paleomix_1.2.7-1_all.deb


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Description

paleomix - pipelines and tools for the processing of ancient and modern HTS data

Property Value
Distribution Ubuntu 17.10 (Artful Aardvark)
Repository Ubuntu Universe i386
Package name paleomix
Package version 1.2.7
Package release 1
Package architecture all
Package type deb
Installed size 7.70 KB
Download size 4.45 MB
Official Mirror archive.ubuntu.com
The PALEOMIX pipelines are a set of pipelines and tools designed to aid
the rapid processing of High-Throughput Sequencing (HTS) data: The BAM
pipeline processes de-multiplexed reads from one or more samples,
through sequence processing and alignment, to generate BAM alignment
files useful in downstream analyses; the Phylogenetic pipeline carries
out genotyping and phylogenetic inference on BAM alignment files, either
produced using the BAM pipeline or generated elsewhere; and the Zonkey
pipeline carries out a suite of analyses on low coverage equine
alignments, in order to detect the presence of F1-hybrids in
archaeological assemblages. In addition, PALEOMIX aids in metagenomic
analysis of the extracts.
The pipelines have been designed with ancient DNA (aDNA) in mind, and
includes several features especially useful for the analyses of ancient
samples, but can all be for the processing of modern samples, in order
to ensure consistent data processing.

Alternatives

Package Version Architecture Repository
paleomix_1.2.7-1_all.deb 1.2.7 all Ubuntu Universe
paleomix - - -

Requires

Name Value
adapterremoval -
bcftools -
bedtools -
bowtie2 -
bwa -
examl -
mafft -
mapdamage -
phylip -
picard-tools -
python-coverage -
python-flexmock -
python-pysam -
python-setproctitle -
python:any << 2.8
python:any >= 2.7.5-5~
r-base-core -
radiant -
raxml -
samtools -

Download

Type URL
Binary Package paleomix_1.2.7-1_all.deb
Source Package paleomix

Install Howto

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

Files

Path
/usr/bin/bam_pipeline
/usr/bin/bam_rmdup_collapsed
/usr/bin/conv_gtf_to_bed
/usr/bin/paleomix
/usr/bin/phylo_pipeline
/usr/bin/trim_pipeline
/usr/lib/python2.7/dist-packages/paleomix/__init__.py
/usr/lib/python2.7/dist-packages/paleomix/config.py
/usr/lib/python2.7/dist-packages/paleomix/logger.py
/usr/lib/python2.7/dist-packages/paleomix/main.py
/usr/lib/python2.7/dist-packages/paleomix/node.py
/usr/lib/python2.7/dist-packages/paleomix/nodegraph.py
/usr/lib/python2.7/dist-packages/paleomix/pipeline.py
/usr/lib/python2.7/dist-packages/paleomix/ui.py
/usr/lib/python2.7/dist-packages/paleomix-1.2.7.egg-info/PKG-INFO
/usr/lib/python2.7/dist-packages/paleomix-1.2.7.egg-info/dependency_links.txt
/usr/lib/python2.7/dist-packages/paleomix-1.2.7.egg-info/entry_points.txt
/usr/lib/python2.7/dist-packages/paleomix-1.2.7.egg-info/not-zip-safe
/usr/lib/python2.7/dist-packages/paleomix-1.2.7.egg-info/requires.txt
/usr/lib/python2.7/dist-packages/paleomix-1.2.7.egg-info/top_level.txt
/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/__init__.py
/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/builder.py
/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/command.py
/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/pprint.py
/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/sets.py
/usr/lib/python2.7/dist-packages/paleomix/common/__init__.py
/usr/lib/python2.7/dist-packages/paleomix/common/bamfiles.py
/usr/lib/python2.7/dist-packages/paleomix/common/bedtools.py
/usr/lib/python2.7/dist-packages/paleomix/common/console.py
/usr/lib/python2.7/dist-packages/paleomix/common/fileutils.py
/usr/lib/python2.7/dist-packages/paleomix/common/makefile.py
/usr/lib/python2.7/dist-packages/paleomix/common/procs.py
/usr/lib/python2.7/dist-packages/paleomix/common/rtools.py
/usr/lib/python2.7/dist-packages/paleomix/common/sampling.py
/usr/lib/python2.7/dist-packages/paleomix/common/sequences.py
/usr/lib/python2.7/dist-packages/paleomix/common/signals.py
/usr/lib/python2.7/dist-packages/paleomix/common/system.py
/usr/lib/python2.7/dist-packages/paleomix/common/testing.py
/usr/lib/python2.7/dist-packages/paleomix/common/text.py
/usr/lib/python2.7/dist-packages/paleomix/common/timer.py
/usr/lib/python2.7/dist-packages/paleomix/common/utilities.py
/usr/lib/python2.7/dist-packages/paleomix/common/vcffilter.py
/usr/lib/python2.7/dist-packages/paleomix/common/vcfwrap.py
/usr/lib/python2.7/dist-packages/paleomix/common/versions.py
/usr/lib/python2.7/dist-packages/paleomix/common/formats/__init__.py
/usr/lib/python2.7/dist-packages/paleomix/common/formats/_common.py
/usr/lib/python2.7/dist-packages/paleomix/common/formats/_graph.py
/usr/lib/python2.7/dist-packages/paleomix/common/formats/fasta.py
/usr/lib/python2.7/dist-packages/paleomix/common/formats/fastq.py
/usr/lib/python2.7/dist-packages/paleomix/common/formats/msa.py
/usr/lib/python2.7/dist-packages/paleomix/common/formats/newick.py
/usr/lib/python2.7/dist-packages/paleomix/common/formats/phylip.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/__init__.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/adapterremoval.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/bedtools.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/bowtie2.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/bwa.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/commands.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/examl.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/formats.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/gatk.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/mafft.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/mapdamage.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/misc.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/newick.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/phylip.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/picard.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/raxml.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/samtools.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/sequences.py
/usr/lib/python2.7/dist-packages/paleomix/nodes/validation.py
/usr/lib/python2.7/dist-packages/paleomix/resources/__init__.py
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_makefile.yaml
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_01.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_02.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_03.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_04.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_01.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_02.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_03.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_04.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_01.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_02.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_03.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_01.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_02.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_03.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_01.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_02.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_03.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_01.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_02.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_03.fastq.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.truncated.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.singleton.truncated.gz
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_prefixes/rCRS.fasta
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_makefile.yaml
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_prefixes/README
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_prefixes/setup.sh
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/setup.sh
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A/000_ENA
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/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Length_plot.pdf
/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Runtime_log.txt
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Changelog

2017-02-23 - Andreas Tille <tille@debian.org>
paleomix (1.2.7-1) unstable; urgency=medium
* Initial release (Closes: #855900)

See Also

Package Description
palo_1.97_i386.deb Linux boot loader for HP PA-RISC
palp_2.1-4_i386.deb Package for Analyzing Lattice Polytopes
pam-dbus-notify_0.2.1-3_all.deb Handler for the pam-dbus module, using notification-daemon
paman_0.9.4-1ubuntu5_i386.deb PulseAudio Manager
pamtester_0.1.2-2_i386.deb utility program to test the PAM facility
pamu2fcfg_1.0.4-2_i386.deb universal 2nd factor (U2F) PAM module command-line helper tool
pan_0.142-1_i386.deb newsreader based on GTK2, which looks like Forte Agent
pandoc-citeproc-preamble_1.2.3_i386.deb insert a preamble before pandoc-citeproc's bibliography
pandoc-citeproc_0.10.4.1-2build3_i386.deb Pandoc support for Citation Style Language - tools
pandoc-data_1.19.2.1.0-1_all.deb general markup converter - data files
pandoc_1.19.2.1.0-1_i386.deb general markup converter
pandora-build_0.171.1-0ubuntu2_all.deb autotools made better, faster stronger
pandora_0.7.1-0ubuntu3_i386.deb GIMP Plugin For Creating Panoramas
pandorafms-agent_4.1-1_all.deb Pandora FMS - The Flexible Monitoring System (agent)
pango1.0-tests_1.40.12-1_i386.deb Layout and rendering of internationalized text - installed tests
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