Package - paleomix
Primary informations
Download package: http://deb.debian.org/debian/pool/main/p/paleomix/paleomix_1.3.8-2_amd64.deb (Size: 961.0KiB)| Property | Value |
|---|---|
| Package | paleomix |
| Version | 1.3.8-2 |
| Installed-Size | 2006 |
| Maintainer | Debian Med Packaging Team |
| Architecture | amd64 |
| Depends | python3-coloredlogs, python3-configargparse, python3-pysam, python3-ruamel.yaml, python3-setproctitle, python3:any, adapterremoval, bedtools, bowtie2, bwa, bcftools, examl, mafft, mapdamage, phylip, picard-tools, r-base-core, radiant, raxml, samtools |
| Description | pipelines and tools for the processing of ancient and modern HTS data |
| Description-md5 | 7cb3c4aa709e51b480a41a73961d7253 |
| Homepage | https://geogenetics.ku.dk/publications/paleomix |
| Section | science |
| Priority | optional |
| Filename | pool/main/p/paleomix/paleomix_1.3.8-2_amd64.deb |
| Size | 984108 |
| MD5sum | 002d92f28755caf1c12004da66a7964a |
| SHA256 | 56fcce16061450d75d95b3db3d8169aee8f8e810f5ac2a725ea57c7dce44864e |
Files in package
- /usr/bin/paleomix
- /usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/PKG-INFO
- /usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/dependency_links.txt
- /usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/entry_points.txt
- /usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/not-zip-safe
- /usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/requires.txt
- /usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/top_level.txt
- /usr/lib/python3/dist-packages/paleomix/__init__.py
- /usr/lib/python3/dist-packages/paleomix/atomiccmd/__init__.py
- /usr/lib/python3/dist-packages/paleomix/atomiccmd/builder.py
- /usr/lib/python3/dist-packages/paleomix/atomiccmd/command.py
- /usr/lib/python3/dist-packages/paleomix/atomiccmd/pprint.py
- /usr/lib/python3/dist-packages/paleomix/atomiccmd/sets.py
- /usr/lib/python3/dist-packages/paleomix/common/__init__.py
- /usr/lib/python3/dist-packages/paleomix/common/argparse.py
- /usr/lib/python3/dist-packages/paleomix/common/bamfiles.py
- /usr/lib/python3/dist-packages/paleomix/common/bedtools.py
- /usr/lib/python3/dist-packages/paleomix/common/fileutils.py
- /usr/lib/python3/dist-packages/paleomix/common/formats/__init__.py
- /usr/lib/python3/dist-packages/paleomix/common/formats/_common.py
- /usr/lib/python3/dist-packages/paleomix/common/formats/_graph.py
- /usr/lib/python3/dist-packages/paleomix/common/formats/fasta.py
- /usr/lib/python3/dist-packages/paleomix/common/formats/fastq.py
- /usr/lib/python3/dist-packages/paleomix/common/formats/msa.py
- /usr/lib/python3/dist-packages/paleomix/common/formats/newick.py
- /usr/lib/python3/dist-packages/paleomix/common/formats/phylip.py
- /usr/lib/python3/dist-packages/paleomix/common/logging.py
- /usr/lib/python3/dist-packages/paleomix/common/makefile.py
- /usr/lib/python3/dist-packages/paleomix/common/procs.py
- /usr/lib/python3/dist-packages/paleomix/common/rtools.py
- /usr/lib/python3/dist-packages/paleomix/common/sampling.py
- /usr/lib/python3/dist-packages/paleomix/common/sequences.py
- /usr/lib/python3/dist-packages/paleomix/common/system.py
- /usr/lib/python3/dist-packages/paleomix/common/testing.py
- /usr/lib/python3/dist-packages/paleomix/common/text.py
- /usr/lib/python3/dist-packages/paleomix/common/timer.py
- /usr/lib/python3/dist-packages/paleomix/common/utilities.py
- /usr/lib/python3/dist-packages/paleomix/common/vcffilter.py
- /usr/lib/python3/dist-packages/paleomix/common/vcfwrap.py
- /usr/lib/python3/dist-packages/paleomix/common/versions.py
- /usr/lib/python3/dist-packages/paleomix/main.py
- /usr/lib/python3/dist-packages/paleomix/node.py
- /usr/lib/python3/dist-packages/paleomix/nodegraph.py
- /usr/lib/python3/dist-packages/paleomix/nodes/__init__.py
- /usr/lib/python3/dist-packages/paleomix/nodes/adapterremoval.py
- /usr/lib/python3/dist-packages/paleomix/nodes/bedtools.py
- /usr/lib/python3/dist-packages/paleomix/nodes/bowtie2.py
- /usr/lib/python3/dist-packages/paleomix/nodes/bwa.py
- /usr/lib/python3/dist-packages/paleomix/nodes/commands.py
- /usr/lib/python3/dist-packages/paleomix/nodes/examl.py
- /usr/lib/python3/dist-packages/paleomix/nodes/formats.py
- /usr/lib/python3/dist-packages/paleomix/nodes/mafft.py
- /usr/lib/python3/dist-packages/paleomix/nodes/mapdamage.py
- /usr/lib/python3/dist-packages/paleomix/nodes/newick.py
- /usr/lib/python3/dist-packages/paleomix/nodes/phylip.py
- /usr/lib/python3/dist-packages/paleomix/nodes/picard.py
- /usr/lib/python3/dist-packages/paleomix/nodes/raxml.py
- /usr/lib/python3/dist-packages/paleomix/nodes/samtools.py
- /usr/lib/python3/dist-packages/paleomix/nodes/sequences.py
- /usr/lib/python3/dist-packages/paleomix/nodes/validation.py
- /usr/lib/python3/dist-packages/paleomix/pipeline.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/__init__.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/__init__.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/config.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/makefile.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/mkfile.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/nodes.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/__init__.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/lane.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/library.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/prefix.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/reads.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/sample.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/statistics.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/summary.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/parts/target.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/paths.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/pipeline.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/bam/trim_pipeline.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/__init__.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/config.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/example.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/makefile.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/mkfile.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/__init__.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/genotype.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/msa.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/parts/phylo.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/phylo/pipeline.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/__init__.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/build_db.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/build_mito.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/build_tped.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/common.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/config.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/database.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/__init__.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/admixture.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/common.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/mitochondria.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/nuclear.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/report.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/parts/summary.py
- /usr/lib/python3/dist-packages/paleomix/pipelines/zonkey/pipeline.py
- /usr/lib/python3/dist-packages/paleomix/resources/__init__.py
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz
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- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz
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- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/makefile.yaml
- /usr/lib/python3/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/setup.sh
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/setup.sh
- /usr/lib/python3/dist-packages/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py
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