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Biorepo containers: Difference between revisions
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# Containers with mature workflows, especially for the clinical studies, that are needed for long-term projects (3-5 years). These types of containers can provide reproducible workflows and tools commonly used in this type of research. | # Containers with mature workflows, especially for the clinical studies, that are needed for long-term projects (3-5 years). These types of containers can provide reproducible workflows and tools commonly used in this type of research. | ||
# Containers that require [[Anaconda/en|Conda]] and can not easily be ported to use [[Python#Creating_and_using_a_virtual_environment|pip]] and our [[Available_software|modules]]. This type of container can be used when the desired tools must be or are much more easily installed through Conda or a similar running environment. | # Containers that require [[Anaconda/en|Conda]] and can not easily be ported to use [[Python#Creating_and_using_a_virtual_environment|pip]] and our [[Available_software|modules]]. This type of container can be used when the desired tools must be or are much more easily installed through Conda or a similar running environment. | ||
# Containers with most of the tools, packages or libraries installed for a certain workflow, such as scRNA-seq. This type of container has the commonly used tools as well as the prerequisite libraries and system files which make it easier to update the version of the desired tools or install new ones. | # Containers with most of the tools, packages or libraries installed for a certain workflow, such as [https://en.wikipedia.org/wiki/Single-cell_sequencing scRNA-seq]. This type of container has the commonly used tools as well as the prerequisite libraries and system files which make it easier to update the version of the desired tools or install new ones. | ||
Additionally, all applications in a container must be open source and governed by a license that allows us to distribute the software in this manner. | Additionally, all applications in a container must be open source and governed by a license that allows us to distribute the software in this manner. | ||
Only the sandbox format of container images (i.e. an unpacked directory) should be published on CVMFS, not .sif files. | Only the sandbox format of container images (i.e. an unpacked directory) should be published on CVMFS, not .sif files. | ||