recipe ucsc-bamtopsl

Convert a bam file to a psl and optionally also a fasta file that contains the reads.

Homepage

http://hgdownload.cse.ucsc.edu/admin/exe/

License

varies; see http://genome.ucsc.edu/license

Recipe

/ucsc-bamtopsl/meta.yaml

package ucsc-bamtopsl

(downloads) docker_ucsc-bamtopsl

Versions

377-1, 377-0, 366-0, 357-2, 357-1, 357-0

Depends libgcc-ng

>=7.3.0

Depends libpng

>=1.6.35,<1.7.0a0

Depends libuuid

>=2.32.1,<3.0a0

Depends mysql-connector-c

>=6.1.11,<6.1.12.0a0

Depends openssl

>=1.1.1a,<1.1.2a

Depends zlib

>=1.2.11,<1.3.0a0

Requirements

Installation

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

conda install ucsc-bamtopsl

and update with:

conda update ucsc-bamtopsl

or use the docker container:

docker pull quay.io/biocontainers/ucsc-bamtopsl:<tag>

(see ucsc-bamtopsl/tags for valid values for <tag>)