macsyfinder_1.0.5-2_all.deb


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Description

macsyfinder - detection of macromolecular systems in protein datasets

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main i386
Package filename macsyfinder_1.0.5-2_all.deb
Package name macsyfinder
Package version 1.0.5
Package release 2
Package architecture all
Package type deb
Category science
Homepage https://github.com/gem-pasteur/macsyfinder
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 6.75 MB
Installed size 21.99 MB
MacSyFinder is a program to model and detect macromolecular systems,
genetic pathways... in protein datasets. In prokaryotes, these systems
have often evolutionarily conserved properties: they are made of conserved
components, and are encoded in compact loci (conserved genetic architecture).
The user models these systems with MacSyFinder to reflect these conserved
features, and to allow their efficient detection
This package presents the Open Source Java API to biological databases
and a series of mostly sequence-based algorithms.

Alternatives

Package Version Architecture Repository
macsyfinder_1.0.5-2_all.deb 1.0.5 all Debian Main
macsyfinder - - -

Requires

Name Value
hmmer -
libjs-jquery -
libjs-underscore -
ncbi-blast+ -
python:any << 2.8
python:any >= 2.7~

Download

Type URL
Mirror ftp.br.debian.org
Binary Package macsyfinder_1.0.5-2_all.deb
Source Package macsyfinder

Install Howto

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

Files

Path
/etc/macsyfinder/macsyfinder.conf
/usr/bin/macsyfinder
/usr/lib/python2.7/dist-packages/macsyfinder-1.0.5.egg-info
/usr/lib/python2.7/dist-packages/macsypy/__init__.py
/usr/lib/python2.7/dist-packages/macsypy/config.py
/usr/lib/python2.7/dist-packages/macsypy/database.py
/usr/lib/python2.7/dist-packages/macsypy/gene.py
/usr/lib/python2.7/dist-packages/macsypy/macsypy_error.py
/usr/lib/python2.7/dist-packages/macsypy/registries.py
/usr/lib/python2.7/dist-packages/macsypy/report.py
/usr/lib/python2.7/dist-packages/macsypy/search_genes.py
/usr/lib/python2.7/dist-packages/macsypy/search_systems.py
/usr/lib/python2.7/dist-packages/macsypy/system.py
/usr/lib/python2.7/dist-packages/macsypy/system_parser.py
/usr/lib/python2.7/dist-packages/macsypy/utils.py
/usr/share/doc-base/macsyfinder
/usr/share/doc/macsyfinder/README.test
/usr/share/doc/macsyfinder/changelog.Debian.gz
/usr/share/doc/macsyfinder/copyright
/usr/share/doc/macsyfinder/run-unit-test
/usr/share/doc/macsyfinder/examples/formatdb.err
/usr/share/doc/macsyfinder/examples/ordered_replicon_base.gz
/usr/share/doc/macsyfinder/examples/test_aesu.fa.gz
/usr/share/doc/macsyfinder/examples/test_aesu.fa.idx.gz
/usr/share/doc/macsyfinder/examples/test_aesu.fa.phr.gz
/usr/share/doc/macsyfinder/examples/test_aesu.fa.pin.gz
/usr/share/doc/macsyfinder/examples/test_aesu.fa.pog.gz
/usr/share/doc/macsyfinder/examples/test_aesu.fa.psd.gz
/usr/share/doc/macsyfinder/examples/test_aesu.fa.psi
/usr/share/doc/macsyfinder/examples/test_aesu.fa.psq.gz
/usr/share/doc/macsyfinder/examples/test_base.fa.gz
/usr/share/doc/macsyfinder/html/.buildinfo
/usr/share/doc/macsyfinder/html/HMMReport.html
/usr/share/doc/macsyfinder/html/config.html
/usr/share/doc/macsyfinder/html/database.html
/usr/share/doc/macsyfinder/html/functioning.html
/usr/share/doc/macsyfinder/html/gembase_convention.html
/usr/share/doc/macsyfinder/html/gene.html
/usr/share/doc/macsyfinder/html/genindex.html
/usr/share/doc/macsyfinder/html/implementation.html
/usr/share/doc/macsyfinder/html/index.html
/usr/share/doc/macsyfinder/html/input.html
/usr/share/doc/macsyfinder/html/installation.html
/usr/share/doc/macsyfinder/html/macsypy_error.html
/usr/share/doc/macsyfinder/html/macsyview.html
/usr/share/doc/macsyfinder/html/objects.inv
/usr/share/doc/macsyfinder/html/outputs.html
/usr/share/doc/macsyfinder/html/profile.html
/usr/share/doc/macsyfinder/html/py-modindex.html
/usr/share/doc/macsyfinder/html/quickstart.html
/usr/share/doc/macsyfinder/html/search.html
/usr/share/doc/macsyfinder/html/search_genes.html
/usr/share/doc/macsyfinder/html/search_systems.html
/usr/share/doc/macsyfinder/html/searchindex.js
/usr/share/doc/macsyfinder/html/system.html
/usr/share/doc/macsyfinder/html/system_definition.html
/usr/share/doc/macsyfinder/html/system_parser.html
/usr/share/doc/macsyfinder/html/_images/Figure1_figure_system_no_mb-new3_2col.svg
/usr/share/doc/macsyfinder/html/_images/FigureS2_figure_TXSScan_last-new.svg
/usr/share/doc/macsyfinder/html/_images/fig_capture.svg
/usr/share/doc/macsyfinder/html/_images/figure_main-2.svg
/usr/share/doc/macsyfinder/html/_images/graphviz-376edbfab4341f66eb110fe7f2529b708ff6bb79.png
/usr/share/doc/macsyfinder/html/_images/graphviz-376edbfab4341f66eb110fe7f2529b708ff6bb79.png.map
/usr/share/doc/macsyfinder/html/_modules/abc.html
/usr/share/doc/macsyfinder/html/_modules/collections.html
/usr/share/doc/macsyfinder/html/_modules/index.html
/usr/share/doc/macsyfinder/html/_modules/macsypy/database.html
/usr/share/doc/macsyfinder/html/_modules/macsypy/gene.html
/usr/share/doc/macsyfinder/html/_modules/macsypy/macsypy_error.html
/usr/share/doc/macsyfinder/html/_modules/macsypy/report.html
/usr/share/doc/macsyfinder/html/_modules/macsypy/search_genes.html
/usr/share/doc/macsyfinder/html/_modules/macsypy/system.html
/usr/share/doc/macsyfinder/html/_modules/macsypy/system_parser.html
/usr/share/doc/macsyfinder/html/_sources/HMMReport.rst.txt
/usr/share/doc/macsyfinder/html/_sources/config.rst.txt
/usr/share/doc/macsyfinder/html/_sources/database.rst.txt
/usr/share/doc/macsyfinder/html/_sources/functioning.rst.txt
/usr/share/doc/macsyfinder/html/_sources/gembase_convention.rst.txt
/usr/share/doc/macsyfinder/html/_sources/gene.rst.txt
/usr/share/doc/macsyfinder/html/_sources/implementation.rst.txt
/usr/share/doc/macsyfinder/html/_sources/index.rst.txt
/usr/share/doc/macsyfinder/html/_sources/input.rst.txt
/usr/share/doc/macsyfinder/html/_sources/installation.rst.txt
/usr/share/doc/macsyfinder/html/_sources/macsypy_error.rst.txt
/usr/share/doc/macsyfinder/html/_sources/macsyview.rst.txt
/usr/share/doc/macsyfinder/html/_sources/outputs.rst.txt
/usr/share/doc/macsyfinder/html/_sources/profile.rst.txt
/usr/share/doc/macsyfinder/html/_sources/quickstart.rst.txt
/usr/share/doc/macsyfinder/html/_sources/search_genes.rst.txt
/usr/share/doc/macsyfinder/html/_sources/search_systems.rst.txt
/usr/share/doc/macsyfinder/html/_sources/system.rst.txt
/usr/share/doc/macsyfinder/html/_sources/system_definition.rst.txt
/usr/share/doc/macsyfinder/html/_sources/system_parser.rst.txt
/usr/share/doc/macsyfinder/html/_static/ajax-loader.gif
/usr/share/doc/macsyfinder/html/_static/basic.css
/usr/share/doc/macsyfinder/html/_static/classic.css
/usr/share/doc/macsyfinder/html/_static/comment-bright.png
/usr/share/doc/macsyfinder/html/_static/comment-close.png
/usr/share/doc/macsyfinder/html/_static/comment.png
/usr/share/doc/macsyfinder/html/_static/default.css
/usr/share/doc/macsyfinder/html/_static/doctools.js
/usr/share/doc/macsyfinder/html/_static/documentation_options.js
/usr/share/doc/macsyfinder/html/_static/down-pressed.png
/usr/share/doc/macsyfinder/html/_static/down.png
/usr/share/doc/macsyfinder/html/_static/file.png
/usr/share/doc/macsyfinder/html/_static/jquery.js
/usr/share/doc/macsyfinder/html/_static/minus.png
/usr/share/doc/macsyfinder/html/_static/plus.png
/usr/share/doc/macsyfinder/html/_static/pygments.css
/usr/share/doc/macsyfinder/html/_static/searchtools.js
/usr/share/doc/macsyfinder/html/_static/sidebar.js
/usr/share/doc/macsyfinder/html/_static/underscore.js
/usr/share/doc/macsyfinder/html/_static/up-pressed.png
/usr/share/doc/macsyfinder/html/_static/up.png
/usr/share/doc/macsyfinder/html/_static/websupport.js
/usr/share/doc/macsyfinder/pdf/Macsyfinder.pdf.gz
/usr/share/macsyfinder/DEF/CAS-TypeIA.xml
/usr/share/macsyfinder/DEF/CAS-TypeIB.xml
/usr/share/macsyfinder/DEF/CAS-TypeIC.xml
/usr/share/macsyfinder/DEF/CAS-TypeID.xml
/usr/share/macsyfinder/DEF/CAS-TypeIE.xml
/usr/share/macsyfinder/DEF/CAS-TypeIF.xml
/usr/share/macsyfinder/DEF/CAS-TypeIIA.xml
/usr/share/macsyfinder/DEF/CAS-TypeIIB.xml
/usr/share/macsyfinder/DEF/CAS-TypeIIIA.xml
/usr/share/macsyfinder/DEF/CAS-TypeIIIB.xml
/usr/share/macsyfinder/DEF/CAS-TypeIIIU.xml
/usr/share/macsyfinder/DEF/CAS-TypeIIU.xml
/usr/share/macsyfinder/DEF/CAS-TypeIU.xml
/usr/share/macsyfinder/DEF/CAS-TypeU.xml
/usr/share/macsyfinder/DEF/CAS.xml
/usr/share/macsyfinder/profiles/cas10_TypeIIIA.hmm
/usr/share/macsyfinder/profiles/cas10_TypeIIIB.hmm
/usr/share/macsyfinder/profiles/cas10d_TypeID.hmm
/usr/share/macsyfinder/profiles/cas1_TypeI-II-III.hmm
/usr/share/macsyfinder/profiles/cas1_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas1_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas1_TypeIC.hmm
/usr/share/macsyfinder/profiles/cas1_TypeID.hmm
/usr/share/macsyfinder/profiles/cas1_TypeIE.hmm
/usr/share/macsyfinder/profiles/cas1_TypeIF.hmm
/usr/share/macsyfinder/profiles/cas1_TypeII.hmm
/usr/share/macsyfinder/profiles/cas1_TypeU.hmm
/usr/share/macsyfinder/profiles/cas2_TypeI-II-III.hmm
/usr/share/macsyfinder/profiles/cas2_TypeIE.hmm
/usr/share/macsyfinder/profiles/cas3-cas2_TypeIF.hmm
/usr/share/macsyfinder/profiles/cas3_TypeI.hmm
/usr/share/macsyfinder/profiles/cas3_TypeID.hmm
/usr/share/macsyfinder/profiles/cas3_TypeIU.hmm
/usr/share/macsyfinder/profiles/cas3a_TypeI.hmm
/usr/share/macsyfinder/profiles/cas4_TypeI-II.hmm
/usr/share/macsyfinder/profiles/cas4_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas4_TypeU.hmm
/usr/share/macsyfinder/profiles/cas5_TypeI.hmm
/usr/share/macsyfinder/profiles/cas5_TypeIE.hmm
/usr/share/macsyfinder/profiles/cas5a2_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas5a_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas5b2_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas5b_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas5c2_TypeIC.hmm
/usr/share/macsyfinder/profiles/cas5c_TypeIC.hmm
/usr/share/macsyfinder/profiles/cas6_TypeI-III.hmm
/usr/share/macsyfinder/profiles/cas6_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas6_TypeIE.hmm
/usr/share/macsyfinder/profiles/cas6_TypeIF.hmm
/usr/share/macsyfinder/profiles/cas7_TypeI.hmm
/usr/share/macsyfinder/profiles/cas7_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas7_TypeIE.hmm
/usr/share/macsyfinder/profiles/cas7b2_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas7b3_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas7b_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas7c2_TypeIC.hmm
/usr/share/macsyfinder/profiles/cas7c_TypeIC.hmm
/usr/share/macsyfinder/profiles/cas8a1a2_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas8a1a3_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas8a1b2_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas8a1b3_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas8a1b_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas8a2a2_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas8a2a_TypeIA.hmm
/usr/share/macsyfinder/profiles/cas8b_TypeIB.hmm
/usr/share/macsyfinder/profiles/cas8c2_TypeIC.hmm
/usr/share/macsyfinder/profiles/cas8c_TypeIC.hmm
/usr/share/macsyfinder/profiles/cas9_TypeII.hmm
/usr/share/macsyfinder/profiles/cas9_TypeIIB.hmm
/usr/share/macsyfinder/profiles/casRa_TypeIA.hmm
/usr/share/macsyfinder/profiles/cmr1_TypeIIIB.hmm
/usr/share/macsyfinder/profiles/cmr3_TypeIIIB.hmm
/usr/share/macsyfinder/profiles/cmr4_TypeIIIB.hmm
/usr/share/macsyfinder/profiles/cmr5_TypeIIIB.hmm
/usr/share/macsyfinder/profiles/cmr6_TypeIIIB.hmm
/usr/share/macsyfinder/profiles/cpf1_TypeU.hmm
/usr/share/macsyfinder/profiles/csa5_TypeIA.hmm
/usr/share/macsyfinder/profiles/csaX_TypeIA.hmm
/usr/share/macsyfinder/profiles/csb1_TypeIU.hmm
/usr/share/macsyfinder/profiles/csb2_TypeIU.hmm
/usr/share/macsyfinder/profiles/csb3_TypeIU.hmm
/usr/share/macsyfinder/profiles/csc1_TypeID.hmm
/usr/share/macsyfinder/profiles/csc2_TypeID.hmm
/usr/share/macsyfinder/profiles/cse1_TypeIE.hmm
/usr/share/macsyfinder/profiles/cse2_TypeIE.hmm
/usr/share/macsyfinder/profiles/csf1_TypeU.hmm
/usr/share/macsyfinder/profiles/csf2_TypeU.hmm
/usr/share/macsyfinder/profiles/csf3_TypeU.hmm
/usr/share/macsyfinder/profiles/csf4_TypeU.hmm
/usr/share/macsyfinder/profiles/csm2_TypeIIIA.hmm
/usr/share/macsyfinder/profiles/csm3_TypeIIIA.hmm
/usr/share/macsyfinder/profiles/csm4_TypeIIIA.hmm
/usr/share/macsyfinder/profiles/csm5_TypeIIIA.hmm
/usr/share/macsyfinder/profiles/csm6_TypeIIIA.hmm
/usr/share/macsyfinder/profiles/csn2_TypeIIA.hmm
/usr/share/macsyfinder/profiles/csx10_TypeIIIU.hmm
/usr/share/macsyfinder/profiles/csx16_TypeIIIU.hmm
/usr/share/macsyfinder/profiles/csx17_TypeIU.hmm
/usr/share/macsyfinder/profiles/csx1u2_TypeIIIU.hmm
/usr/share/macsyfinder/profiles/csx1u_TypeIIIU.hmm
/usr/share/macsyfinder/profiles/csx3_TypeIIIU.hmm
/usr/share/macsyfinder/profiles/csy1_TypeIF.hmm
/usr/share/macsyfinder/profiles/csy2_TypeIF.hmm
/usr/share/macsyfinder/profiles/csy3_TypeIF.hmm
/usr/share/macsyfinder/sequence_data/datatest_gembase.fasta
/usr/share/macsyfinder/sequence_data/datatest_gembase.topology
/usr/share/macsyfinder/sequence_data/results.macsyfinder.json
/usr/share/man/man1/macsyfinder.1.gz

Changelog

2018-10-29 - Andreas Tille <tille@debian.org>
macsyfinder (1.0.5-2) unstable; urgency=medium
[ Jelmer Vernooij ]
* Team Upload.
* Trim trailing whitespace.
* Remove unnecessary X-Python{,3}-Version field in debian/control.
* Use secure copyright file specification URI.
[ Andreas Tille ]
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Remove trailing whitespace in debian/rules
2018-02-06 - Andreas Tille <tille@debian.org>
macsyfinder (1.0.5-1) unstable; urgency=medium
* Team upload
* New upstream version
* cme fix dpkg-control
* debhelper 11
* Build-Depends: s/python-sphinx/python3-sphinx/
2017-10-22 - Andreas Tille <tille@debian.org>
macsyfinder (1.0.2-5) unstable; urgency=medium
* Team upload.
* Add graphviz to Build-Depends
Closes: #878503
* Standards-Version: 4.1.1
2017-09-11 - Andreas Tille <tille@debian.org>
macsyfinder (1.0.2-4) unstable; urgency=medium
* Team upload
* Build-Depends: latexmk
Closes: #872232
* Build-Depends: dh-python
* Standards-Version: 4.1.0 (no changes needed)
2016-12-13 - Canberk Koç <canberkkoc@gmail.com>
macsyfinder (1.0.2-3) unstable; urgency=medium
* Team upload
[ Andreas Tille ]
* Move packaging from SVN to Git
* Add missing X-Python-Version
* Hack around results of broken setup.py
* debhelper 10
* d/watch: version=4
[ Canberk Koç ]
* Autopkgtest added
2016-07-08 - Andreas Tille <tille@debian.org>
macsyfinder (1.0.2-2) unstable; urgency=medium
* Team upload
* debian/upstream/metadata: Fix citation syntax and add some more
information
* cme fix dpkg-control
* Add missing Build-Depends texlive-generic-extra
Closes: #830407
* Fix short description
* Fix manpage
* DEP5 fix
2015-01-31 - bertrand Neron <bneron@pasteur.fr>
macsyfinder (1.0.2-1) unstable; urgency=medium
* first package import (Closes: #776722).

See Also

Package Description
mactelnet-client_0.4.4-4_i386.deb Console tools for telneting and pinging via MAC addresses
mactelnet-server_0.4.4-4_i386.deb Telnet daemon for accepting connections via MAC addresses
macutils_2.0b3-16+b2_i386.deb Set of tools to deal with specially encoded Macintosh files
madbomber-data_0.2.5-8_all.deb Datafiles for madbomber
madbomber_0.2.5-8_i386.deb Kaboom! clone
madison-lite_0.24_all.deb display versions of Debian packages in an archive
madlib-doc_1.3.0-2.1_all.deb mesh adaptation library
madplay_0.15.2b-8.3_i386.deb MPEG audio player in fixed point
madwimax_0.1.1-1+b2_i386.deb user-space driver for mWiMAX equipment based on Samsung CMC-730
maelstrom_1.4.3-L3.0.6+main-9_i386.deb Arcade-style game resembling Asteroids
maffilter-examples_1.3.1+dfsg-1_all.deb process genome alignment in the Multiple Alignment Format (example data)
maffilter_1.3.1+dfsg-1+b1_i386.deb process genome alignment in the Multiple Alignment Format
mafft_7.407-2_i386.deb Multiple alignment program for amino acid or nucleotide sequences
magic-wormhole-transit-relay_0.1.2-1_all.deb Transit Relay server for Magic-Wormhole
magic-wormhole_0.11.2-1_all.deb Securely and simply transfer data between computers
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