- recipe jalview
Jalview is a free program for multiple sequence alignment editing, visualisation, analysis and figure generation.
- Homepage:
- License:
GPL-3.0-only
- Recipe:
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¶
- Versions:
2.11.5.1-0,2.11.5.0-0,2.11.4.1-0,2.11.4.0-0,2.11.3.3-0,2.11.3.2-0,2.11.3.1-0,2.11.3.0-0,2.11.2.7-0,2.11.5.1-0,2.11.5.0-0,2.11.4.1-0,2.11.4.0-0,2.11.3.3-0,2.11.3.2-0,2.11.3.1-0,2.11.3.0-0,2.11.2.7-0,2.11.2.6-0,2.11.2.4-0,2.11.2.3-0,2.11.2.1-0,2.11.1.5-0,2.11.1.4-2,2.11.1.4-1,2.11.1.4-0,2.11.1.3-0,2.11.1.2-0,2.11.1.0-1,2.11.1.0-0,2.11.0-1,2.11.0-0,2.10.5-3,2.10.4-0,2.10.4b1-2,2.10.4b1-0,2.10.3-1,2.10.3-0,2.10.3b1-0,2.10.2b2-2,2.10.2b2-1,2.10.2b2-0- Depends:
on openjdk
>=8.0.192,!=9.*,!=10.*,!=11.0.9.*,<12on psutil
on xorg-libxtst
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install jalview
to add into an existing workspace instead, run:
pixi add jalview
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install jalview
Alternatively, to install into a new environment, run:
conda create -n envname jalview
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/jalview:<tag>
(see jalview/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
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).
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/jalview/README.html)
