recipe jalview

Jalview is a free program for multiple sequence alignment editing, visualisation, analysis and figure generation.

Homepage:

https://www.jalview.org/

License:

GPL-3.0-only

Recipe:

/jalview/meta.yaml

Jalview is a free program for multiple sequence alignment editing, visualisation, analysis and figure generation. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. It is also able to import and annotate DNA and Protein products from VCF files and retrieve data and annotation from 3D-Beacons, Uniprot, Ensembl, ENA, Rfam, Pfam and the PDBe.

package jalview

(downloads) docker_jalview

versions:
2.11.4.1-0,  2.11.4.0-0,  2.11.3.3-0,  2.11.3.2-0,  2.11.3.1-0,  2.11.3.0-0,  2.11.2.7-0,  2.11.2.6-0,  2.11.2.4-0, 

2.11.4.1-0,  2.11.4.0-0,  2.11.3.3-0,  2.11.3.2-0,  2.11.3.1-0,  2.11.3.0-0,  2.11.2.7-0,  2.11.2.6-0,  2.11.2.4-0,  2.11.2.3-0,  2.11.2.1-0,  2.11.1.5-0,  2.11.1.4-2,  2.11.1.4-1,  2.11.1.4-0,  2.11.1.3-0,  2.11.1.2-0,  2.11.1.0-1,  2.11.1.0-0,  2.11.0-1,  2.11.0-0,  2.10.5-3,  2.10.4-0,  2.10.4b1-2,  2.10.4b1-0,  2.10.3-1,  2.10.3-0,  2.10.3b1-0,  2.10.2b2-2,  2.10.2b2-1,  2.10.2b2-0

depends openjdk:

>=8.0.192,!=9.*,!=10.*,!=11.0.9.*,<12

depends psutil:

depends xorg-libxtst:

requirements:

additional platforms:

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 jalview

and update with::

   mamba update jalview

To create a new environment, run:

mamba create --name myenvname jalview

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/jalview:<tag>

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

Notes

This wrapper and installation is primarily for commandline use. Set JALVIEW_JRE=j1.8 or JALVIEW_JRE=j11 to specify the java runtime if you need jalview to start up as quickly as possible Set JALVIEW_MAXMEM=2g to restrict jalviews maximal memory consumption (here to 2G RAM). Otherwise 90% of physical memory (capped at 32G) is allocated. Memory allocation can also be set in Tools->Preferences->Startup or specified with command- line arguments --jvmmempc=90 (percentage of total physical memory, default 90) and --jvmmemmax=2g (set a different cap, default 32G if total physical memory can be detected or 8G if total physical memory cannot be detected).

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