mapdamage_2.0.8+dfsg-1_all.deb


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Description

mapdamage - tracking and quantifying damage patterns in ancient DNA sequences

Property Value
Distribution Ubuntu 18.04 LTS (Bionic Beaver)
Repository Ubuntu Universe amd64
Package filename mapdamage_2.0.8+dfsg-1_all.deb
Package name mapdamage
Package version 2.0.8+dfsg
Package release 1
Package architecture all
Package type deb
Category universe/science
Homepage https://ginolhac.github.io/mapDamage/
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 38.38 KB
Installed size 184.00 KB
MapDamage is a computational framework written in Python and R, which
tracks and quantifies DNA damage patterns among ancient DNA sequencing
reads generated by Next-Generation Sequencing platforms.
MapDamage is developed at the Centre for GeoGenetics by the
Orlando Group.

Alternatives

Package Version Architecture Repository
mapdamage_2.0.8+dfsg-1_all.deb 2.0.8+dfsg all Ubuntu Universe
mapdamage - - -

Requires

Name Value
libatlas-base-dev -
libblas-dev -
libblas.so -
liblapack-dev -
liblapack.so -
libopenblas-dev -
python-pysam -
python:any >= 2.7.5-5~
python:any << 2.8
r-base-core -
r-cran-gam -
r-cran-ggplot2 -
r-cran-inline -
r-cran-rcpp -
r-cran-rcppgsl -
seqtk -

Download

Type URL
Mirror archive.ubuntu.com
Binary Package mapdamage_2.0.8+dfsg-1_all.deb
Source Package mapdamage

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install mapdamage deb package:
    # sudo apt-get install mapdamage

Files

Path
/usr/bin/mapDamage
/usr/lib/python2.7/dist-packages/mapdamage-2.0.8.egg-info
/usr/lib/python2.7/dist-packages/mapdamage/__init__.py
/usr/lib/python2.7/dist-packages/mapdamage/align.py
/usr/lib/python2.7/dist-packages/mapdamage/composition.py
/usr/lib/python2.7/dist-packages/mapdamage/parseoptions.py
/usr/lib/python2.7/dist-packages/mapdamage/rescale.py
/usr/lib/python2.7/dist-packages/mapdamage/rscript.py
/usr/lib/python2.7/dist-packages/mapdamage/seq.py
/usr/lib/python2.7/dist-packages/mapdamage/tables.py
/usr/lib/python2.7/dist-packages/mapdamage/version.py
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/lengths.R
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/mapDamage.R
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/checkLibraries.R
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/data.R
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/function.R
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/main.R
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/postConditonal.R
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/priorPropose.R
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/runGeneral.R
/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/start.R
/usr/share/doc/mapdamage/README.test
/usr/share/doc/mapdamage/changelog.Debian.gz
/usr/share/doc/mapdamage/copyright
/usr/share/doc/mapdamage/ref_T.fa
/usr/share/doc/mapdamage/run-r-packages-check
/usr/share/doc/mapdamage/run-unit-test
/usr/share/doc/mapdamage/tests/rescale_test.py
/usr/share/doc/mapdamage/tests/rescale_test/long_align/pe.sam
/usr/share/doc/mapdamage/tests/rescale_test/long_align/ref.fa
/usr/share/doc/mapdamage/tests/rescale_test/long_align/pe_output/Stats_out_MCMC_correct_prob.csv
/usr/share/doc/mapdamage/tests/rescale_test/pe_test/pe.sam
/usr/share/doc/mapdamage/tests/rescale_test/pe_test/pe_rescaled_correct.sam
/usr/share/doc/mapdamage/tests/rescale_test/pe_test/ref.fa
/usr/share/doc/mapdamage/tests/rescale_test/pe_test/pe_output/Stats_out_MCMC_correct_prob.csv
/usr/share/man/man1/mapDamage.1.gz

Changelog

2017-06-19 - Andreas Tille <tille@debian.org>
mapdamage (2.0.8+dfsg-1) unstable; urgency=medium
* New upstream version
* debhelper 10
* d/watch: version=4
2017-03-23 - Nadiya Sitdykova <rovenskasa@gmail.com>
mapdamage (2.0.6+dfsg-2) unstable; urgency=medium
* Team upload
[ Andreas Tille ]
* Spelling
[ Nadiya Sitdykova ]
* Add simple tests for examples
* Move pysam dependency from tests/control to control as it's needed
not only for test, but for package
* Add test checking stdin redirect
* Add simple test to demonstrate the problems with installing
r-cran-rcppgsl package
* Edit path to seqtk in composition.py
Closes: #859090
* Fix typo in tests/control 
* Add patch to fix quantile call to remove NA and NaNs
* Add dependency providing liblapack.so and libblas.so
Closes: #859091
* Add file with reference containing all types of nucleotides
* Add information how to check R libraries and what to do in case of errors
to README.test
* Provide tests for examples from documentation
Closes: #848326 
* Fixed typo in README.test
2016-08-03 - Andreas Tille <tille@debian.org>
mapdamage (2.0.6+dfsg-1) unstable; urgency=medium
* Initial release (Closes: #833387)

See Also

Package Description
mapivi_0.9.7-1.1_all.deb Photo viewer and organizer with emphasis on IPTC fields
mapnik-doc_3.0.19+ds-1_all.deb C++ toolkit for developing GIS applications (doc)
mapnik-reference_8.5.6-1~exp1ubuntu1_all.deb Parseable specifications of mapnik - Node.js module
mapnik-utils_3.0.19+ds-1_amd64.deb C++ toolkit for developing GIS applications (utilities)
mapnik-vector-tile_1.6.1+dfsg-2_all.deb Vector tiles integration with mapnik - development files
mapproxy-doc_1.11.0-1_all.deb open source proxy for geospatial data - documentation
mapproxy_1.11.0-1_all.deb open source proxy for geospatial data
mapsembler2_2.2.4+dfsg-1_amd64.deb bioinformatics targeted assembly software
mapserver-bin_7.0.7-1build2_amd64.deb MapServer utilities
mapserver-doc_7.0.7-1build2_all.deb documentation for MapServer
maptool_0.5.0+dfsg.1-2build1_amd64.deb Converts OpenStreetMap maps to Navit
maptransfer-server_0.3-2_all.deb upload/download maps to/from a VALVe game server (Server)
maptransfer_0.3-2_all.deb upload/download maps to/from a VALVe game server (Client)
maq_0.7.1-7_amd64.deb maps short fixed-length polymorphic DNA sequence reads to reference sequences
maqview_0.2.5-8_amd64.deb graphical read alignment viewer for short gene sequences
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