Package Recipe 'arb-bio'

recipe arb-bio

ARB 6 Sequence Analysis Suite

Homepage:: http://www.arb-home.de
Documentation:: http://www.arb-home.de/documentation.html
Developer docs:: http://bugs.arb-home.de/
License:: ARB
Recipe:: /arb-bio/meta.yaml
Links:: biotools: arb, doi: 10.1002/9781118010518.ch46

"ARB (ARBor, Latin: tree): A software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction.

The programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database.

The ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. The majority of operations can be controlled using the mouse for moving the pointer and the left mouse button for initiating and performing operations"

package arb-bio¶

Versions:

6.0.6-8, 6.0.6-7, 6.0.6-6, 6.0.6-5, 6.0.6-4, 6.0.6-3, 6.0.6-1, 6.0.6-0

Depends:

on arb-bio-tools 6.0.6 haa8b8d8_8
on fasttree
on fig2dev
on gettext >=0.19.8.1,<1.0a0
on glib >=2.58.2,<3.0a0
on gnuplot
on libgcc-ng >=7.3.0
on libpng >=1.6.35,<1.7.0a0
on libstdcxx-ng >=7.3.0
on libtiff >=4.0.9,<5.0a0
on libxslt >=1.1.32,<2.0a0
on mafft
on mrbayes
on muscle
on openmotif
on perl >=5.26.2,<5.26.3.0a0
on phylip
on phyml 3.2.0.*
on raxml
on sed >=4.4
on xerces-c >=3.2.2,<3.2.3.0a0
on xfig
on xorg-libxaw
on xorg-libxft
on xorg-libxi
on xorg-libxmu
on xorg-libxp
on xorg-libxpm
on xorg-libxt

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 arb-bio

to add into an existing workspace instead, run:

pixi add arb-bio

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 arb-bio

Alternatively, to install into a new environment, run:

conda create -n envname arb-bio

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/arb-bio:<tag>

(see arb-bio/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.

package arb-bio-devel¶

Versions:

6.0.6-8, 6.0.6-7, 6.0.6-6, 6.0.6-5, 6.0.6-4, 6.0.6-3

Depends:

on arb-bio 6.0.6 pl526h7ded70a_8
on libgcc-ng >=7.3.0
on libstdcxx-ng >=7.3.0
on openmotif-dev

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 arb-bio-devel

to add into an existing workspace instead, run:

pixi add arb-bio-devel

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 arb-bio-devel

Alternatively, to install into a new environment, run:

conda create -n envname arb-bio-devel

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/arb-bio-devel:<tag>

(see arb-bio-devel/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.

package arb-bio-tools¶

Versions:

6.0.6-8, 6.0.6-7, 6.0.6-6, 6.0.6-5, 6.0.6-4, 6.0.6-3

Depends:

on glib >=2.58.2,<3.0a0
on libarbdb 6.0.6 haa8b8d8_8
on libgcc-ng >=7.3.0
on libstdcxx-ng >=7.3.0

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 arb-bio-tools

to add into an existing workspace instead, run:

pixi add arb-bio-tools

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 arb-bio-tools

Alternatively, to install into a new environment, run:

conda create -n envname arb-bio-tools

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/arb-bio-tools:<tag>

(see arb-bio-tools/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.

package libarbdb¶

Versions:

6.0.6-8, 6.0.6-7, 6.0.6-6, 6.0.6-5, 6.0.6-4, 6.0.6-3

Depends:

on gettext
on glib >=2.58.2,<3.0a0
on libgcc-ng >=7.3.0
on libstdcxx-ng >=7.3.0

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 libarbdb

to add into an existing workspace instead, run:

pixi add libarbdb

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 libarbdb

Alternatively, to install into a new environment, run:

conda create -n envname libarbdb

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/libarbdb:<tag>

(see libarbdb/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.

Download stats¶

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/arb-bio/README.html)