debian-med 3.4 source package in Ubuntu
Changelog
debian-med (3.4) unstable; urgency=medium * Standards-Version: 4.4.1 * Use debhelper-compat * Re-render dependencies without Python2 packages * start of automatic changelog entry * * Changes in metapackage dependencies -med-bio added: Recommends: python3-deeptoolsintervals, skesa, python3-orange, vg, mmseqs2, mindthegap, kaptive, r-cran-tsne, python3-deeptools, r-cran-seurat, python3-cogent, kleborate, python3-reaper, python3-treetime, pizzly, trim-galore, pigx-scrnaseq, pigx-rnaseq, r-bioc-multiassayexperiment, wham-align, r-other-wgcna, r-bioc-mofa, seqcluster, r-cran-kaos, r-cran-drinsight Suggests: r-bioc-tximport, r-bioc-qusage, python3-pyflow, python3-alignlib, r-cran-corrplot, r-cran-fitdistrplus, r-cran-dynamictreecut, python3-loompy, strelka, r-cran-gprofiler, python3-py2bit, r-cran-sctransform removed: Recommends: python-orange, python-treetime, python-reaper, python-cogent -med-bio-dev added: Recommends: python3-roadrunner, python3-deeptoolsintervals, r-other-hms-dbmi-spp, python3-loompy, python3-py2bit, r-cran-rotl, r-cran-seqinr, libseqan2-dev, r-cran-boolnet, r-other-apmswapp, r-cran-vegan, r-cran-tsne, gffread, python3-deeptools, r-cran-seurat, r-cran-corrplot, r-cran-fitdistrplus, r-cran-qqman, r-cran-metamix, r-cran-pscbs, r-cran-pheatmap, r-cran-sctransform, r-cran-adephylo, r-cran-phangorn, r-cran-distory, python3-htseq, libmaus2-dev, python3-rdkit, r-cran-samr, r-cran-webgestaltr, python3-freecontact, libseqan3-dev, r-cran-rentrez, r-cran-adegenet, r-cran-dynamictreecut, r-cran-gprofiler, r-cran-forecast, libgclib, python3-biom-format, r-cran-drinsight Suggests: r-cran-rann, r-bioc-biostrings, r-bioc-deseq2, r-bioc-mergeomics, r-cran-metap, r-bioc-qusage, python3-pyflow, python3-pycosat, r-bioc-metagenomeseq, r-bioc-annotate, r-bioc-cner, r-bioc-geneplotter, r-bioc-ensembldb, r-bioc-rentrez, r-bioc-tximport, r-bioc-rtracklayer, r-bioc-annotationhub, r-bioc-ebseq, r-bioc-go.db, r-bioc-limma, r-cran-ica, r-bioc-pcamethods, r-bioc-savr, r-cran-rsvd, python3-alignlib, r-cran-future.batchtools, r-bioc-tfbstools, r-bioc-bitseq, r-bioc-cummerbund, r-bioc-multiassayexperiment, r-bioc-gviz, r-bioc-genefilter, r-bioc-phyloseq, r-bioc-impute, r-bioc-aroma.light, r-cran-future.apply, r-bioc-mofa, r-bioc-dnacopy removed: Recommends: python-htseq, python-mmtk, python-rdkit, python-screed, python-biom-format, python-roadrunner, python-freecontact Suggests: python-pyflow, r-cran-rentrez -med-bio-ngs added: Recommends: wham-align -med-cloud removed: Recommends: python-biopython -med-data added: Recommends: python3-hl7 Suggests: oscar removed: Recommends: python-hl7 -med-epi added: Recommends: python3-treetime removed: Recommends: python-treetime -med-imaging added: Recommends: python3-nibabel, python3-mvpa2, python3-dicom, python3-surfer, tifffile removed: Recommends: python-surfer, python-mvpa2, python-dicom, python-nibabel, python-tifffile -med-imaging-dev added: Recommends: python3-mia, python3-mvpa2, python3-dicom, python3-openslide, python3-gdcm, python3-imageio, python3-mne, python3-nibabel Suggests: tifffile removed: Recommends: python-mia | python3-mia, python-gdcm, python-mne, python-mvpa2, python-dicom, python-nibabel, python-imageio, python-openslide Suggests: python-libavg, python-tifffile -med-physics added: Suggests: python3-multipletau removed: Suggests: python-multipletau -med-practice added: Recommends: oscar -med-psychology removed: Suggests: python-visionegg -med-tools added: Recommends: python3-fitbit Suggests: oscar removed: Recommends: python-clips, python-fitbit -- Andreas Tille <email address hidden> Sat, 05 Oct 2019 12:02:38 +0200
Upload details
- Uploaded by:
- Debian Med
- Uploaded to:
- Sid
- Original maintainer:
- Debian Med
- Architectures:
- all
- Section:
- misc
- Urgency:
- Medium Urgency
See full publishing history Publishing
Series | Published | Component | Section |
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Downloads
File | Size | SHA-256 Checksum |
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debian-med_3.4.dsc | 2.9 KiB | 63d4f1abd7c173956cec9a6035eeb1be8e5aa24851425e2d1a16ede336bf2f83 |
debian-med_3.4.tar.xz | 102.8 KiB | 5b51b9c4751ee6f3c0f70be4498303836f6b285ecb75eef3340fb7f6db46c7f4 |
Available diffs
- diff from 3.3 to 3.4 (18.6 KiB)
No changes file available.
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: 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.
- med-cloud: 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
depend on graphical toolkits and therefore can fit on system images for use
in cloud computing clusters, where space can be limited.
- 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: 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.
- 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: 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
continuous work going on to package a ready to install system currently
only preconditions are finished but hopefully helpful in hospitals
anyway.
- med-imaging: Debian Med image processing and visualization packages
This metapackage will install Debian packages which might be useful in
medical image processing and visualization.
.
On one hand, it installs several packages supporting various image file
formats and image management, like DICOM (Digital Imaging and
Communications in Medicine) which is the de-facto standard for medical
image management, and NIFTI. On the other hand, it provides a variety of
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.
- 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: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
oncology.
- 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-research: Debian Med packages for medical research
This metapackage will install tools that are useful for
medical research.
- 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
https://blends. debian. org/med/ 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.