debian-med 3.0.1ubuntu1 source package in Ubuntu
Changelog
debian-med (3.0.1ubuntu1) artful; urgency=medium
* Merge from Debian unstable. Remaining changes:
- Regenerate control file for artful.
debian-med (3.0.1) unstable; urgency=medium
* Re-render before Stretch release
debian-med (3.0) unstable; urgency=medium
* Bump version for Stretch release
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-tools
added:
Depends: r-cran-fitcoach, pesco
-med-typesetting
added:
Suggests: r-cran-qqman
-med-bio
added:
Depends: euler2, nextsv, r-bioc-metagenomeseq, diamond-aligner,
bedops, ccs, euler-sr, r-bioc-mergeomics, baitfisher,
libvcflib-tools, r-bioc-phyloseq, r-cran-rotl, tvc
Suggests: r-cran-qqman, r-bioc-savr, r-cran-rentrez
removed:
Depends: fermi-lite
-med-imaging
added:
Depends: bart-view, dcm2niix
-med-bio-dev
added:
Depends: python3-gffutils, libjloda-java, libbio-eutilities-perl,
libvcflib-dev, python3-pybedtools, python3-fast5 | python-fast5,
python3-misopy | python-misopy, libbio-coordinate-perl,
python3-skbio, python3-bx | python-bx, libswiss-perl,
python3-bd2k | python-bd2k
Suggests: r-bioc-biomformat, r-bioc-rbgl, ruby-rgfa, r-cran-rentrez,
libpbcopper-dev
removed:
Depends: libbiojava3-java, libvcflib, python3-skbio | python-skbio,
python-miso, unanimity
debian-med (2.4) unstable; urgency=medium
* rebuild using blends-dev 0.6.96
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-tools
added:
Depends: nutsqlite
-med-bio
added:
Depends: dascrubber, manta, blobology, bio-eagle, malt, atac, qtltools, deepnano, contrafold, nanocall, falcon
Suggests: biomaj
removed:
Depends: falconkit, biomaj
-med-imaging-dev
added:
Depends: libcifti-dev, libcamitk-dev
removed:
Depends: libcamitk4-dev
-med-bio-dev
added:
Depends: libgkarrays-dev, unanimity
debian-med (2.3) unstable; urgency=medium
* blends-dev 0.6.93 does not add single packages to tasksel control file
but only the metapackage itself
* med-bio: Add mgltools-pmv, mgltools-vision, mgltools-cadd
Closes: #732069
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-tools
added:
Depends: galileo, r-cran-fitbitscraper
Suggests: sleepyhead
-med-statistics
added:
Depends: r-cran-ade4, rstudio, r-bioc-multtest
-med-bio-ngs
added:
Depends: sprai, rna-star, daligner, mhap, dindel, blasr, bcftools
-med-bio
added:
Depends: pbbarcode, spaced, varmatch, cgview, phipack, ffp,
snap-aligner, plast, kineticstools, brig, harvest-tools,
transrate-tools, meryl, metabit, parsnp, beagle, maffilter,
pbhoney, jmodeltest, mgltools-cadd, roadtrips, roary,
sim4db, alter-sequence-alignment, graphlan,
ncbi-entrez-direct, falconkit, partitionfinder,
art-nextgen-simulation-tools, sspace, phybin, fastahack,
phylophlan, crux-toolkit, varna, dindel, smithwaterman,
r-bioc-geneplotter, dawg, lefse, r-bioc-deseq2, fsm-lite,
nanopolish, physamp, minimap, kmc, snpomatic, proteinortho,
phast, prottest, qualimap, sprai, fml-asm, circlator, inspect,
pipasic, hilive, mgltools-pmv, fastqtl, piler,
r-cran-adephylo, r-cran-pscbs, hisat2, ssw-align, garli, pssh2,
plink1.9, r-cran-adegenet, velvet | velvet-long, condetri,
fastml, mapdamage, rsat, r-cran-distory, segemehl, andi,
ncl-tools, sumaclust, sniffles, pbalign, scrm, miniasm,
poretools, sparta, pbh5tools, r-cran-bio3d, kronatools,
beast2-mcmc, clustalw, dwgsim, pirs, reapr, r-cran-treescape,
leaff, seer, surankco, tide, placnet, canu, rambo-k, lofreq,
artfastqgenerator, lambda-align, rapmap, metaphlan2,
r-bioc-dnacopy, mgltools-vision, indelible, salmon, dazzdb,
srst2, king-probe, cutadapt, pbgenomicconsensus, ariba,
pbsuite, adapterremoval, kraken, pbjelly, mash, fermi-lite,
pbsim, bcftools
Suggests: science-workflow, r-bioc-aroma.light, r-cran-pheatmap, mrs,
r-bioc-annotationhub, r-bioc-ensembldb, r-bioc-go.db
removed:
Depends: python-kineticstools, r-other-bio3d, velvet, tigr-assembler,
clustalw | clustalw-mpi, python-pbalign, wgsim, wgs-assembler,
mrs, act, r8s, fastml2
-med-his
added:
Depends: openmaxims
-med-practice
added:
Depends: sleepyhead, orthanc
removed:
Depends: clinica
-med-imaging-dev
added:
Depends: libinsighttoolkit4-dev, octave-bart, libvtk-dicom-dev,
libbart-dev, libodil0-dev, libmia-2.4-dev, libcamitk4-dev,
libopenigtlink-dev, libvtk6-dev
Suggests: libcamp0.7-dev, libfreeimage-dev
removed:
Depends: libopenigtlink1-dev, libactiviz.net-cil, libvtk5-dev,
libinsighttoolkit3-dev | libinsighttoolkit4-dev,
libvtk-dicom0.5-dev, libmia-2.2-dev, libcamitk3-dev
Suggests: libvtk5.4, insighttoolkit3-examples
-med-imaging
added:
Depends: fw4spl, python-tifffile, bart
Suggests: science-workflow, orthanc-postgresql, orthanc-imagej,
orthanc-dicomweb
removed:
Depends: tifffile
-med-data
added:
Suggests: sleepyhead
-med-bio-phylogeny
added:
Depends: iqtree, clustalw
removed:
Depends: clustalw | clustalw-mpi
-med-bio-dev
added:
Depends: python3-pyvcf | python-pyvcf, libsmithwaterman-dev,
mgltools-vision, libbpp-phyl-omics-dev,
python3-csb | python-csb, libqcpp-dev, libbio-das-lite-perl,
libhtsjdk-java, libqes-dev,
python3-biopython | python-biopython, python-kineticstools,
libfreecontact-dev, libssw-dev, libminimap-dev, r-cran-rnexml,
libssw-java, r-cran-rncl, python3-pymummer,
python3-ngs | python-ngs, libpbdata-dev, libbpp-raa-dev,
python3-pbconsensuscore | python-pbconsensuscore, libblasr-dev,
libbpp-qt-dev,
python3-intervaltree-bio | python-intervaltree-bio, libncl-dev,
libngs-java, python3-pyfaidx | python-pyfaidx, libbpp-seq-dev,
libfast5-dev, r-cran-phylobase, python-pbcommand,
libncbi-vdb-dev, libbpp-core-dev, libpbbam-dev,
libconsensuscore-dev, libpbihdf-dev, libtabixpp-dev,
python3-pyfasta | python-pyfasta, libbpp-phyl-dev, libfml-dev,
python3-consensuscore2 | python-consensuscore2,
mgltools-networkeditor, libpbseq-dev, libgff-dev,
libngs-sdk-dev, octave-bioinfo, libbpp-popgen-dev,
mgltools-pybabel, libfastahack-dev, ruby-crb-blast,
libbpp-seq-omics-dev
Suggests: python3-biopython-sql | python-biopython-sql, libdisorder-dev,
libbam-dev
removed:
Depends: libgbfp-dev, python-biopython | python3-biopython, libtabixpp,
libfreecontact0-dev, python-csb | python3-csb, libbio-das-perl
Suggests: python-biopython-sql | python3-biopython-sql
-med-epi
added:
Suggests: r-cran-cmprsk
debian-med (2.2) unstable; urgency=medium
* Moved to Git
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-tools
removed:
Depends: python3-fitbitscraper
-med-bio
added:
Depends: sortmerna, r-bioc-limma, r-cran-metamix, iqtree,
relion-bin+gui | relion-bin+mpi+gui, berkeley-express,
daligner, mhap, sumatra, hyphy-mpi | hyphy-pt,
python-pbalign, bio-rainbow, python-kineticstools,
ea-utils, suitename, wgsim, r-bioc-annotate, r-bioc-edger,
adun-core, r-bioc-genefilter, hyphygui, sumtrees, blasr,
repeatmasker-recon, pbdagcon, relion-bin | relion-bin+mpi,
axe-demultiplexer, tantan
Suggests: adun.app
removed:
Depends: relion-bin | relion-bin-mpi, express, relion-gui, hyphy,
adun.app
-med-imaging-dev
added:
Depends: libvtk-dicom-java, libmaxflow-dev, libvtk-dicom0.5-dev
Suggests: liblimereg-dev
removed:
Depends: libvtk-dicom0.4-dev
Suggests: limereg-dev
-med-bio-dev
added:
Depends: libdivsufsort-dev, python3-cutadapt | python-cutadapt,
python3-skbio | python-skbio, python3-dendropy |
python-dendropy, python3-ruffus | python-ruffus,
python3-hyphy | python-hyphy
removed:
Depends: librdp-readseq-java, librdp-alignment-java
-- Bhavani Shankar <email address hidden> Wed, 24 May 2017 17:31:34 +0530
Upload details
- Uploaded by:
- Bhavani Shankar
- Uploaded to:
- Artful
- Original maintainer:
- Ubuntu Developers
- Architectures:
- all
- Section:
- misc
- Urgency:
- Medium Urgency
See full publishing history Publishing
| Series | Published | Component | Section | |
|---|---|---|---|---|
| Bionic | release | universe | misc |
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| debian-med_3.0.1ubuntu1.tar.xz | 104.5 KiB | 195a4aa65533dd2f939e7745c9ef2f4fea02dc2cc3d9acdaa63719e111f6a190 |
| debian-med_3.0.1ubuntu1.dsc | 2.5 KiB | 0ec1e5a7df048a6759cafe4deee5419792e866788885571409520b0b1cc45b48 |
Available diffs
- diff from 2.1ubuntu6 to 3.0.1ubuntu1 (38.7 KiB)
Binary packages built by this source
- med-all: 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.
- med-bio: Debian Med bioinformatics packages
This metapackage will install Debian packages for use in molecular biology,
structural biology and other biological sciences.
- med-bio-dev: No summary available for med-bio-dev in ubuntu artful.
No description available for med-bio-dev in ubuntu artful.
- med-cloud: No summary available for med-cloud in ubuntu cosmic.
No description available for med-cloud in ubuntu cosmic.
- med-config: Debian Med general config package
This package provides the basic infrastructure of all metapackages assembled
by the Debian Med team.
.
This metapackage provides common features shared between the different
metapackages of the project. Moreover it introduces a method to handle a
'med' system users group using debconf.
.
The Debian Med Project include metapackages for different tasks, which are:
* applications for microbiological research and support for development of
biological applications
* cloud computing in microbiological research
* drug databases
* dental surgery practice
* epidemiology and medical statistics
* image processing and support for imaging application development
* pharmacological research
* radiation oncology, diagnostic imaging and related fields
* medical practice
* psychological research and practice
* rehabilitation
* typesetting and publishing
* miscellaneous tools
.
Each task is represented by a metapackage. Metapackages do not contain
executable programs, but rather dependencies from other packages. This way
you will conveniently get all free medical software which is available for
Debian by simply installing the relevant metapackage
- med-data: No summary available for med-data in ubuntu artful.
No description available for med-data in ubuntu artful.
- med-dental: 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.
- med-epi: 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
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
- med-his: No summary available for med-his in ubuntu artful.
No description available for med-his in ubuntu artful.
- med-imaging: No summary available for med-imaging in ubuntu artful.
No description available for med-imaging in ubuntu artful.
- med-imaging-dev: 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.
- med-laboratory: Debian Med suggestions for medical laboratories
This metapackage contains dependencies for software and that could
be useful ro run a medical laboratory.
- med-oncology: No summary available for med-oncology in ubuntu cosmic.
No description available for med-oncology in ubuntu cosmic.
- med-pharmacy: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
collection of software and documentation which is useful for
pharmaceutical research.
- med-physics: Debian Med packages for medical physicists
This metapackage contains dependencies for a
collection of software and documentation which is useful for
medical physicists in radiation oncology, diagnostics imaging
and related fields.
- med-practice: 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.
- med-psychology: Debian Med packages for psychology
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
- med-rehabilitation: No summary available for med-rehabilitation in ubuntu cosmic.
No description available for med-rehabilitation in ubuntu cosmic.
- med-statistics: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
- med-tasks: Debian Med tasks for tasksel
This package provides Debian Med tasks in tasksel.
.
These tasks are described in detail at
http://debian- med.alioth. debian. org/tasks/
- med-tools: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
- med-typesetting: 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.
