recipe pysam

Pysam is a python module for reading and manipulating Samfiles. It is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

Homepage

https://github.com/pysam-developers/pysam

License

MIT

Recipe

/pysam/meta.yaml

Links

biotools: pysam, doi: 10.1093/bioinformatics/btp352

package pysam

Versions

0.15.3-1, 0.15.3-0, 0.15.2-3, 0.15.2-2, 0.15.2-1, 0.15.2-0, 0.15.1-0, 0.15.0.1-1, 0.15.0.1-0, 0.15.0-0, 0.14.1-1, 0.14.1-0, 0.14.0-2, 0.14.0-1, 0.14.0-0, 0.13.0-0, 0.12.0.1-2, 0.12.0.1-1, 0.12.0.1-0, 0.11.2.2-2, 0.11.2.2-1, 0.11.2.2-0, 0.11.2.1-0, 0.11.1-0, 0.11.0-0, 0.10.0-8, 0.10.0-7, 0.10.0-6, 0.10.0-5, 0.10.0-4, 0.10.0-3, 0.10.0-1, 0.9.1.4-1, 0.9.1.4-0, 0.9.1-6, 0.9.1-5, 0.9.1-4, 0.9.1-3, 0.9.1-2, 0.9.1-1, 0.9.1-0, 0.9.0-2, 0.9.0-1, 0.9.0-0, 0.8.4-0, 0.8.4pre0-0, 0.8.3-6, 0.8.3-5, 0.8.3-4, 0.8.3-3, 0.8.3-2, 0.8.3-1, 0.8.3-0, 0.7.7-3, 0.7.7-2, 0.7.7-1, 0.7.7-0

Depends

• bzip2 >=1.0.8,<2.0a0

• curl

• libdeflate >=1.0,<1.1.0a0

• libgcc-ng >=7.3.0

• python >=2.7,<2.8.0a0

• xz >=5.2.4,<5.3.0a0

• zlib >=1.2.11,<1.3.0a0

Required By

• cpat

• pepr

• slamdunk

• iclipro

• counterr

• icount

• igv-reports

• sqt

• nanosv

• clinvar-tsv

• phyluce

• rseqc

• misopy

• python-bioext

• tapestry

• peakachu

• plastid

• tobias

• nanosim

• seroba

• pysamstats

• besst

• wisecondorx

• athena_meta

• crossmap

• ebfilter

• lumpy-sv

• metaseq

• nanocomp

• paragraph

• dr-disco

• gimmemotifs

• riboraptor

• spliceai

• aquila_stlfr

• svtyper

• vcfpy

• samsift

• smcounter2

• wisestork

• rnftools

• atactk

• gretel

• deeptools

• monovar

• patholive

• relocate2

• rmats2sashimiplot

• segmentation-fold

• strainest

• tetoolkit

• mark-nonconverted-reads

• whatshap

• confindr

• mgkit

• outrigger

• advntr

• emirge

• spliceai-wrapper

• comparative-annotation-toolkit

• pneumocat

• kipoi_veff

• hap.py

• riboplot

• ariba

• pbalign

• pbcoretools

• tiddit

• trnanalysis

• ctat-mutations

• gemini

• uropa

• pomoxis

• pydnase

• sequana

• biofluff

• pynnotator

• rna-cd

• rgt

• circlator

• pbcore

• afplot

• cgat-apps

• telescope

• samplot

• refinem

• breakseq2

• iva

• vqsr_cnn

• connor

• ipyrad

• sccaller

• epic2

• oncotator

• probamconvert

• atropos

• ngsutils

• metaphlan2

• tophat-recondition

• microhapulator

• dupre

• metasv

• mqc

• anvio-minimal

• targqc

• pygenometracks

• ribocode

• umi_tools

• compare-reads

• checkm-genome

• guidescan

• aquila_umap

• svim

• tepid

• cooler

• bactopia

• flair

• svviz

• pyloh

• eagle

• mockinbird

• hifive

• medaka

• seqcluster

• smallgenomeutilities

• hicexplorer

• rpkmforgenes

• cgat-daisy

• imfusion

• pybedtools

• ribotish

• umitools

• mapdamage2

• blockclust

• moca

• edd

• scanindel

• sv2

• wg-blimp

• wub

• optitype

• fings

• umis

• bcbio-nextgen-vm

• hits

• tigmint

• rop

• guessmylt

• insilicoseq

• nanoplot

• somaticseq

• ribotricer

• htseq

• mirtop

• pb-falcon

• circle-map

• reparation_blast

• riboseed

• genomelake

• qcat

• fast5seek

• nanoget

• prophyle

• cnvkit

• daisysuite

• midas

• desman

• vamb

• circexplorer

• xyalign

• spanki

• mvp

• genomicassertions

• bcbio-nextgen

• circexplorer2

• cgat-scripts

• simlord

• nucleoatac

• bamread

• dkfz-bias-filter

• quasitools

• phenix

• sixgill

• starseqr

• recycler

• pyseer

• discasm

• bs-seeker2

• flaimapper

• aquila

• bioconvert

• transposcope

• riboseq-rust

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install pysam

and update with:

conda update pysam

or use the docker container:

docker pull quay.io/biocontainers/pysam:<tag>

(see pysam/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pysam/README.html)