khmer_2.1.2+dfsg-6_amd64.deb


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Description

khmer - in-memory DNA sequence kmer counting, filtering & graph traversal

Property Value
Distribution Ubuntu 19.04 (Disco Dingo)
Repository Ubuntu Universe amd64
Package filename khmer_2.1.2+dfsg-6_amd64.deb
Package name khmer
Package version 2.1.2+dfsg
Package release 6
Package architecture amd64
Package type deb
Category universe/python
Homepage http://khmer.readthedocs.org
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 6.38 MB
Installed size 28.87 MB
khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as that
produced by the Illumina platform. khmer takes a k-mer-centric approach to
sequence analysis, hence the name.

Alternatives

Package Version Architecture Repository
khmer - - -

Requires

Name Value
cython3 >= 0.26.1
khmer-common -
libbz2-1.0 -
libc6 >= 2.14
libgcc1 >= 1:3.4
libgomp1 >= 4.9
libstdc++6 >= 5.2
python3 >= 3.7~
python3 << 3.8
python3-bz2file -
python3-screed >= 1.0
python3:any -
zlib1g >= 1:1.2.3.4

Download

Type URL
Mirror archive.ubuntu.com
Binary Package khmer_2.1.2+dfsg-6_amd64.deb
Source Package khmer

Install Howto

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

Files

Path
/usr/bin/khmer
/usr/lib/khmer/bin/abundance-dist-single.py
/usr/lib/khmer/bin/abundance-dist.py
/usr/lib/khmer/bin/annotate-partitions.py
/usr/lib/khmer/bin/count-median.py
/usr/lib/khmer/bin/do-partition.py
/usr/lib/khmer/bin/extract-long-sequences.py
/usr/lib/khmer/bin/extract-paired-reads.py
/usr/lib/khmer/bin/extract-partitions.py
/usr/lib/khmer/bin/fastq-to-fasta.py
/usr/lib/khmer/bin/filter-abund-single.py
/usr/lib/khmer/bin/filter-abund.py
/usr/lib/khmer/bin/filter-stoptags.py
/usr/lib/khmer/bin/find-knots.py
/usr/lib/khmer/bin/interleave-reads.py
/usr/lib/khmer/bin/load-graph.py
/usr/lib/khmer/bin/load-into-counting.py
/usr/lib/khmer/bin/make-initial-stoptags.py
/usr/lib/khmer/bin/merge-partitions.py
/usr/lib/khmer/bin/normalize-by-median.py
/usr/lib/khmer/bin/partition-graph.py
/usr/lib/khmer/bin/readstats.py
/usr/lib/khmer/bin/sample-reads-randomly.py
/usr/lib/khmer/bin/split-paired-reads.py
/usr/lib/khmer/bin/trim-low-abund.py
/usr/lib/khmer/bin/unique-kmers.py
/usr/lib/python3/dist-packages/khmer/__init__.py
/usr/lib/python3/dist-packages/khmer/_khmer.cpython-37m-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/khmer/_version.py
/usr/lib/python3/dist-packages/khmer/kfile.py
/usr/lib/python3/dist-packages/khmer/khmer_args.py
/usr/lib/python3/dist-packages/khmer/khmer_logger.py
/usr/lib/python3/dist-packages/khmer/thread_utils.py
/usr/lib/python3/dist-packages/khmer/trimming.py
/usr/lib/python3/dist-packages/khmer/utils.py
/usr/lib/python3/dist-packages/khmer-2.1.2.egg-info/PKG-INFO
/usr/lib/python3/dist-packages/khmer-2.1.2.egg-info/dependency_links.txt
/usr/lib/python3/dist-packages/khmer-2.1.2.egg-info/not-zip-safe
/usr/lib/python3/dist-packages/khmer-2.1.2.egg-info/requires.txt
/usr/lib/python3/dist-packages/khmer-2.1.2.egg-info/top_level.txt
/usr/lib/python3/dist-packages/khmer/_oxli/__init__.py
/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpp
/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-37m-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/khmer/_oxli/assembly.pxd
/usr/lib/python3/dist-packages/khmer/_oxli/assembly.pyx
/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpp
/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-37m-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/khmer/_oxli/graphs.pxd
/usr/lib/python3/dist-packages/khmer/_oxli/graphs.pyx
/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpp
/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-37m-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/khmer/_oxli/hashing.pxd
/usr/lib/python3/dist-packages/khmer/_oxli/hashing.pyx
/usr/lib/python3/dist-packages/khmer/_oxli/hllcounter.pxd
/usr/lib/python3/dist-packages/khmer/_oxli/oxli_types.pxd
/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpp
/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-37m-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/khmer/_oxli/parsing.pxd
/usr/lib/python3/dist-packages/khmer/_oxli/parsing.pyx
/usr/lib/python3/dist-packages/khmer/_oxli/traversal.pxd
/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpp
/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-37m-x86_64-linux-gnu.so
/usr/lib/python3/dist-packages/khmer/_oxli/utils.pxd
/usr/lib/python3/dist-packages/khmer/_oxli/utils.pyx
/usr/lib/python3/dist-packages/khmer/tests/__init__.py
/usr/lib/python3/dist-packages/khmer/tests/graph_features.py
/usr/lib/python3/dist-packages/khmer/tests/khmer_tst_utils.py
/usr/lib/python3/dist-packages/khmer/tests/test_banding.py
/usr/lib/python3/dist-packages/khmer/tests/test_countgraph.py
/usr/lib/python3/dist-packages/khmer/tests/test_counting_single.py
/usr/lib/python3/dist-packages/khmer/tests/test_counttable.py
/usr/lib/python3/dist-packages/khmer/tests/test_cpython_hierarchy.py
/usr/lib/python3/dist-packages/khmer/tests/test_cython_assembly.py
/usr/lib/python3/dist-packages/khmer/tests/test_cython_parsing.py
/usr/lib/python3/dist-packages/khmer/tests/test_filter_abund.py
/usr/lib/python3/dist-packages/khmer/tests/test_functions.py
/usr/lib/python3/dist-packages/khmer/tests/test_graph.py
/usr/lib/python3/dist-packages/khmer/tests/test_hashset.py
/usr/lib/python3/dist-packages/khmer/tests/test_hll.py
/usr/lib/python3/dist-packages/khmer/tests/test_labelhash.py
/usr/lib/python3/dist-packages/khmer/tests/test_lump.py
/usr/lib/python3/dist-packages/khmer/tests/test_nibblestorage.py
/usr/lib/python3/dist-packages/khmer/tests/test_nodegraph.py
/usr/lib/python3/dist-packages/khmer/tests/test_normalize_by_median.py
/usr/lib/python3/dist-packages/khmer/tests/test_oxli_functions.py
/usr/lib/python3/dist-packages/khmer/tests/test_read_aligner.py
/usr/lib/python3/dist-packages/khmer/tests/test_read_handling.py
/usr/lib/python3/dist-packages/khmer/tests/test_read_parsers.py
/usr/lib/python3/dist-packages/khmer/tests/test_sandbox_scripts.py
/usr/lib/python3/dist-packages/khmer/tests/test_script_arguments.py
/usr/lib/python3/dist-packages/khmer/tests/test_script_output.py
/usr/lib/python3/dist-packages/khmer/tests/test_scripts.py
/usr/lib/python3/dist-packages/khmer/tests/test_sequence_validation.py
/usr/lib/python3/dist-packages/khmer/tests/test_streaming_io.py
/usr/lib/python3/dist-packages/khmer/tests/test_subset_graph.py
/usr/lib/python3/dist-packages/khmer/tests/test_tabletype.py
/usr/lib/python3/dist-packages/khmer/tests/test_threaded_sequence_processor.py
/usr/lib/python3/dist-packages/khmer/tests/test_version.py
/usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.bz2
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/usr/lib/python3/dist-packages/khmer/tests/test-data/README.rst
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/usr/lib/python3/dist-packages/khmer/tests/test-data/badversion-k32.stoptags
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/usr/lib/python3/dist-packages/khmer/tests/test-data/fakelump.fa.stoptags.txt
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/usr/lib/python3/dist-packages/oxli/__init__.py
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/usr/lib/python3/dist-packages/oxli/functions.py
/usr/lib/python3/dist-packages/oxli/partition.py
/usr/share/doc/khmer/changelog.Debian.gz
/usr/share/doc/khmer/copyright
/usr/share/lintian/overrides/khmer
/usr/share/man/man1/khmer.1.gz
/usr/share/metainfo/khmer.metainfo.xml
/usr/share/python3/runtime.d/khmer.rtupdate

Changelog

2019-01-09 - Michael R. Crusoe <michael.crusoe@gmail.com>
khmer (2.1.2+dfsg-6) unstable; urgency=medium
* Fix building arch-independent packages separately.
2019-01-08 - Michael R. Crusoe <michael.crusoe@gmail.com>
khmer (2.1.2+dfsg-5) unstable; urgency=medium
* Fix liboxli-dev autopkgtest.
* debian/khmer.metainfo.xml: Use a component ID in reverse domain-name
format.
* shrink khmer-common and silence many lintian warnings by symlinking to the
relevant files in python3-guzzle-sphinx-theme
2019-01-07 - Andreas Tille <tille@debian.org>
khmer (2.1.2+dfsg-4) unstable; urgency=medium
* Team upload.
[ Michael R. Crusoe ]
* deal with embedded-javascript-library.
[ Andreas Tille ]
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.3.0
* Drop useless get-orig-source target
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
* Drop ancient X-Python-Version field
* package khmer is: Multi-Arch: foreign
2018-02-11 - Michael R. Crusoe <michael.crusoe@gmail.com>
khmer (2.1.2+dfsg-3) unstable; urgency=medium
* Drop unsupported archs (mips*, ppc*).
2017-12-15 - Andreas Tille <tille@debian.org>
khmer (2.1.2+dfsg-2) unstable; urgency=medium
* Team upload
* debhelper 10
* Specify compression option from d/rules directly inside watch file
* Fix clean target ba removing possibly existing __pycache__ and .eggs
* Autopkgtest is making use of third-party header file - install this into
liboxli-dev package and add according -I directive to test
Closes: #851830
* Standards-Version: 4.1.2
2017-10-07 - Michael R. Crusoe <michael.crusoe@gmail.com>
khmer (2.1.2+dfsg-1) unstable; urgency=medium
* New upstream version 2.1.2
2017-08-29 - Michael R. Crusoe <michael.crusoe@gmail.com>
khmer (2.1.1+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* Remove empty field
[ Michael R. Crusoe ]
* New upstream version 2.1.1
* Incorporate patch from Ubuntu, thank you Michael Hudson-Doyle.
Closes: #862380
2017-05-12 - Michael Hudson-Doyle <michael.hudson@ubuntu.com>
khmer (2.0+dfsg-10ubuntu1) artful; urgency=medium
* Fix build with Python 3.6.
2017-04-06 - Mattia Rizzolo <mattia@debian.org>
khmer (2.0+dfsg-10) unstable; urgency=medium
* Team upload.
* Revert "Drop arm64 due to failing tests."  Closes: #859752
2017-01-24 - Michael R. Crusoe <michael.crusoe@gmail.com>
khmer (2.0+dfsg-9) unstable; urgency=medium
* Drop arm64 due to failing tests. (Closes: #851830)

See Also

Package Description
khmerconverter_1.4-1.2_all.deb converts between legacy Khmer encodings and Unicode
khotkeys-data_5.15.4-0ubuntu1_all.deb configure input actions settings
khotkeys-dev_5.15.4-0ubuntu1_amd64.deb configure input actions settings
khotkeys_5.15.4-0ubuntu1_amd64.deb configure input actions settings
khronos-api_4.6+git20180514-1_all.deb Khronos XML API Registry
kicad-common_5.0.2+dfsg1-1_all.deb Old common files used by kicad - Transitional Package
kicad-demos_5.0.2+dfsg1-1_all.deb Demo projects for kicad
kicad-doc-ca_5.0.2+dfsg1-1_all.deb Kicad help files (Catalan)
kicad-doc-de_5.0.2+dfsg1-1_all.deb Kicad help files (German)
kicad-doc-en_5.0.2+dfsg1-1_all.deb Kicad help files (English)
kicad-doc-es_5.0.2+dfsg1-1_all.deb Kicad help files (Spanish)
kicad-doc-fr_5.0.2+dfsg1-1_all.deb Kicad help files (French)
kicad-doc-id_5.0.2+dfsg1-1_all.deb Kicad help files (Indonesian)
kicad-doc-it_5.0.2+dfsg1-1_all.deb Kicad help files (Italian)
kicad-doc-ja_5.0.2+dfsg1-1_all.deb Kicad help files (Japanese)
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