mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-29 17:42:12 +08:00
63 lines
2.5 KiB
Plaintext
63 lines
2.5 KiB
Plaintext
# This is an example mapping file for the module (http://modules.sourceforge.net/) Dependency resolver (in YAML format)
|
|
#
|
|
# The goal of this file is to map tool's requirements to existing modules available on your system
|
|
# Of course, if the name of a requirement and the name of a module match perfectly, there is no need to map them together through this mapping file.
|
|
#
|
|
# This is a sample file so the first thing to do to activate the mapping system is to create a copy of this file called "environment_modules_mapping.yml".
|
|
# The module dependency resolver is programmed to search and use this YAML file automatically if it exists in the "config" folder of your Galaxy instance.
|
|
# Alternatively, you can also use the "mapping_files" attribute of the <modules /> resolver in the dependency_resolvers_conf.xml file to specify a custom mapping file
|
|
#
|
|
# Example 1:
|
|
#
|
|
# Let's say that one of the wrapper installed on your Galaxy instance has the following requirement:
|
|
#
|
|
# <requirements>
|
|
# <requirement type="package" version="1.5.0">PIPITS</requirement>
|
|
# </requirements>
|
|
#
|
|
# But unfortunately, the name of the corresponding module file on your system is "pipits_pipeline/1.5.0"
|
|
#
|
|
# Then, to make Galaxy load/unload the appropriate module, you just have to add the following lines (without the #) to the "environment_modules_mapping.yml" file:
|
|
#
|
|
#- from:
|
|
# name: PIPITS
|
|
# version: 1.5.0
|
|
# to:
|
|
# name: pipits_pipeline
|
|
# version: 1.5.0.6
|
|
#
|
|
#
|
|
# Example 2:
|
|
#
|
|
# The requirements section specify a requirement on the PIPITS tool but do not ask for a specific version of it:
|
|
#
|
|
# <requirements>
|
|
# <requirement type="package">PIPITS</requirement>
|
|
# </requirements>
|
|
#
|
|
# Although, there is no version required you may want to force the loading of a version that is known to run well on your system.
|
|
#
|
|
# In that case you can add the following lines to the "environment_modules_mapping.yml" file:
|
|
#
|
|
#- from:
|
|
# name: PIPITS
|
|
# unversioned: true
|
|
# to:
|
|
# name: pipits_pipeline
|
|
# version: 1.4.0
|
|
#
|
|
#
|
|
# ## WARNING ##
|
|
#
|
|
# YAML is a typed language, and types are inferred. Thus, the unquoted version 1.10 (for example) will be read by the YAML parser as the floating
|
|
# point number 1.1, which will not match module version 1.10 on your system. To avoid type inference, such values should be quoted with single (')
|
|
# or double (") quotes like so:
|
|
#
|
|
#- from:
|
|
# name: bcftools
|
|
# version: "1.10"
|
|
# to:
|
|
# name: biotools/bcftools
|
|
#
|
|
# Values that cannot be inferred as numbers (such as 1.4.0) do not need to be quoted, but can be, if you prefer.
|