recipe spaln

Map and align a set of cDNA/EST or protein sequences onto a genome

Homepage:

https://github.com/ogotoh/spaln

Documentation:

https://github.com/ogotoh/spaln/blob/ver.3.0.6b/README.md

License:

GPL / GPL-2.0-or-later

Recipe:

/spaln/meta.yaml

Links:

doi: 10.1093/nar/gks708, doi: 10.1093/bioinformatics/btl067, usegalaxy-eu: spaln

Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. Spaln also performs spliced or ordinary alignment after rapid similarity search against a protein sequence database, if a genomic segment or an amino acid sequence is given as a query.

package spaln

versions:

3.0.6-0,  3.0.6b-1,  3.0.6b-0,  3.0.4-0,  3.0.1-0,  3.0.0-0,  2.4.13-2,  2.4.13-1,  2.4.13-0, 

3.0.6-0,  3.0.6b-1,  3.0.6b-0,  3.0.4-0,  3.0.1-0,  3.0.0-0,  2.4.13-2,  2.4.13-1,  2.4.13-0,  2.4.13g-0,  2.4.13f-0,  2.4.9-0,  2.4.8-0,  2.4.7-2,  2.4.7-1,  2.4.7-0,  2.4.6-1,  2.4.6-0,  2.4.5-0,  2.4.4-0,  2.4.03-1,  2.4.03-0,  2.4.02-0,  2.4.01-0,  2.3.3-0,  2.3.3c-0,  2.3.3b-0,  2.3.3a-0,  2.3.2-0

depends libgcc:

>=12

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

requirements:

additional platforms:

linux-aarch64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install spaln

and update with::

   mamba update spaln

To create a new environment, run:

mamba create --name myenvname spaln

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `spaln/tags`_ for valid values for ``<tag>``)

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