
+ science-workflow,
+ scoary,
+ segemehl,
+ seq-gen,
+ sequenceconverter.app,
+ sift,
+ sistr,
+ situs,
+ snpeff,
+ soapaligner,
+ soapsnp,
+ solvate,
+ sparta,
+ spice,
+ splitstree,
+ ssaha,
+ strap,
+ strap-base,
+ tab2mage,
+ tacg,
+ taverna,
+ taxinspector,
+ tetra,
+ tide,
+ tigr-glimmer-mg,
+ tn-seqexplorer,
+ toil,
+ trace2dbest,
+ tracetuner,
+ treebuilder3d,
+ treetime,
+ tripal,
+ trnascan-se,
+ tvc,
+ twain,
+ ugene,
+ umap,
+ unc-fish,
+ uniprime,
+ varmatch,
+ varscan,
+ vienna-rna,
+ vmd,
+ x-tandem-pipeline,
+ zodiac-zeden
Description: Debian Med bioinformatics packages
This metapackage will install Debian packages for use in molecular biology,
structural biology and other biological sciences.
@@ -766,208 +776,204 @@ Description: Debian Med bioinformatics packages
Package: med-bio-dev
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: bio-tradis,
- bioperl,
- bioperl-run,
- biosquid,
- libace-perl,
- libai-fann-perl,
- libbambamc-dev,
- libbamtools-dev,
- libbio-coordinate-perl,
- libbio-das-lite-perl,
- libbio-eutilities-perl,
- libbio-graphics-perl,
- libbio-mage-perl,
- libbio-mage-utils-perl,
- libbio-primerdesigner-perl,
- libbiococoa-dev,
- libbiod-dev,
- libbiojava-java,
- libbiojava4-java,
- libblasr-dev,
- libbpp-core-dev,
- libbpp-phyl-dev,
- libbpp-phyl-omics-dev,
- libbpp-popgen-dev,
- libbpp-qt-dev,
- libbpp-raa-dev,
- libbpp-seq-dev,
- libbpp-seq-omics-dev,
- libchado-perl,
- libconsensuscore-dev,
- libdivsufsort-dev,
- libfast5-dev,
- libfastahack-dev,
- libffindex0-dev,
- libfml-dev,
- libfreecontact-dev,
- libfreecontact-perl,
- libgenome-1.3-dev,
- libgenome-model-tools-music-perl,
- libgenome-perl,
- libgenometools0-dev,
- libgff-dev,
- libgkarrays-dev,
- libgo-perl,
- libhmsbeagle-dev,
- libhts-dev,
- libhtsjdk-java,
- libjebl2-java,
- libjloda-java,
- libkmer-dev,
- libmems-1.6-dev,
- libminimap-dev,
- libmuscle-3.7-dev,
- libncbi-vdb-dev,
- libncbi6-dev,
- libncl-dev,
- libngs-java,
- libngs-sdk-dev,
- libnhgri-blastall-perl,
- libopenms-dev,
- libpal-java,
- libpbbam-dev,
- libpbdata-dev,
- libpbihdf-dev,
- libpbseq-dev,
- libqes-dev,
- librcsb-core-wrapper0-dev,
- librdp-taxonomy-tree-java,
- librelion-dev,
- librg-blast-parser-perl,
- librg-reprof-bundle-perl,
- librostlab-blast0-dev,
- librostlab3-dev,
- libsbml5-dev,
- libseqlib-dev,
- libsmithwaterman-dev,
- libsnp-sites1-dev,
- libsort-key-top-perl,
- libsrf-dev,
- libssm-dev,
- libssw-dev,
- libssw-java,
- libstaden-read-dev,
- libswiss-perl,
- libtabixpp-dev,
- libtfbs-perl,
- libvcflib-dev,
- libvibrant6-dev,
- libzerg-perl,
- libzerg0-dev,
- mcl,
- pyfai,
- python-bd2k,
- python-biom-format,
- python-cobra,
- python-cogent,
- python-corepywrap,
- python-freecontact,
- python-htseq,
- python-kineticstools,
- python-pbcommand,
- python-pbcore,
- python-pbh5tools,
- python-pysam,
- python-rdkit,
- python3-biomaj3,
- python3-biopython | python-biopython,
- python3-biotools | python-biotools,
- python3-csb | python-csb,
- python3-cutadapt | python-cutadapt,
- python3-dendropy | python-dendropy,
- python3-fast5 | python-fast5,
- python3-gfapy,
- python3-gffutils,
- python3-intervaltree-bio | python-intervaltree-bio,
- python3-ngs | python-ngs,
- python3-pbconsensuscore | python-pbconsensuscore,
- python3-pybedtools,
- python3-pyfaidx | python-pyfaidx,
- python3-pymummer,
- python3-pyvcf | python-pyvcf,
- python3-ruffus | python-ruffus,
- python3-skbio,
- r-bioc-biobase,
- r-cran-genetics,
- r-cran-haplo.stats,
- r-cran-phylobase,
- r-cran-rncl,
- r-cran-rnexml,
- ruby-bio,
- ruby-crb-blast,
- sbmltoolbox,
- seqan-dev
+ bioperl,
+ bioperl-run,
+ biosquid,
+ libace-perl,
+ libai-fann-perl,
+ libbambamc-dev,
+ libbamtools-dev,
+ libbio-coordinate-perl,
+ libbio-das-lite-perl,
+ libbio-eutilities-perl,
+ libbio-graphics-perl,
+ libbio-mage-perl,
+ libbio-mage-utils-perl,
+ libbio-primerdesigner-perl,
+ libbiococoa-dev,
+ libbiod-dev,
+ libbiojava-java,
+ libbiojava4-java,
+ libblasr-dev,
+ libbpp-core-dev,
+ libbpp-phyl-dev,
+ libbpp-phyl-omics-dev,
+ libbpp-popgen-dev,
+ libbpp-qt-dev,
+ libbpp-raa-dev,
+ libbpp-seq-dev,
+ libbpp-seq-omics-dev,
+ libchado-perl,
+ libconsensuscore-dev,
+ libdivsufsort-dev,
+ libfast5-dev,
+ libfastahack-dev,
+ libffindex0-dev,
+ libfml-dev,
+ libfreecontact-dev,
+ libfreecontact-perl,
+ libgenome-1.3-dev,
+ libgenome-model-tools-music-perl,
+ libgenome-perl,
+ libgenometools0-dev,
+ libgff-dev,
+ libgkarrays-dev,
+ libgo-perl,
+ libhmsbeagle-dev,
+ libhts-dev,
+ libhtsjdk-java,
+ libjebl2-java,
+ libjloda-java,
+ libkmer-dev,
+ libmems-1.6-dev,
+ libminimap-dev,
+ libmuscle-3.7-dev,
+ libncbi-vdb-dev,
+ libncbi6-dev,
+ libncl-dev,
+ libngs-java,
+ libngs-sdk-dev,
+ libnhgri-blastall-perl,
+ libopenms-dev,
+ libpal-java,
+ libpbbam-dev,
+ libpbdata-dev,
+ libpbihdf-dev,
+ libpbseq-dev,
+ libqes-dev,
+ librcsb-core-wrapper0-dev,
+ librdp-taxonomy-tree-java,
+ librelion-dev,
+ librg-blast-parser-perl,
+ librg-reprof-bundle-perl,
+ librostlab-blast0-dev,
+ librostlab3-dev,
+ libsbml5-dev,
+ libseqlib-dev,
+ libsmithwaterman-dev,
+ libsnp-sites1-dev,
+ libsort-key-top-perl,
+ libsrf-dev,
+ libssm-dev,
+ libssw-dev,
+ libssw-java,
+ libstaden-read-dev,
+ libswiss-perl,
+ libtabixpp-dev,
+ libtfbs-perl,
+ libvcflib-dev,
+ libvibrant6-dev,
+ libzerg-perl,
+ libzerg0-dev,
+ mcl,
+ pyfai,
+ python-bd2k,
+ python-biom-format,
+ python-cobra,
+ python-cogent,
+ python-corepywrap,
+ python-freecontact,
+ python-htseq,
+ python-kineticstools,
+ python-pbcommand,
+ python-pbcore,
+ python-pbh5tools,
+ python-pysam,
+ python-rdkit,
+ python3-biomaj3,
+ python3-biopython | python-biopython,
+ python3-biotools | python-biotools,
+ python3-csb | python-csb,
+ python3-cutadapt | python-cutadapt,
+ python3-dendropy | python-dendropy,
+ python3-fast5 | python-fast5,
+ python3-gfapy,
+ python3-intervaltree-bio | python-intervaltree-bio,
+ python3-ngs | python-ngs,
+ python3-pbconsensuscore | python-pbconsensuscore,
+ python3-pyfaidx | python-pyfaidx,
+ python3-pymummer,
+ python3-pyvcf | python-pyvcf,
+ python3-ruffus | python-ruffus,
+ python3-skbio,
+ r-bioc-biobase,
+ r-cran-genetics,
+ r-cran-haplo.stats,
+ r-cran-phylobase,
+ r-cran-rncl,
+ r-cran-rnexml,
+ ruby-bio,
+ sbmltoolbox,
+ seqan-dev
Suggests: bioclipse,
- libbam-dev,
- libdisorder-dev,
- libforester-java,
- libfreecontact-doc,
- libgatbcore-dev,
- libgff-perl,
- libgoby-java,
- libgtextutils-dev,
- libpbcopper-dev,
- libqcpp-dev,
- libroadrunner-dev,
- librostlab-blast-doc,
- librostlab-doc,
- libswarm2-dev,
- mgltools-networkeditor,
- mgltools-pybabel,
- mgltools-vision,
- octace-bioinfo,
- octave-bioinfo,
- python-biomaj3,
- python-biopython-doc,
- python-bx,
- python-consensuscore2,
- python-ete3,
- python-hyphy,
- python-misopy,
- python-mmtk,
- python-pyfasta,
- python-pyflow,
- python-roadrunner,
- python-screed,
- python3-bd2k,
- python3-biopython-sql | python-biopython-sql,
- python3-bx,
- python3-consensuscore2,
- python3-ete3,
- python3-hyphy,
- python3-misopy,
- python3-pyfasta,
- r-bioc-affy,
- r-bioc-affyio,
- r-bioc-altcdfenvs,
- r-bioc-annotationdbi,
- r-bioc-biocgenerics,
- r-bioc-biomart,
- r-bioc-biomformat,
- r-bioc-biovizbase,
- r-bioc-bsgenome,
- r-bioc-genomeinfodb,
- r-bioc-genomicalignments,
- r-bioc-genomicfeatures,
- r-bioc-genomicranges,
- r-bioc-graph,
- r-bioc-hypergraph,
- r-bioc-iranges,
- r-bioc-makecdfenv,
- r-bioc-preprocesscore,
- r-bioc-rbgl,
- r-bioc-rsamtools,
- r-bioc-shortread,
- r-bioc-snpstats,
- r-bioc-variantannotation,
- r-bioc-xvector,
- r-cran-natserv,
- r-cran-rentrez,
- r-cran-rocr,
- ruby-rgfa
+ libbam-dev,
+ libdisorder-dev,
+ libforester-java,
+ libfreecontact-doc,
+ libgatbcore-dev,
+ libgff-perl,
+ libgoby-java,
+ libgtextutils-dev,
+ libpbcopper-dev,
+ libqcpp-dev,
+ libroadrunner-dev,
+ librostlab-blast-doc,
+ librostlab-doc,
+ libswarm2-dev,
+ mgltools-networkeditor,
+ mgltools-pybabel,
+ mgltools-vision,
+ octace-bioinfo,
+ octave-bioinfo,
+ python-biomaj3,
+ python-biopython-doc,
+ python-mmtk,
+ python-pyflow,
+ python-roadrunner,
+ python-screed,
+ python3-bd2k,
+ python3-biopython-sql | python-biopython-sql,
+ python3-bx | python-bx,
+ python3-consensuscore2 | python-consensuscore2,
+ python3-ete3 | python-ete3,
+ python3-gffutils,
+ python3-hyphy | python-hyphy,
+ python3-misopy | python-misopy,
+ python3-pybedtools,
+ python3-pyfasta | python-pyfasta,
+ r-bioc-affy,
+ r-bioc-affyio,
+ r-bioc-altcdfenvs,
+ r-bioc-annotationdbi,
+ r-bioc-biocgenerics,
+ r-bioc-biomart,
+ r-bioc-biomformat,
+ r-bioc-biovizbase,
+ r-bioc-bsgenome,
+ r-bioc-genomeinfodb,
+ r-bioc-genomicalignments,
+ r-bioc-genomicfeatures,
+ r-bioc-genomicranges,
+ r-bioc-graph,
+ r-bioc-hypergraph,
+ r-bioc-iranges,
+ r-bioc-makecdfenv,
+ r-bioc-preprocesscore,
+ r-bioc-rbgl,
+ r-bioc-rsamtools,
+ r-bioc-shortread,
+ r-bioc-snpstats,
+ r-bioc-variantannotation,
+ r-bioc-xvector,
+ r-cran-natserv,
+ r-cran-rentrez,
+ r-cran-rocr,
+ ruby-crb-blast,
+ ruby-rgfa
Description: Debian Med packages for development of bioinformatics applications
This metapackage will install Debian packages which might be helpful
for development of applications for biological research.
@@ -975,155 +981,157 @@ Description: Debian Med packages for development of bioinformatics applications
Package: med-cloud
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: abyss,
- acedb-other,
- aevol,
- alien-hunter,
- altree,
- amap-align,
- ampliconnoise,
- anfo,
- aragorn,
- arden,
- autodock,
- autodock-vina,
- autogrid,
- bamtools,
- bedtools,
- bioperl,
- bioperl-run,
- biosquid,
- blast2,
- bowtie,
- bowtie2,
- boxshade,
- bwa,
- cain,
- cassiopee,
- cd-hit,
- cdbfasta,
- circos,
- clearcut,
- clonalframe,
- clustalo,
- clustalw,
- concavity,
- conservation-code,
- datamash,
- dialign,
- dialign-tx,
- discosnp,
- disulfinder,
- dnaclust,
- dssp,
- embassy-domainatrix,
- embassy-domalign,
- embassy-domsearch,
- emboss,
- exonerate,
- fastdnaml,
- fastlink,
- fastqc,
- fasttree,
- fastx-toolkit,
- fitgcp,
- flexbar,
- freecontact,
- gasic,
- genometools,
- gff2aplot,
- gff2ps,
- giira,
- glam2,
- grinder,
- gromacs,
- hhsuite,
- hmmer,
- idba,
- infernal,
- jellyfish,
- kalign,
- kissplice,
- last-align,
- loki,
- macs,
- mafft,
- mapsembler2,
- maq,
- melting,
- minia,
- mipe,
- mira-assembler,
- mlv-smile,
- mothur,
- mrbayes,
- mummer,
- muscle,
- mustang,
- ncbi-epcr,
- ncbi-tools-bin,
- ncoils,
- neobio,
- paraclu,
- parsinsert,
- pdb2pqr,
- perm,
- phyml,
- phyutility,
- picard-tools,
- plink,
- poa,
- prank,
- prime-phylo,
- primer3,
- probabel,
- probcons,
- proda,
- prodigal,
- pynast,
- python-biopython,
- python-cogent,
- python3-biomaj3-cli,
- python3-biopython,
- qiime,
- r-bioc-hilbertvis,
- r-cran-pvclust,
- r-cran-qtl,
- r-cran-vegan,
- r-other-mott-happy.hbrem,
- raster3d,
- readseq,
- rnahybrid,
- rtax,
- samtools,
- seqan-apps,
- sibsim4,
- sigma-align,
- sim4,
- smalt,
- snap,
- soapdenovo,
- soapdenovo2,
- squizz,
- sra-toolkit,
- ssake,
- staden-io-lib-utils,
- t-coffee,
- tabix,
- theseus,
- tigr-glimmer,
- tophat,
- tree-puzzle | tree-ppuzzle,
- vcftools,
- velvet,
- wise,
- zalign
+ acedb-other,
+ aevol,
+ alien-hunter,
+ altree,
+ amap-align,
+ ampliconnoise,
+ anfo,
+ aragorn,
+ arden,
+ autodock,
+ autodock-vina,
+ autogrid,
+ bamtools,
+ bedtools,
+ bioperl,
+ bioperl-run,
+ biosquid,
+ blast2,
+ bowtie,
+ bowtie2,
+ boxshade,
+ bwa,
+ cain,
+ cassiopee,
+ cd-hit,
+ cdbfasta,
+ circos,
+ clearcut,
+ clonalframe,
+ clustalo,
+ clustalw,
+ concavity,
+ conservation-code,
+ datamash,
+ dialign,
+ dialign-tx,
+ discosnp,
+ disulfinder,
+ dnaclust,
+ dssp,
+ embassy-domainatrix,
+ embassy-domalign,
+ embassy-domsearch,
+ emboss,
+ exonerate,
+ fastdnaml,
+ fastlink,
+ fastqc,
+ fasttree,
+ fastx-toolkit,
+ filo,
+ fitgcp,
+ flexbar,
+ freecontact,
+ gasic,
+ genometools,
+ gff2aplot,
+ gff2ps,
+ giira,
+ glam2,
+ grinder,
+ gromacs,
+ hhsuite,
+ hmmer,
+ idba,
+ infernal,
+ jellyfish,
+ kalign,
+ kissplice,
+ last-align,
+ loki,
+ macs,
+ mafft,
+ mapsembler2,
+ maq,
+ melting,
+ minia,
+ mipe,
+ mira-assembler,
+ mlv-smile,
+ mothur,
+ mrbayes,
+ mummer,
+ muscle,
+ mustang,
+ ncbi-epcr,
+ ncbi-tools-bin,
+ ncoils,
+ neobio,
+ paraclu,
+ parsinsert,
+ pdb2pqr,
+ perm,
+ phyml,
+ phyutility,
+ picard-tools,
+ plink,
+ poa,
+ prank,
+ prime-phylo,
+ primer3,
+ probabel,
+ probcons,
+ proda,
+ prodigal,
+ pynast,
+ python-biopython,
+ python-cogent,
+ python3-biomaj3-cli,
+ python3-biopython,
+ qiime,
+ r-bioc-hilbertvis,
+ r-cran-pvclust,
+ r-cran-qtl,
+ r-cran-vegan,
+ r-other-mott-happy.hbrem,
+ raster3d,
+ readseq,
+ rnahybrid,
+ rtax,
+ samtools,
+ seqan-apps,
+ sibsim4,
+ sigma-align,
+ sim4,
+ smalt,
+ snap,
+ soapdenovo,
+ soapdenovo2,
+ squizz,
+ sra-toolkit,
+ ssake,
+ staden-io-lib-utils,
+ t-coffee,
+ tabix,
+ theseus,
+ tigr-glimmer,
+ tophat,
+ tree-puzzle | tree-ppuzzle,
+ vcftools,
+ velvet,
+ wise,
+ zalign
Suggests: bagpipe,
- cufflinks,
- embassy-phylip,
- filo,
- gmap
+ cufflinks,
+ embassy-phylip,
+ gmap
Description: Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences, that do not
@@ -1133,12 +1141,14 @@ Description: Debian Med bioinformatics applications usable in cloud computing
Package: med-data
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: freediams,
- freemedforms-freedata,
- python-hl7
+ freemedforms-freedata,
+ python-hl7
Suggests: drugref.org,
- sleepyhead
+ sleepyhead
Description: Debian Med drug databases
This metapackage will install free drug databases and related
applications. The database can be accessed by any EMR using
@@ -1147,10 +1157,12 @@ Description: Debian Med drug databases
Package: med-dental
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: entangle,
- imagetooth,
- openmolar
+ imagetooth,
+ openmolar
Description: Debian Med packages related to dental practice
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
@@ -1158,25 +1170,27 @@ Description: Debian Med packages related to dental practice
Package: med-epi
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: epigrass,
- python-treetime,
- r-cran-diagnosismed,
- r-cran-epi,
- r-cran-epibasix,
- r-cran-epicalc,
- r-cran-epir,
- r-cran-epitools,
- r-cran-lexrankr,
- r-cran-seroincidence,
- r-cran-surveillance
+ python-treetime,
+ r-cran-diagnosismed,
+ r-cran-epi,
+ r-cran-epibasix,
+ r-cran-epicalc,
+ r-cran-epir,
+ r-cran-epitools,
+ r-cran-lexrankr,
+ r-cran-seroincidence,
+ r-cran-surveillance
Suggests: netepi-analysis,
- netepi-collection,
- r-cran-cmprsk,
- r-cran-msm,
- repast,
- shiny-server,
- ushahidi
+ netepi-collection,
+ r-cran-cmprsk,
+ r-cran-msm,
+ repast,
+ shiny-server,
+ ushahidi
Description: Debian Med epidemiology related packages
This metapackage will install tools that are useful in epidemiological
research. Several packages making use of the GNU R data language for
@@ -1187,21 +1201,23 @@ Description: Debian Med epidemiology related packages
Package: med-his
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: fis-gtm,
- orthanc-wsi
+ orthanc-wsi
Suggests: care2x,
- ewd-920,
- hkma-cms,
- ipath,
- openeyes,
- openmaxims,
- openmrs,
- oscar-mcmaster,
- patientos,
- tryton-modules-health,
- vista-foia,
- world-vista
+ ewd-920,
+ hkma-cms,
+ ipath,
+ openeyes,
+ openmaxims,
+ openmrs,
+ oscar-mcmaster,
+ patientos,
+ tryton-modules-health,
+ vista-foia,
+ world-vista
Description: Debian Med suggestions for Hospital Information Systems
This metapackage contains dependencies for software and that could
be useful ro run a Hospital Information System. While there is
@@ -1212,140 +1228,143 @@ Description: Debian Med suggestions for Hospital Information Systems
Package: med-imaging
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: aeskulap,
- amide,
- ants,
- bart,
- bart-view,
- biosig-tools,
- camitk-imp,
- ctn,
- ctsim,
- dcm2niix,
- dcmtk,
- dicom3tools,
- dicomnifti,
- dicomscope,
- fw4spl,
- gdf-tools,
- ginkgocadx,
- gwyddion,
- imagej,
- imagevis3d,
- invesalius,
- ismrmrd-tools,
- itksnap,
- king,
- libgdcm-tools,
- medcon,
- mia-tools,
- mia-viewit,
- mialmpick,
- minc-tools,
- mriconvert,
- mricron,
- mrtrix,
- nifti-bin,
- odin,
- openslide-tools,
- orthanc,
- orthanc-wsi,
- pixelmed-apps,
- plastimatch,
- python-dicom,
- python-mvpa2,
- python-nibabel,
- python-nipy,
- python-nipype,
- python-nitime,
- python-surfer,
- python-tifffile,
- sigviewer,
- sofa-apps,
- teem-apps,
- voxbo,
- vtk-dicom-tools,
- xmedcon
+ amide,
+ ants,
+ bart,
+ bart-view,
+ biosig-tools,
+ camitk-imp,
+ ctn,
+ ctsim,
+ dcm2niix,
+ dcmtk,
+ dicom3tools,
+ dicomnifti,
+ dicomscope,
+ fw4spl,
+ gdf-tools,
+ ginkgocadx,
+ gwyddion,
+ imagej,
+ imagevis3d,
+ invesalius,
+ ismrmrd-tools,
+ itksnap,
+ king,
+ libgdcm-tools,
+ medcon,
+ mia-tools,
+ mia-viewit,
+ mialmpick,
+ minc-tools,
+ mriconvert,
+ mricron,
+ mrtrix,
+ nifti-bin,
+ odin,
+ openslide-tools,
+ orthanc,
+ orthanc-wsi,
+ pixelmed-apps,
+ plastimatch,
+ python-dicom,
+ python-dipy,
+ python-mvpa2,
+ python-nibabel,
+ python-nipy,
+ python-nipype,
+ python-nitime,
+ python-surfer,
+ python-tifffile,
+ sigviewer,
+ sofa-apps,
+ teem-apps,
+ voxbo,
+ vtk-dicom-tools,
+ xmedcon
Suggests: afni,
- bioimagesuite,
- bioimagexd,
- blox,
- brainvisa,
- caret,
- cdmedicpacs,
- cellprofiler,
- cmtk,
- connectomeviewer,
- conquest-common,
- conquest-dbase,
- conquest-mysql,
- conquest-postgres,
- conquest-sqlite,
- crea,
- dcm4chee,
- devide,
- dicom4j,
- dicoogle,
- drjekyll,
- dti-query,
- dtitk,
- ecg2png,
- eeglab,
- elastix,
- fiji,
- freesurfer,
- fsl,
- fslview,
- gimias,
- hid,
- imagemagick,
- imview,
- incf-nidash-oneclick-clients,
- insightapplications,
- isis,
- jemris,
- jist,
- kradview,
- libdcm4che-java,
- lipsia,
- maris,
- mayam,
- medisnap,
- mesa-test-tools,
- micromanager,
- mipav,
- miview,
- mni-autoreg,
- mni-colin27-nifti,
- mni-icbm152-nlin-2009,
- mni-n3,
- mrisim,
- omero,
- opendicom.net,
- openelectrophy,
- openmeeg-tools,
- opensourcepacs,
- openwalnut-qt4,
- orthanc-dicomweb,
- orthanc-imagej,
- orthanc-postgresql,
- orthanc-webviewer,
- paraview,
- piano,
- pngquant,
- pymeg,
- python-pyxid,
- science-workflow,
- slicer,
- stabilitycalc,
- stir,
- tempo,
- trimage,
- via-bin,
- visit,
- vmtk,
- xnat
+ bioimagesuite,
+ bioimagexd,
+ blox,
+ brainvisa,
+ caret,
+ cdmedicpacs,
+ cellprofiler,
+ cmtk,
+ connectomeviewer,
+ conquest-common,
+ conquest-dbase,
+ conquest-mysql,
+ conquest-postgres,
+ conquest-sqlite,
+ crea,
+ dcm4chee,
+ devide,
+ dicom4j,
+ dicoogle,
+ drjekyll,
+ dti-query,
+ dtitk,
+ ecg2png,
+ eeglab,
+ elastix,
+ fiji,
+ freesurfer,
+ fsl,
+ fslview,
+ gimias,
+ hid,
+ imagemagick,
+ imview,
+ incf-nidash-oneclick-clients,
+ insightapplications,
+ isis,
+ jemris,
+ jist,
+ kradview,
+ libdcm4che-java,
+ lipsia,
+ maris,
+ mayam,
+ medisnap,
+ mesa-test-tools,
+ micromanager,
+ mipav,
+ miview,
+ mni-autoreg,
+ mni-colin27-nifti,
+ mni-icbm152-nlin-2009,
+ mni-n3,
+ mrisim,
+ omero,
+ opendicom.net,
+ openelectrophy,
+ openmeeg-tools,
+ opensourcepacs,
+ openwalnut-qt4,
+ orthanc-dicomweb,
+ orthanc-imagej,
+ orthanc-postgresql,
+ orthanc-webviewer,
+ paraview,
+ piano,
+ pngquant,
+ pymeg,
+ python-pyxid,
+ science-workflow,
+ slicer,
+ stabilitycalc,
+ stir,
+ tempo,
+ trimage,
+ via-bin,
+ visit,
+ vmtk,
+ xnat
Description: Debian Med image processing and visualization packages
This metapackage will install Debian packages which might be useful in
medical image processing and visualization.
@@ -1361,78 +1380,80 @@ Description: Debian Med image processing and visualization packages
Package: med-imaging-dev
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: cimg-dev,
- ctn-dev,
- gmic,
- libbart-dev,
- libbiosig-dev,
- libcamitk-dev,
- libcifti-dev,
- libedf-dev,
- libgdcm2-dev,
- libgdf-dev,
- libgiftiio-dev,
- libinsighttoolkit4-dev,
- libismrmrd-dev,
- libmaxflow-dev,
- libmdc2-dev,
- libmia-2.4-dev,
- libmialm-dev,
- libmiaviewit-dev,
- libminc-dev,
- libnifti-dev,
- libopenigtlink-dev,
- libopenslide-dev,
- libopensurgsim-dev,
- libpapyrus3-dev,
- libteem-dev,
- libvigraimpex-dev,
- libvistaio-dev,
- libvolpack1-dev,
- libvtk-dicom-dev,
- libvtk6-dev,
- octave-bart,
- octave-gdf,
- odin,
- python-casmoothing,
- python-cfflib,
- python-dicom,
- python-dipy,
- python-gdcm,
- python-imageio,
- python-mia | python3-mia,
- python-mne,
- python-mvpa2,
- python-nibabel,
- python-nipy,
- python-nipype,
- python-nitime,
- python-openslide,
- python-pyxnat,
- python-vigra,
- r-cran-rniftilib
+ ctn-dev,
+ gmic,
+ libbart-dev,
+ libbiosig-dev,
+ libcamitk-dev,
+ libcifti-dev,
+ libedf-dev,
+ libgdcm2-dev,
+ libgdf-dev,
+ libgiftiio-dev,
+ libinsighttoolkit4-dev,
+ libismrmrd-dev,
+ libmaxflow-dev,
+ libmdc2-dev,
+ libmia-2.4-dev,
+ libmialm-dev,
+ libmiaviewit-dev,
+ libminc-dev,
+ libnifti-dev,
+ libodil0-dev,
+ libopenigtlink-dev,
+ libopenslide-dev,
+ libopensurgsim-dev,
+ libpapyrus3-dev,
+ libteem-dev,
+ libvigraimpex-dev,
+ libvistaio-dev,
+ libvolpack1-dev,
+ libvtk-dicom-dev,
+ libvtk6-dev,
+ octave-bart,
+ octave-gdf,
+ odin,
+ python-casmoothing,
+ python-cfflib,
+ python-dicom,
+ python-dipy,
+ python-gdcm,
+ python-imageio,
+ python-mia | python3-mia,
+ python-mne,
+ python-mvpa2,
+ python-nibabel,
+ python-nipy,
+ python-nipype,
+ python-nitime,
+ python-openslide,
+ python-pyxnat,
+ python-vigra,
+ r-cran-rniftilib
Suggests: emokit,
- libbio-formats-java,
- libcamp-dev,
- libctk-dev,
- libcv-dev,
- libeegdev-dev,
- libfreeimage-dev,
- libics-dev,
- liblimereg-dev,
- libmni-perllib-perl,
- libnifti-doc,
- libodil0-dev,
- libopenmeeg-dev,
- libopenslide-java,
- libvia-dev,
- libvmtk-dev,
- libxdffileio-dev,
- octave-dicom,
- python-libavg,
- python-tifffile,
- python-vmtk
+ libbio-formats-java,
+ libcamp-dev,
+ libctk-dev,
+ libcv-dev,
+ libeegdev-dev,
+ libfreeimage-dev,
+ libics-dev,
+ liblimereg-dev,
+ libmni-perllib-perl,
+ libnifti-doc,
+ libopenmeeg-dev,
+ libopenslide-java,
+ libvia-dev,
+ libvmtk-dev,
+ libxdffileio-dev,
+ octave-dicom,
+ python-libavg,
+ python-tifffile,
+ python-vmtk
Description: Debian Med image processing and visualization packages development
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing and
@@ -1441,12 +1462,14 @@ Description: Debian Med image processing and visualization packages development
Package: med-laboratory
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: opencfu,
- orthanc-wsi
+ orthanc-wsi
Suggests: catissuesuite,
- openelis,
- openfreezer
+ openelis,
+ openfreezer
Description: Debian Med suggestions for medical laboratories
This metapackage contains dependencies for software and that could
be useful ro run a medical laboratory.
@@ -1454,11 +1477,13 @@ Description: Debian Med suggestions for medical laboratories
Package: med-oncology
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: dicompyler,
- orthanc-wsi
+ orthanc-wsi
Suggests: planunc,
- uw-prism
+ uw-prism
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
oncology.
@@ -1466,9 +1491,11 @@ Description: Debian Med packages for oncology
Package: med-pharmacy
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: chemtool,
- r-cran-dosefinding
+ r-cran-dosefinding
Suggests: raccoon
Description: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
@@ -1478,20 +1505,22 @@ Description: Debian Med packages for pharmaceutical research
Package: med-physics
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: biosig-tools,
- gdf-tools,
- octave,
- paw,
- paw++,
- r-base
+ gdf-tools,
+ octave,
+ paw,
+ paw++,
+ r-base
Suggests: gate,
- libbiosig-dev,
- octave-biosig,
- openvibe,
- paw-demos,
- python-biosig,
- python-multipletau
+ libbiosig-dev,
+ octave-biosig,
+ openvibe,
+ paw-demos,
+ python-biosig,
+ python-multipletau
Description: Debian Med packages for medical physicists
This metapackage contains dependencies for a
collection of software and documentation which is useful for
@@ -1501,38 +1530,40 @@ Description: Debian Med packages for medical physicists
Package: med-practice
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: entangle,
- freediams,
- freemedforms-emr,
- ginkgocadx,
- gnumed-client,
- gnumed-server,
- libchipcard-tools,
- orthanc,
- orthanc-wsi,
- qrisk2,
- r-cran-medadherence,
- sleepyhead
+ freediams,
+ freemedforms-emr,
+ ginkgocadx,
+ gnumed-client,
+ gnumed-server,
+ libchipcard-tools,
+ orthanc,
+ orthanc-wsi,
+ qrisk2,
+ r-cran-medadherence,
+ sleepyhead
Suggests: clearhealth,
- elementalclinic,
- elexis,
- freeb,
- freemed,
- freeshim,
- libctapimkt1,
- medintux,
- mirrormed,
- mirth,
- openemr,
- openpms,
- openrep,
- proteus,
- remitt,
- resmedicinae,
- sqlclinic,
- thera-pi,
- tinyheb
+ elementalclinic,
+ elexis,
+ freeb,
+ freemed,
+ freeshim,
+ libctapimkt1,
+ medintux,
+ mirrormed,
+ mirth,
+ openemr,
+ openpms,
+ openrep,
+ proteus,
+ remitt,
+ resmedicinae,
+ sqlclinic,
+ thera-pi,
+ tinyheb
Description: Debian Med packages for practice management
This metapackage contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
@@ -1540,21 +1571,23 @@ Description: Debian Med packages for practice management
Package: med-psychology
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: praat,
- psignifit,
- psychopy,
- python-pyepl,
- r-cran-foreign,
- r-cran-psy
+ psignifit,
+ psychopy,
+ python-pyepl,
+ r-cran-foreign,
+ r-cran-psy
Suggests: miscpsycho,
- psych,
- psychometric,
- psychotree,
- psyphy,
- python-pypsignifit,
- python-visionegg,
- science-psychophysics
+ psych,
+ psychometric,
+ psychotree,
+ psyphy,
+ python-pypsignifit,
+ python-visionegg,
+ science-psychophysics
Description: Debian Med packages for psychology
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
@@ -1562,26 +1595,45 @@ Description: Debian Med packages for psychology
Package: med-rehabilitation
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: sitplus
Suggests: aghermann
Description: Debian Med packages for rehabilitation technologies
This metapackage will install tools that are useful for
rehabilitation and therapy.
+Package: med-research
+Section: metapackages
+Architecture: all
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
+Suggests: openclinica
+Description: Debian Med packages for medical research
+ This metapackage will install tools that are useful for
+ medical research.
+
Package: med-statistics
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: r-bioc-limma,
- r-bioc-multtest,
- r-bioc-qvalue,
- r-cran-ade4,
- r-cran-beeswarm,
- r-cran-pvclust,
- r-cran-randomforest
+ r-bioc-multtest,
+ r-bioc-qvalue,
+ r-cran-ade4,
+ r-cran-beeswarm,
+ r-cran-pvclust,
+ r-cran-randomforest,
+ r-cran-rwave,
+ r-cran-snowfall,
+ r-cran-waveslim,
+ r-cran-wavethresh
Suggests: rstudio,
- science-statistics
+ science-statistics
Description: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
@@ -1589,30 +1641,32 @@ Description: Debian Med statistics
Package: med-tools
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: cronometer,
- edfbrowser,
- galileo,
- hunspell-de-med,
- hunspell-en-med,
- nutsqlite,
- pcalendar,
- pondus,
- python-clips,
- python-fitbit,
- quitcount,
- r-cran-fitbitscraper,
- r-cran-fitcoach,
- wgerman-medical,
- workrave
+ edfbrowser,
+ galileo,
+ hunspell-de-med,
+ hunspell-en-med,
+ nutsqlite,
+ pcalendar,
+ pondus,
+ python-clips,
+ python-fitbit,
+ quitcount,
+ r-cran-fitbitscraper,
+ r-cran-fitcoach,
+ wgerman-medical,
+ workrave
Suggests: cycle,
- entangle,
- goldencheetah,
- mencal,
- mssstest,
- nut-nutrition,
- pesco,
- sleepyhead
+ entangle,
+ goldencheetah,
+ mencal,
+ mssstest,
+ nut-nutrition,
+ pesco,
+ sleepyhead
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
@@ -1620,16 +1674,18 @@ Description: Debian Med several tools
Package: med-typesetting
Section: metapackages
Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
Recommends: king,
- texlive-latex-extra,
- texlive-science
+ texlive-latex-extra,
+ texlive-science
Suggests: biber,
- bibus,
- jabref-plugin-oo,
- kbibtex,
- r-cran-qqman,
- referencer
+ bibus,
+ jabref-plugin-oo,
+ kbibtex,
+ r-cran-qqman,
+ referencer
Description: Debian Med support for typesetting and publishing
This metapackage will install Debian packages that might be helpful
for typesetting and publishing in medical care and structural
=====================================
dependency_data/debian-med_3.1.json
=====================================
--- a/dependency_data/debian-med_3.1.json
+++ b/dependency_data/debian-med_3.1.json
@@ -1 +1 @@
-{"oncology": {"ignore": [], "suggests": [], "depends": [], "recommends": ["uw-prism", "orthanc-wsi", "planunc", "dicompyler"], "avoid": []}, "laboratory": {"ignore": [], "suggests": [], "depends": [], "recommends": ["opencfu", "orthanc-wsi", "openelis", "openfreezer", "catissuesuite"], "avoid": []}, "research": {"ignore": [], "suggests": [], "depends": [], "recommends": ["openclinica"], "avoid": []}, "tools": {"ignore": [], "suggests": ["cycle", "mencal", "entangle", "goldencheetah", "sleepyhead"], "depends": [], "recommends": ["pcalendar", "pondus", "mssstest", "wgerman-medical", "hunspell-de-med", "quitcount", "workrave", "edfbrowser", "hunspell-en-med", "python-clips", "cronometer", "python-fitbit", "r-cran-fitcoach", "r-cran-fitbitscraper", "galileo", "nut-nutrition", "nutsqlite", "pesco"], "avoid": []}, "cloud": {"ignore": [], "suggests": [], "depends": [], "recommends": ["altree", "clearcut", "fastdnaml", "fasttree", "parsinsert", "phyml", "phyutility", "prime-phylo", "mrbayes", "tree-puzzle | tree-ppuzzle", "alien-hunter", "bagpipe", "fastlink", "loki", "gasic", "genometools", "plink", "probabel", "r-cran-qtl", "r-other-valdar-bagphenotype.library", "r-other-mott-happy.hbrem", "amap-align", "blast2", "biosquid", "boxshade", "cassiopee", "cdbfasta", "cd-hit", "clustalo", "clustalw", "conservation-code", "dialign", "dialign-tx", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "exonerate", "gff2aplot", "gff2ps", "glam2", "gmap", "hmmer", "jellyfish", "kalign", "mafft", "mlv-smile", "mummer", "muscle", "neobio", "poa", "prank", "probcons", "proda", "pynast", "sibsim4", "sigma-align", "sim4", "snap", "squizz", "t-coffee", "wise", "zalign", "bamtools", "bedtools", "fastx-toolkit", "flexbar", "picard-tools", "samtools", "tabix", "vcftools", "anfo", "cufflinks", "bowtie", "bowtie2", "bwa", "last-align", "maq", "perm", "tophat", "smalt", "soapdenovo", "soapdenovo2", "abyss", "mapsembler2", "idba", "minia", "mira-assembler", "ssake", "velvet", "ampliconnoise", "arden", "fastqc", "discosnp", "dnaclust", "fitgcp", "giira", "grinder", "kissplice", "macs", "mothur", "paraclu", "r-bioc-hilbertvis", "sra-toolkit", "aragorn", "infernal", "rnahybrid", "rtax", "autodock", "autodock-vina", "autogrid", "concavity", "dssp", "freecontact", "gromacs", "hhsuite", "mustang", "pdb2pqr", "raster3d", "theseus", "melting", "mipe", "ncbi-epcr", "primer3", "acedb-other", "disulfinder", "ncbi-tools-bin", "ncoils", "python-cogent", "readseq", "tigr-glimmer", "seqan-apps", "staden-io-lib-utils", "aevol", "biomaj", "bioperl", "bioperl-run", "cain", "clonalframe", "circos", "datamash", "filo", "prodigal", "python-biopython", "python3-biopython", "qiime", "r-cran-pvclust", "r-cran-vegan"], "avoid": []}, "statistics": {"ignore": [], "suggests": ["science-statistics"], "depends": [], "recommends": ["r-bioc-limma", "r-bioc-qvalue", "r-cran-randomforest", "r-cran-beeswarm", "r-cran-pvclust", "rstudio", "r-bioc-multtest", "r-cran-ade4"], "avoid": []}, "psychology": {"ignore": [], "suggests": ["science-psychophysics", "python-visionegg"], "depends": [], "recommends": ["python-pyepl", "praat", "r-cran-foreign", "psignifit", "python-pypsignifit", "r-cran-psy", "psychopy", "miscpsycho", "psych", "psychometric", "psychotree", "psyphy"], "avoid": []}, "pharmacy": {"ignore": [], "suggests": [], "depends": [], "recommends": ["chemtool", "raccoon", "r-cran-dosefinding"], "avoid": []}, "typesetting": {"ignore": [], "suggests": ["kbibtex", "biber", "bibus", "referencer", "jabref-plugin-oo", "r-cran-qqman"], "depends": [], "recommends": ["texlive-science", "texlive-latex-extra", "king"], "avoid": []}, "dental": {"ignore": [], "suggests": [], "depends": [], "recommends": ["openmolar", "imagetooth", "entangle"], "avoid": []}, "bio": {"ignore": ["mozilla-biofox", "riso", "catissuecore", "trapss"], "suggests": ["dascrubber", "emboss-explorer", "adun.app", "melting-gui", "biomaj", "biomaj-watcher", "cain", "science-workflow", "getdata", "metastudent-data", "metastudent-data-2", "metastudent-data-3", "mrs", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-ensembldb", "r-bioc-go.db", "r-bioc-savr", "r-cran-qqman", "r-cran-rentrez", "r-cran-boolnet", "r-cran-pheatmap", "mobyle", "mobyle-programs", "mobyle-tutorials", "maude"], "depends": [], "recommends": ["altree", "beast-mcmc", "beast2-mcmc", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle", "probalign", "treeviewx", "figtree", "hyphygui", "hyphy-mpi | hyphy-pt", "spread-phy", "phylip", "fastlink", "loki", "plink", "plink1.9", "r-cran-qtl", "r-cran-genabel", "amap-align", "boxshade", "fastx-toolkit", "gff2aplot", "muscle", "sim4", "sibsim4", "tabix", "tophat", "wise", "maqview", "blasr", "daligner", "mhap", "bwa", "mummer", "e-mem", "ncbi-blast+-legacy", "plast", "ncbi-blast+", "mafft", "sra-toolkit", "t-coffee", "kalign", "hmmer", "exonerate", "dialign", "dialign-tx", "poa", "probcons", "proda", "seaview", "sigma-align", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "arb", "clustalx", "clustalo", "clustalw", "mothur", "bowtie", "bowtie2", "transtermhp", "last-align", "maq", "ssake", "velvet | velvet-long", "qiime", "scoary", "umap", "infernal", "rnahybrid", "adun-core", "garlic", "gamgi", "gdpc", "ghemical", "jmol", "pymol", "r-cran-bio3d", "massxpert", "gromacs", "rasmol", "modeller", "plasmidomics", "gff2ps", "ncbi-epcr", "ncbi-tools-bin", "ncbi-tools-x11", "perlprimer", "readseq", "tigr-glimmer", "melting", "mipe", "primer3", "artemis", "gbrowse", "python3-biomaj3", "glam2", "raster3d", "phyml", "autodock", "autogrid", "autodock-vina", "autodocktools", "mgltools-pmv", "mgltools-vision", "mgltools-cadd", "mustang", "probabel", "theseus", "staden-io-lib-utils", "samtools", "bedtools", "filo", "datamash", "gassst", "hinge", "r-bioc-hilbertvis", "r-other-mott-happy.hbrem", "seq-gen", "snp-sites", "mira-assembler", "alien-hunter", "seqan-apps", "ncoils", "gentle", "gmap", "igv", "picard-tools", "acedb-other-dotter", "acedb-other-belvu", "acedb-other", "python-cogent", "paml", "velvetoptimiser", "ensembl", "mrbayes", "pdb2pqr", "squizz", "clonalframe", "clonalframeml", "dssp", "jellyfish", "ballview", "pynast", "raxml", "mlv-smile", "cd-hit", "cufflinks", "r-bioc-cummerbund", "eigensoft", "grinder", "jalview", "reprof", "tm-align", "norsnet", "norsp", "predictnls", "prime-phylo", "proftmb", "profbval", "profisis", "hhsuite", "ffindex", "flexbar", "blimps-utils", "sift", "neobio", "ray", "ugene", "logol-bin", "soapdenovo", "soapdenovo2", "microbiomeutil", "chimeraslayer", "nast-ier", "wigeon", "minia", "trimmomatic", "saint", "rtax", "rate4site", "rna-star", "topp", "openms", "scythe", "sickle", "kmc", "king-probe", "ncl-tools", "tvc", "libvcflib-tools", "bppsuite", "bppphyview", "acacia", "adapterremoval", "aegean", "andi", "arden", "artfastqgenerator", "art-nextgen-simulation-tools", "augustus", "baitfisher", "bandage", "beagle", "bedops", "biceps", "cnvkit", "csb", "diamond-aligner", "emperor", "euler2", "euler-sr", "fitgcp", "gasic", "giira", "ipig", "aevol", "alter-sequence-alignment", "amos-assembler", "hawkeye", "anfo", "apollo", "aragorn", "ariba", "atac", "axe-demultiplexer", "axparafit", "axpcoords", "barrnap", "bamtools", "bagpipe", "bcftools", "bigsdb", "bio-eagle", "bio-tradis", "bitseq", "blat", "blobology", "bio-rainbow", "card-rgi", "cassiopee", "ccs", "cdbfasta", "centrifuge", "cgview", "brig", "cinema", "circlator", "clearcut", "clonalorigin", "cluster3", "codonw", "condetri", "contrafold", "crac", "crossbow", "crux-toolkit", "cutadapt", "cytoscape", "dawg", "dazzdb", "dazzle", "deepnano", "dindel", "dwgsim", "ea-utils", "ecell", "ecopcr", "edtsurf", "emmax", "examl", "raxml-ng", "exabayes", "berkeley-express", "falcon", "fasta3", "fasttree", "fastahack", "fastaq", "fastml", "fastqc", "fastqtl", "ffp", "unc-fish", "fml-asm", "forester", "freecontact", "freebayes", "fsa", "fsm-lite", "garli", "gatb-core", "gatk", "genometools", "grabix", "graphlan", "grogui", "gwama", "gubbins", "haploview", "harvest-tools", "hilive", "hisat2", "hmmer2", "htqc", "idba", "indelible", "iqtree", "iva", "jaligner", "jbrowse", "jmodeltest", "kempbasu", "kineticstools", "kissplice", "kraken", "lagan", "lambda-align", "leaff", "ltrsift", "lofreq", "logomat-m", "kclust", "khmer", "kmer", "radiant", "lefse", "mach-haplotyper", "macs", "macsyfinder", "maffilter", "mage2tab", "malt", "manta", "mapdamage", "martj", "mash", "progressivemauve", "mauve-aligner", "meme", "meryl", "metabit", "metaphlan2", "metastudent", "microbegps", "miniasm", "minimap", "molekel", "mosaik-aligner", "mpsqed", "mptp", "mugsy", "murasaki", "nanocall", "nanook", "nanopolish", "ncbi-entrez-direct", "ncbi-seg", "nextsv", "ngila", "ngsqctoolkit", "nw-align", "oases", "obitools", "r-other-apmswapp", "pal2nal", "paleomix", "paraclu", "parsinsert", "parsnp", "partitionfinder", "patman", "patristic", "pbalign", "pbbarcode", "pbdagcon", "pbsuite", "pbgenomicconsensus", "pbjelly", "pbhoney", "pbh5tools", "pbsim", "pcma", "perm", "pftools", "phast", "phipack", "phybin", "phylophlan", "phyloviz-core", "phyutility", "piler", "pipasic", "inspect", "tide", "physamp", "pirs", "placnet", "plato", "plip", "poretools", "prank", "predictprotein", "proalign", "prodigal", "prokka", "proteinortho", "prottest", "psortb", "pscan-tfbs", "psipred", "pssh2", "pycorrfit", "pyscanfcs", "python-reaper", "python-treetime", "qcumber", "qtltools", "qualimap", "quorum", "rambo-k", "rapmap", "r-bioc-rtracklayer", "r-bioc-gviz", "r-bioc-biostrings", "r-bioc-annotate", "r-bioc-genefilter", "r-bioc-deseq2", "r-bioc-dnacopy", "r-bioc-geneplotter", "r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-phyloseq", "r-bioc-ebseq", "r-bioc-limma", "r-cran-rotl", "r-cran-adegenet", "r-cran-adephylo", "r-cran-distory", "r-cran-metamix", "r-cran-phangorn", "r-cran-pscbs", "r-cran-seqinr", "r-cran-vegan", "relion-bin+gui | relion-bin+mpi+gui", "relion-bin | relion-bin+mpi", "r-other-valdar-bagphenotype.library", "rdp-alignment", "rdp-readseq", "rdp-classifier", "reapr", "repeatmasker-recon", "repeatmasker", "roadtrips", "roary", "roguenarok", "rosetta", "rsat", "rsem", "sambamba", "salmon", "sap", "scrm", "sga", "seer", "segemehl", "seqprep", "seqsero", "seqtk", "sequenceconverter.app", "sistr", "situs", "sim4db", "smalt", "smithwaterman", "ssw-align", "smrtanalysis", "snpeff", "snpomatic", "sortmerna", "snap-aligner", "sniffles", "spaced", "spades", "sparta", "sprai", "srst2", "ssaha", "sspace", "staden", "stacks", "strap", "strap-base", "subread", "suitename", "sumatra", "sumaclust", "sumtrees", "surankco", "swarm", "tacg", "tantan", "toppred", "transdecoder", "tnseq-transit", "tn-seqexplorer", "transrate-tools", "treeview", "trinityrnaseq", "uc-echo", "varna", "varmatch", "varscan", "vienna-rna", "vmd", "vsearch", "canu", "zalign", "zodiac-zeden", "discosnp", "mapsembler2", "dnaclust", "copycat", "btk-core", "asap", "cactus", "contralign", "concavity", "conservation-code", "galaxy", "genographer", "pftools", "phylographer", "phylowin", "gbioseq", "phpphylotree", "tracetuner", "twain", "rose", "glimmerhmm", "genezilla", "exalt", "jigsaw", "genesplicer", "mummergpu", "amoscmp", "minimus", "bambus", "gmv", "pyrophosphate-tools", "figaro", "mirbase", "elph", "uniprime", "genetrack", "operondb", "trnascan-se", "cdna-db", "das-proserver", "spice", "decipher", "est-db", "finex", "hexamer", "coot", "r-cran-ape", "r-cran-treescape", "caftools", "roche454ace2caf", "big-blast", "blixem", "dotter", "belvu", "estferret", "estscan", "fasta", "lamarc", "lucy", "maxd", "mesquite", "migrate", "msatfinder", "mview", "oligoarrayaux", "omegamap", "partigene", "pfaat", "prot4est", "qtlcart", "rbs-finder", "splitstree", "taverna", "taxinspector", "tetra", "trace2dbest", "profit", "obo-edit", "jstreeview", "phagefinder", "compclust", "treebuilder3d", "excavator", "treetime", "abacas", "profnet-bval", "profnet-chop", "profnet-con", "profnet-isis", "profnet-md", "profnet-norsnet", "profnet-prof", "profnet-snapfun", "profphd-net", "profphd-utils", "profphd", "abyss", "ampliconnoise", "disulfinder", "circos", "runcircos-gui", "populations", "raccoon", "librg-utils-perl", "snap", "vcftools", "hilbertvisgui", "beads", "x-tandem-pipeline", "forge", "metarep", "arachne", "maker2", "rmblast", "e-hive", "cmap", "gbrowse-syn", "tripal", "genemark", "annovar", "python-orange", "tigr-glimmer-mg"], "avoid": []}, "his": {"ignore": [], "suggests": [], "depends": [], "recommends": ["care2x", "fis-gtm", "vista-foia", "ewd-920", "orthanc-wsi", "tryton-modules-health", "openmaxims", "world-vista", "ipath", "patientos", "openmrs", "hkma-cms", "oscar-mcmaster", "openeyes"], "avoid": []}, "bio-ngs": {"ignore": [], "suggests": [], "depends": [], "recommends": ["bedtools", "bwa", "bowtie", "blasr", "daligner", "mhap", "fastx-toolkit", "last-align", "maq", "picard-tools", "r-bioc-hilbertvis", "rna-star", "samtools", 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\ No newline at end of file
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"libmdc2-dev", "libvtk6-dev", "libnifti-dev", "libinsighttoolkit4-dev", "libvolpack1-dev", "libgdcm2-dev", "python-gdcm", "libopensurgsim-dev", "libmaxflow-dev", "python-mvpa2", "python-nipy", "python-nipype", "python-nitime", "python-casmoothing", "libvia-dev", "odin", "libcv-dev", "libteem-dev", "gmic", "libgiftiio-dev", "libvistaio-dev", "libmia-2.4-dev", "libmiaviewit-dev", "libmialm-dev", "python-mia | python3-mia", "libopenigtlink-dev", "r-cran-rniftilib", "libmni-perllib-perl", "python-dicom", "libopenmeeg-dev", "python-nibabel", "libgdf-dev", "octave-gdf", "python-pyxnat", "python-dipy", "libbiosig-dev", "libctk-dev", "python-cfflib", "libopenslide-dev", "python-openslide", "libopenslide-java", "libbio-formats-java", "octave-dicom", "libcamitk-dev", "libpapyrus3-dev", "python-mne", "python-vmtk", "libvmtk-dev", "libvigraimpex-dev", "python-vigra", "libvtk-dicom-dev", "libedf-dev", "python-imageio", "libismrmrd-dev", "libodil0-dev", "libbart-dev", "octave-bart", "libcifti-dev"], "ignore": [], "avoid": []}}
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/blends-team/med/compare/6451da2d816f762cf391f048676c79eee1c25431...98bc56e01882a1dbeedbdccf469ab3cc4c99f3ab
---
View it on GitLab: https://salsa.debian.org/blends-team/med/compare/6451da2d816f762cf391f048676c79eee1c25431...98bc56e01882a1dbeedbdccf469ab3cc4c99f3ab
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