Package Recipe 'perl-atlas-modules' — Bioconda documentation

recipe perl-atlas-modules

A package exporting in-house perl functions and classes used in the data production of EMBL-EBI Expression Atlas data.

Homepage:: ebi-gene-expression-group/perl-atlas-modules
License:: APACHE / Apache-2.0
Recipe:: /perl-atlas-modules/meta.yaml

package perl-atlas-modules#

Versions:

0.3.2-0, 0.3.1-5, 0.3.1-4, 0.3.1-3, 0.3.1-2, 0.3.1-0, 0.3.0-0, 0.2.0-0, 0.1.6-2,

0.3.2-0, 0.3.1-5, 0.3.1-4, 0.3.1-3, 0.3.1-2, 0.3.1-0, 0.3.0-0, 0.2.0-0, 0.1.6-2, 0.1.6-1, 0.1.6-0

Depends:

on __osx >=10.13
on libcxx >=19
on perl >=5.32.1,<5.33.0a0 *_perl5
on perl-algorithm-diff
on perl-archive-extract
on perl-archive-zip
on perl-array-compare
on perl-array-utils
on perl-base
on perl-capture-tiny
on perl-carp
on perl-carp-clan
on perl-class-accessor
on perl-class-std
on perl-clone 0.46.*
on perl-data-compare
on perl-data-dumper
on perl-date-manip >=6.99,<7.0a0
on perl-datetime >=1.66,<2.0a0
on perl-datetime-format-strptime >=1.80,<2.0a0
on perl-dbd-mysql >=5.13,<6.0a0
on perl-dbd-pg >=3.20.0,<4.0a0
on perl-dbi
on perl-devel-symdump
on perl-extutils-cbuilder
on perl-extutils-config 0.008.*
on perl-extutils-helpers 0.026.*
on perl-extutils-installpaths 0.012.*
on perl-file-spec
on perl-graphviz >=2.26,<3.0a0
on perl-io-scalar
on perl-io-stringy
on perl-ipc-cmd >=1.4,<1.5.0a0
on perl-ipc-run3 >=0.49,<0.50.0a0
on perl-json >=4.11,<5.0a0
on perl-json-parse >=0.62,<0.63.0a0
on perl-list-moreutils
on perl-log-log4perl
on perl-lwp-protocol-https >=6.15,<7.0a0
on perl-lwp-simple >=6.67,<7.0a0
on perl-mailtools >=2.22,<3.0a0
on perl-mime-lite
on perl-module-build 0.4234.*
on perl-module-build-tiny 0.039.*
on perl-module-pluggable
on perl-moose 2.2207.*
on perl-moosex-types >=0.51,<0.52.0a0
on perl-params-coerce
on perl-params-validate >=1.31,<2.0a0
on perl-parse-recdescent
on perl-path-tiny
on perl-readonly 2.05.*
on perl-scalar-list-utils
on perl-spiffy 0.46.*
on perl-sub-exporter-formethods
on perl-sub-uplevel
on perl-test-exception
on perl-test-inter >=1.12,<2.0a0
on perl-test-needs
on perl-test-nowarnings 1.06.*
on perl-test-pod
on perl-test-pod-coverage >=1.10,<2.0a0
on perl-test-warn
on perl-text-csv
on perl-text-csv_xs >=1.61,<2.0a0
on perl-text-diff
on perl-tie-ixhash
on perl-timedate >=2.35,<3.0a0
on perl-uri 5.34.*
on perl-xml-parser
on perl-xml-simple
on perl-xml-writer
on perl-yaml

Additional platforms:

linux-aarch64

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 perl-atlas-modules

to add into an existing workspace instead, run:

pixi add perl-atlas-modules

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 perl-atlas-modules

Alternatively, to install into a new environment, run:

conda create -n envname perl-atlas-modules

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/perl-atlas-modules:<tag>

(see perl-atlas-modules/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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/perl-atlas-modules/README.html)