├── .gitignore
├── CONTRIBUTING.md
├── LICENSE
├── README.md
├── container-specs.md
└── imgs
├── BioContainers.png
├── biocontainers-logo.png
├── container.png
├── edf3082e-84e4-11e6-95b5-ac8d2a0992b8.png
├── workflow.png
└── workflow.svg
/.gitignore:
--------------------------------------------------------------------------------
1 |
2 | # User-specific stuff:
3 | .idea*
4 | *.iml
5 | .idea/
6 |
--------------------------------------------------------------------------------
/CONTRIBUTING.md:
--------------------------------------------------------------------------------
1 | # Contributing
2 |
3 | This document briefly describes how to contribute to the [BioContainers project](https://github.com/BioContainers/specs).
4 |
5 | ## Before you Begin
6 |
7 | If you have an idea for a feature/container to add or an approach for a bugfix, it is best to communicate with BioContainers developers early. The most
8 | common venues for this are [GitHub issues](https://github.com/BioContainers/specs/issues) for common specification issues and the
9 | [Containers and Tools](https://github.com/BioContainers/containers/issues) for container/docker related issues.
10 | Browse through existing GitHub issues and if one seems related, comment on it. If no existing issue seems appropriate, a new issue can be
11 | opened using [this form](https://github.com/BioContainers/BioContainers/issues/new). BioContainers developers are also generally available via BioContainerss@gmail.com or
12 | [](https://gitter.im/biocontainers/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
13 |
14 | ## How to Contribute
15 |
16 | * All changes to the [specifications BioContainers project](https://github.com/BioContainers/bidocker)
17 | should be made through pull requests to this repository (with just two
18 | exceptions outlined below).
19 |
20 | * If you are new to Git, the [Try Git](http://try.github.com/) tutorial is a good places to start.
21 | More learning resources are listed at https://help.github.com/articles/good-resources-for-learning-git-and-github/ .
22 |
23 | * Make sure you have a free [GitHub](https://github.com/) account.
24 |
25 | * Fork the [container repository](https://github.com/BioContainers/containers) on
26 | GitHub to make your changes. (While many Containers instances track active development
27 | happens in the containers GitHub repository and this is where pull requests
28 | should be made).
29 |
30 | * Choose the correct branch to develop your changes against.
31 |
32 | * Additions of new features to the code base should be pushed to the `dev` branch (`git
33 | checkout dev`).
34 |
35 | * Most bug fixes to previously release components (things in bidocker-dist)
36 | should be made against the recent `release_XX.XX` branch (`git checkout release_XX.XX`).
37 |
38 | * Serious security problems should not be fixed via pull request - please
39 | responsibly disclose these by e-mailing them (with or without patches) to
40 | biodockers@gmail.com . The BioContainers core development team will solve
41 | those issues and we will provide you credit for the discovery when publicly
42 | disclosing the issue.
43 |
44 | * If your changes modify containers/images - please ensure the resulting files
45 | conform to BioContainers Specifications [BioContainers
46 | Specifications](http://biocontainers.pro/docs/developer-manual/biocotainers-dockerfile/).
47 |
48 | * Commit and push your changes to your
49 | [fork](https://help.github.com/articles/pushing-to-a-remote/).
50 |
51 | * Open a [pull
52 | request](https://help.github.com/articles/creating-a-pull-request/)
53 | with these changes. You pull request message ideally should include:
54 |
55 | * A description of why the changes should be made.
56 |
57 | * A description of the implementation of the changes.
58 |
59 | * A description of how to test the changes.
60 |
61 | * The pull request should pass all the continuous integration tests which are
62 | automatically run by GitHub using e.g. Travis CI.
63 |
64 | ## Ideas
65 |
66 | BioContainers's [BioContainers Specification and Design](http://github.com/BioContainers/BioContainers/issues) is filled with comments and ideas
67 | for enhancements and we believe would make the best entry points for new developers.
68 |
69 | ## A Quick Note about Containers
70 |
71 | For the most part, BioContainers containers should be published to the [BioContainers containers](https://github.com/BioContainers/BioContainers) and not in this repository directly.
72 | If you are looking to supply new containers first check if an existing container exists in this repository [BioContainers containers](https://github.com/BioContainers/BioContainers) -
73 | please checkout the repository on GitHub.
74 |
75 | ## Handling Pull Requests
76 |
77 | Everyone is encouraged to express opinions and issue non-binding votes on pull
78 | requests, but only members of the *contributors* group may issue binding votes
79 | on pull requests.
80 |
81 | Votes on pull requests should take the form of
82 | [+1, 0, -1, and fractions](http://www.apache.org/foundation/voting.html)
83 | as outlined by the Apache Foundation.
84 |
85 | Pull requests modifying pre-existing releases should be restricted to bug fixes
86 | and require at least 2 *+1* binding votes from someone other than the author of
87 | the pull request with no *-1* binding votes.
88 |
89 | Pull requests changing or clarifying the procedures governing this repository:
90 |
91 | - Must be made to the ``dev`` branch of this repository.
92 | - Must remain open for at least 192 hours (unless every qualified committer has
93 | voted).
94 | - Require binding *+1* votes from at least 25% of qualified *committers* with no
95 | *-1* binding votes.
96 | - Should be titled with the prefix *[PROCEDURES]* and tagged with
97 | the *procedures* tag in Github.
98 | - Should not be modified once open. If changes are needed, the pull request
99 | should be closed, re-opened with modifications, and votes reset.
100 | - Should be restricted to just modifying the procedures and generally should not
101 | contain code modifications.
102 | - If the pull request adds or removes committers, there must be a separate
103 | pull request for each person added or removed.
104 |
105 | Any other pull request requires at least 1 *+1* binding vote from someone other
106 | than the author of the pull request. A member of the committers group merging a
107 | pull request is considered an implicit +1.
108 |
109 | Pull requests marked *[WIP]* (i.e. work in progress) in the title by the
110 | author(s), or tagged WIP via GitHub tags, may *not* be merged without
111 | coordinating the removal of that tag with the pull request author(s), and
112 | completing the removal of that tag from wherever it is present in the open pull
113 | request.
114 |
115 | ### Timelines
116 |
117 | Except in the case of pull requests modifying governance procedures, there are
118 | generally no objective guidelines defining how long pull requests must remain
119 | open for comment. Subjectively speaking though - larger and more potentially
120 | controversial pull requests containing enhancements should remain open for a at
121 | least a few days to give everyone the opportunity to weigh in.
122 |
123 | ### Vetoes
124 |
125 | A note on vetoes (*-1* votes) taken verbatim from the
126 | [Apache Foundation](http://www.apache.org/foundation/voting.html):
127 |
128 | >"A code-modification proposal may be stopped dead in its tracks by a -1 vote
129 | by a qualified voter. This constitutes a veto, and it cannot be overruled nor
130 | overridden by anyone. Vetoes stand until and unless withdrawn by their casters.
131 | >
132 | >To prevent vetoes from being used capriciously, they must be accompanied by a
133 | technical justification showing why the change is bad (opens a security
134 | exposure, negatively affects performance, etc. ). A veto without a
135 | justification is invalid and has no weight."
136 |
137 | For votes regarding non-coding issues such as procedure changes, the requirement
138 | that a veto is accompanied by a *technical* justification is relaxed somewhat,
139 | though a well reasoned justification must still be included.
140 |
141 | ### Reversions
142 |
143 | A *-1* vote on any recently merged pull request requires an immediate
144 | reversion of the merged pull request. The backout of such a pull request
145 | invokes a mandatory, minimum 72 hour, review period.
146 |
147 | - Recently merged pull requests are defined as a being within the past 168 hours (7
148 | days), so as to not prevent forward progress, while allowing for reversions of
149 | things merged without proper review and consensus.
150 | - The person issuing the -1 vote will, upon commenting `-1` with technical
151 | justification per the vetoes section, immediately open a pull request to
152 | revert the original merge in question. If any committer other than the -1
153 | issuer deems the justification technical - regardless of whether they agree
154 | with justification - that committer must then merge the pull request to
155 | revert.
156 |
157 | ### Direct Commit Access
158 |
159 | The BioContainers *committers* group may only commit directly to BioContainers (i.e. outside
160 | of a pull request and not following the procedures described here) the
161 | following two categories of patches:
162 |
163 | * Patches for serious security vulnerabilities.
164 | * Cherry-picking and/or merging of existing approved commits to other
165 | branches.
166 |
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/README.md:
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1 |
2 |
3 |
4 |
5 | The latest information about BioContainers is available via [https://BioContainers.pro](https://Biocontainers.pro/)
6 |
7 |
8 | [](https://gitter.im/biocontainers/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
9 |
10 |
11 | Containers
12 | --------
13 | Repository of approved bioinformatics containers
14 |
15 | Links:
16 | -------
17 | Web Page : http://biocontainers.pro/
18 |
19 | Project Definition : https://github.com/BioContainers/specs
20 |
21 | Contribution Rules : https://github.com/BioContainers/specs/blob/master/CONTRIBUTING.md
22 |
23 | Containers : https://github.com/BioContainers/containers
24 |
25 | Email : biodockers@gmail.com
26 |
27 | License
28 | ----------
29 |
30 | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0)
31 |
32 | Contents
33 | ----------
34 |
35 | 1. [Essentials](#essentials)
36 | 1.1. [What is BioContainers](#11-what-is-biocontainers)
37 | 1.2. [Objectives](#12-objectives-and-goals)
38 | 2. [Containers](#2-containers)
39 | 2.1. [What is a container?](#21-what-is-a-container)
40 | 2.2. [Why do I need to use a container](#22-what-do-i-need-to-use-a-container)
41 | 2.3. [How to use a BioContainer](#23-how-to-use-a-biocontainer)
42 | 2.4. [BioContainers Architecture](#24-biocontainers-architecture)
43 | 2.4.1 [How to Request a Container](#241-how-to-request-a-container)
44 | 2.4.2 [Add a container](#242-add-a-container)
45 | 2.4.3 [Use a Container](#243-use-a-bioContainer.)
46 | 3. [Developing containers](#3-developing-containers)
47 | 3.1. [How to build BioContainers](#31-how-to-build-biocontainers)
48 | 3.2. [What do I need to develop?](#32-what-do-i-need-to-develop)
49 | 3.3. [How to create a Docker based BioContainer?](#33-how-to-create-a-docker-based-biocontainer)
50 | 4. [Support](#4-support)
51 | 4.1 [Get involved](#41-get-involved)
52 |
53 | ## 1. Essentials
54 | ------------------
55 |
56 | ### 1.1. What is BioContainers?
57 |
58 | The BioContainers project came from the idea of using the containers-based technologies such as [Docker](https://www.docker.com) or [rkt](https://github.com/coreos/rkt) for bioinformatics software. Having a common and controllable environment for running software could help to deal with some of the current problems during software development and distribution. BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics fields such as proteomics, genomics, transcriptomics and metabolomics. The main containers already implemented in BioContainers (https://github.com/BioContainers/containers) are discussed in details including examples on how to use BioContainers.
59 | The currently available BioContainers containers facilitate the usage, and reproducibility of software and algorithms. They can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, Cloud environments or HPC clusters). We also present the guidelines and specifications on how to create new containers, and how to contribute to the BioContainers project.
60 |
61 | ### 1.2. Objectives and Goals
62 |
63 | * Provide a base specification and images to easily build and deploy new bioinformatics/proteomics software
64 | including the source and examples.
65 |
66 | * Provide a series of containers ready to be used by the bioinformatics community (https://github.com/BioContainers/containers).
67 |
68 | * Define a set of guidelines and specifications to build a standardized container that can be
69 | used in combination with other containers and bioinformatics tools.
70 |
71 | * Define a complete infrastructure to develop, deploy and test new bioinformatics containers
72 | using continuous integration suites such as Travis Continuous Integration (https://travisci.
73 | org/), Shippable (https://app.shippable.com/) or manually built solutions.
74 |
75 | * Provide support and help to the bioinformatics community to deploy new containers for researchers that do not have bioinformatics support.
76 |
77 | * Provide guidelines and help on how to create reproducible pipelines by defining, reusing
78 | and reporting specific container versions which will consistently produce the exact same
79 | result and always be available in the history of the container.
80 |
81 | * Coordinate and integrate developers and bioinformaticians to produce best practice of
82 | documentation and software development.
83 |
84 | ## 2. Containers
85 | -------------
86 |
87 | ### 2.1. What is a container?
88 |
89 | Containers are build from existing operating systems. They are different from Virtual machines because they don't possess an entire guest OS inside, instead, containers are built using optimized system libraries and use the host OS memory management and process controls. Containers normally are centralized around a specific software and you can make them executable by instantiating images from them.
90 |
91 | 
92 |
93 | ### 2.2. What do I need to use a container?
94 |
95 | Most of the time when a bioinformatics analysis is performed, several bioinformatics tools and software should be installed and configured. This process can take several hours and demands a lot of efforts including the installation of multiple dependencies and tools. BioContainers provides ready to use packages and tools that can be easily deployed and used in local machines, HPC and cloud architectures.
96 |
97 | ### 2.3. How to use a BioContainer
98 |
99 | BioContainers are listed in two main registries:
100 |
101 | * [Docker Hub](https://hub.docker.com/u/biocontainers/): Docker based containers that can be used using the docker infrastructure.
102 | * [QUAY Hub](https://quay.io/organization/biocontainers): Docker and rkt based containers that can be used using the rkt infrastructure.
103 |
104 | A full documentation about how to use BioContainers to perform bioinformatics analysis: please check the [Full Documentation](http://BioDocker.org/docs)
105 |
106 | ### 2.4. BioContainers Architecture
107 |
108 | BioContainers is a community-driven project that allows bioinformatics to request, build and deploy bioinformatics tools using containers. The following figure present the general BioContainers workflow:
109 |
110 | 
111 |
112 | The next sections explain in details the presented workflow:
113 |
114 | * (i) How to request a workflow
115 | * (ii) Use a BioContainer
116 | * (iii) Developing containers
117 |
118 |
119 | #### 2.4.1 How to Request a Container
120 |
121 | Users can request a container by opening an issue in the [containers
122 | repository] (http://github.com/BioContainers/containers/issues) `(In the previous workflow this is the first step performed by user henrik)`. The issue should contain the name of the software, the url of the code or binary to be package and information about the software [see BioContainers specification](https://github.com/BioContainers/specs/blob/master/container-specs.md). When the container is deployed and fully functional, the issue will be closed by the developer or the contributor to BioContainers.
123 |
124 | #### 2.4.2 Add a container
125 |
126 | Fork the repository and add a container. To add a container:
127 |
128 | * create directory name_of_software/version_of_upstream_software
129 | * in directory add a Dockerfile [following BioContainers specification](https://github.com/BioContainers/specs/blob/master/container-specs.md)
130 | * optionally (but recommended) add a test-cmds.txt file to test automatically the container (list of one-line bash commands
131 |
132 | Example test-cmds.txt
133 |
134 | mytool -v
135 | mytool -h
136 |
137 | Test the container recipe where your Dockerfile is:
138 |
139 | docker build .
140 |
141 | If ok, commit and push your changes to your fork and ask for a pull request to our repository.
142 |
143 | #### 2.4.3 Use a BioContainer
144 |
145 | When a container is deployed and the developer closes the issue in GitHub, the user `(henrik)` receives a notification that the container is ready.
146 | The user can then use [docker](http://www.docker.com) or [rkt](https://coreos.com/rkt/docs/latest/) to pull or fetch the corresponding container.
147 |
148 |
149 | ## 3. Developing containers
150 | -----------------------
151 |
152 | ### 3.1. How to build BioContainers
153 |
154 | There are two different ways to build a container.
155 |
156 | * Go to the GitHub repository with the recipe of the software you want, clone it, and build it yourself on your machine.
157 | * Use the docker daemon to search for a ready-to-use version of the containerized software you want.
158 |
159 | Inside the central repository there is a list of softwares with docker recipes, there you can find more information about how to work with them.
160 |
161 | ### 3.2. What do I need to develop?
162 |
163 | BioContainers are based on Linux systems, so you will need a computer with Linux installed, you also will need the `docker` or `rkt` daemon and the software you want to containerize.
164 |
165 | ### 3.3. How to create a Docker based Biocontainer?
166 |
167 | Having all in hands now you need to create a Dockerfile. Dockerfiles are simple recipes to instruct the daemon on how to set an appropriate OS and how to download, manage, install and give access to the software inside.
168 |
169 | You can check the [Docker](https://docs.docker.com/reference/builder/) documentation for more information.
170 |
171 | Once the container is ready you can get in touch with us so we can make the appropriate arrangements to make your container available to everyone in the community by giving an automated build system.
172 |
173 | ### 3.3. How to create a rkt based Biocontainer?
174 |
175 | Having all in hands now you need to create a rkt. rkt containers are simple recipes to instruct the daemon on how to set an appropriate OS and how to download, manage, install and give access to the software inside.
176 |
177 | You can check the [rkt](https://github.com/coreos/rkt/blob/master/Documentation/getting-started-guide.md) documentation for more information.
178 |
179 | Once the container is ready you can get in touch with us so we can make the appropriate arrangements to make your container available to everyone in the community by giving an automated build system.
180 |
181 |
182 | ## 4. Support
183 | ----------
184 |
185 | ### 4.1. Get involved
186 |
187 | Whether you want to make your own software available to others as a container, to just use them on your pipelines and analysis or just give opinions, you are most welcome. This is a community-driven project, that means everyone has a voice.
188 |
189 | Here are some general ideas:
190 |
191 | * Browse our list of containers
192 | * Propose your own ideas or software
193 | * Interact with other if you think there is something missing.
194 |
195 |
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/container-specs.md:
--------------------------------------------------------------------------------
1 | Container Specifications
2 | ========================
3 |
4 | Each container should provide a well-defined metadata header that allows the final users to test, deploy and get support around the container.
5 | We explain here the containers metadata, their meaning and use in BioContainers:
6 |
7 |
8 |
9 | | Field | Description | Optional | Example |
10 | |----------------|------------ |------------------------------------------------------|-----------|
11 | | LABEL base_image | The original image where the software has been built | **Mandatory** | base_image=" biodckr/biodocker" |
12 | | LABEL version | Version of the tool's Dockerfile | **Mandatory** | version="2" |
13 | | LABEL software.version | Version of the software or tool | **Mandatory** | software.version="2015020" |
14 | | LABEL software | Name of the software or tool | **Mandatory** | software="Comet" |
15 | | LABEL about.summary | A short description of the software or tool. | **Mandatory** | about.summary="Peptide" identification|
16 | | LABEL about.home | The original software website. | **Mandatory** | about.home="http://comet-ms.sourceforge.net/" |
17 | | LABEL about.documentation | URL(s) containing information about software | _Optional_ | about.documentation="http://comet-ms.sourceforge.net/" |
18 | | LABEL about.license | SPDX license specification. If not in the SPDX list, specify URL in license_file> | **Mandatory** | about.license="SPDX:Apache-2.0" |
19 | | LABEL about.license_file | License path location in the container or url (according to license requirements) | _Optional_ | |
20 | | LABEL about.tags | Tags about the software that enable to find and classify the software tool.| _Optional_ | about.tags="proteomics, mass spectrometry, biocontainers" |
21 | | LABEL maintainer | The developer in charge of the container/software | **Mandatory** | maintainer="Yasset Perez-Riverol " |
22 | | LABEL extra.identifiers | Extra identifiers are external identifiers in other resources that will allow to pull metadata, an external information from other resources (e.g biotools). In order to be compatible with Docker specification the domain (database) of the identifiers should be specified in the name of the label. | _Optional_ | extra.identifiers.biotools=abyss |
23 |
24 |
25 | ### Dockerfile example (Single lines LABEL):
26 |
27 | ```Dockerfile
28 | # Base Image
29 | FROM biocontainers/biocontainers:latest
30 |
31 | # Metadata
32 | LABEL base_image="biocontainers:latest"
33 | LABEL version="3"
34 | LABEL software="Comet"
35 | LABEL software.version="2016012"
36 | LABEL about.summary="an open source tandem mass spectrometry sequence database search tool"
37 | LABEL about.home="http://comet-ms.sourceforge.net/"
38 | LABEL about.documentation="http://comet-ms.sourceforge.net/parameters/parameters_2016010/"
39 | LABEL about.license="SPDX:Apache-2.0"
40 | LABEL about.license_file="/usr/share/common-licenses/Apache-2.0"
41 | LABEL about.tags="Proteomics"
42 | LABEL extra.identifiers.biotools=comet
43 | LABEL maintainer="Felipe da Veiga Leprevost "
44 |
45 | USER biodocker
46 |
47 | RUN ZIP=comet_binaries_2016012.zip && \
48 | wget https://github.com/BioDocker/software-archive/releases/download/Comet/$ZIP -O /tmp/$ZIP && \
49 | unzip /tmp/$ZIP -d /home/biodocker/bin/Comet/ && \
50 | chmod -R 755 /home/biodocker/bin/Comet/* && \
51 | rm /tmp/$ZIP
52 |
53 | RUN mv /home/biodocker/bin/Comet/comet_binaries_2016012/comet.2016012.linux.exe /home/biodocker/bin/Comet/comet
54 |
55 | ENV PATH /home/biodocker/bin/Comet:$PATH
56 |
57 | WORKDIR /data/
58 |
59 | ```
60 |
61 |
62 | ### Dockerfile example (Multiple lines LABEL):
63 |
64 | ```Dockerfile
65 |
66 | # Base Image
67 | FROM biocontainers/biocontainers:latest
68 |
69 | # Metadata
70 | LABEL base_image="biocontainers:latest" \
71 | version="3" \
72 | software="Comet" \
73 | software.version="2016012" \
74 | about.summary="an open source tandem mass spectrometry sequence database search tool" \
75 | about.home="http://comet-ms.sourceforge.net/" \
76 | about.documentation="http://comet-ms.sourceforge.net/parameters/parameters_2016010/" \
77 | about.license="SPDX:Apache-2.0" \
78 | about.license_file="/usr/share/common-licenses/Apache-2.0" \
79 | about.tags="Proteomics" \
80 | extra.identifiers.biotools=comet
81 |
82 | # Maintainer
83 | LABEL maintainer="Felipe da Veiga Leprevost "
84 |
85 | USER biodocker
86 |
87 | RUN ZIP=comet_binaries_2016012.zip && \
88 | wget https://github.com/BioDocker/software-archive/releases/download/Comet/$ZIP -O /tmp/$ZIP && \
89 | unzip /tmp/$ZIP -d /home/biodocker/bin/Comet/ && \
90 | chmod -R 755 /home/biodocker/bin/Comet/* && \
91 | rm /tmp/$ZIP
92 |
93 | RUN mv /home/biodocker/bin/Comet/comet_binaries_2016012/comet.2016012.linux.exe /home/biodocker/bin/Comet/comet
94 |
95 | ENV PATH /home/biodocker/bin/Comet:$PATH
96 |
97 | WORKDIR /data/
98 |
99 | ```
100 |
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1 |
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3 |
4 |
5 | The latest information about BioContainers is available via [https://BioContainers.pro](https://Biocontainers.pro/)
6 |
7 |
8 | [](https://gitter.im/biocontainers/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
9 |
10 |
11 | Containers
12 | --------
13 | Repository of approved bioinformatics containers
14 |
15 | Links:
16 | -------
17 | Web Page : http://biocontainers.pro/
18 |
19 | Project Definition : https://github.com/BioContainers/specs
20 |
21 | Contribution Rules : https://github.com/BioContainers/specs/blob/master/CONTRIBUTING.md
22 |
23 | Containers : https://github.com/BioContainers/containers
24 |
25 | Email : biodockers@gmail.com
26 |
27 | License
28 | ----------
29 |
30 | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0)
31 |
32 | Contents
33 | ----------
34 |
35 | 1. [Essentials](#essentials)
36 | 1.1. [What is BioContainers](#11-what-is-biocontainers)
37 | 1.2. [Objectives](#12-objectives-and-goals)
38 | 2. [Containers](#2-containers)
39 | 2.1. [What is a container?](#21-what-is-a-container)
40 | 2.2. [Why do I need to use a container](#22-what-do-i-need-to-use-a-container)
41 | 2.3. [How to use a BioContainer](#23-how-to-use-a-biocontainer)
42 | 2.4. [BioContainers Architecture](#24-biocontainers-architecture)
43 | 2.4.1 [How to Request a Container](#241-how-to-request-a-container)
44 | 2.4.2 [Add a container](#242-add-a-container)
45 | 2.4.3 [Use a Container](#243-use-a-bioContainer.)
46 | 3. [Developing containers](#3-developing-containers)
47 | 3.1. [How to build BioContainers](#31-how-to-build-biocontainers)
48 | 3.2. [What do I need to develop?](#32-what-do-i-need-to-develop)
49 | 3.3. [How to create a Docker based BioContainer?](#33-how-to-create-a-docker-based-biocontainer)
50 | 4. [Support](#4-support)
51 | 4.1 [Get involved](#41-get-involved)
52 |
53 | ## 1. Essentials
54 | ------------------
55 |
56 | ### 1.1. What is BioContainers?
57 |
58 | The BioContainers project came from the idea of using the containers-based technologies such as [Docker](https://www.docker.com) or [rkt](https://github.com/coreos/rkt) for bioinformatics software. Having a common and controllable environment for running software could help to deal with some of the current problems during software development and distribution. BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics fields such as proteomics, genomics, transcriptomics and metabolomics. The main containers already implemented in BioContainers (https://github.com/BioContainers/containers) are discussed in details including examples on how to use BioContainers.
59 | The currently available BioContainers containers facilitate the usage, and reproducibility of software and algorithms. They can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, Cloud environments or HPC clusters). We also present the guidelines and specifications on how to create new containers, and how to contribute to the BioContainers project.
60 |
61 | ### 1.2. Objectives and Goals
62 |
63 | * Provide a base specification and images to easily build and deploy new bioinformatics/proteomics software
64 | including the source and examples.
65 |
66 | * Provide a series of containers ready to be used by the bioinformatics community (https://github.com/BioContainers/containers).
67 |
68 | * Define a set of guidelines and specifications to build a standardized container that can be
69 | used in combination with other containers and bioinformatics tools.
70 |
71 | * Define a complete infrastructure to develop, deploy and test new bioinformatics containers
72 | using continuous integration suites such as Travis Continuous Integration (https://travisci.
73 | org/), Shippable (https://app.shippable.com/) or manually built solutions.
74 |
75 | * Provide support and help to the bioinformatics community to deploy new containers for researchers that do not have bioinformatics support.
76 |
77 | * Provide guidelines and help on how to create reproducible pipelines by defining, reusing
78 | and reporting specific container versions which will consistently produce the exact same
79 | result and always be available in the history of the container.
80 |
81 | * Coordinate and integrate developers and bioinformaticians to produce best practice of
82 | documentation and software development.
83 |
84 | ## 2. Containers
85 | -------------
86 |
87 | ### 2.1. What is a container?
88 |
89 | Containers are build from existing operating systems. They are different from Virtual machines because they don't possess an entire guest OS inside, instead, containers are built using optimized system libraries and use the host OS memory management and process controls. Containers normally are centralized around a specific software and you can make them executable by instantiating images from them.
90 |
91 | 
92 |
93 | ### 2.2. What do I need to use a container?
94 |
95 | Most of the time when a bioinformatics analysis is performed, several bioinformatics tools and software should be installed and configured. This process can take several hours and demands a lot of efforts including the installation of multiple dependencies and tools. BioContainers provides ready to use packages and tools that can be easily deployed and used in local machines, HPC and cloud architectures.
96 |
97 | ### 2.3. How to use a BioContainer
98 |
99 | BioContainers are listed in two main registries:
100 |
101 | * [Docker Hub](https://hub.docker.com/u/biocontainers/): Docker based containers that can be used using the docker infrastructure.
102 | * [QUAY Hub](https://quay.io/organization/biocontainers): Docker and rkt based containers that can be used using the rkt infrastructure.
103 |
104 | A full documentation about how to use BioContainers to perform bioinformatics analysis: please check the [Full Documentation](http://BioDocker.org/docs)
105 |
106 | ### 2.4. BioContainers Architecture
107 |
108 | BioContainers is a community-driven project that allows bioinformatics to request, build and deploy bioinformatics tools using containers. The following figure present the general BioContainers workflow:
109 |
110 | 
111 |
112 | The next sections explain in details the presented workflow:
113 |
114 | * (i) How to request a workflow
115 | * (ii) Use a BioContainer
116 | * (iii) Developing containers
117 |
118 |
119 | #### 2.4.1 How to Request a Container
120 |
121 | Users can request a container by opening an issue in the [containers
122 | repository] (http://github.com/BioContainers/containers/issues) `(In the previous workflow this is the first step performed by user henrik)`. The issue should contain the name of the software, the url of the code or binary to be package and information about the software [see BioContainers specification](https://github.com/BioContainers/specs/blob/master/container-specs.md). When the container is deployed and fully functional, the issue will be closed by the developer or the contributor to BioContainers.
123 |
124 | #### 2.4.2 Add a container
125 |
126 | Fork the repository and add a container. To add a container:
127 |
128 | * create directory name_of_software/version_of_upstream_software
129 | * in directory add a Dockerfile [following BioContainers specification](https://github.com/BioContainers/specs/blob/master/container-specs.md)
130 | * optionally (but recommended) add a test-cmds.txt file to test automatically the container (list of one-line bash commands
131 |
132 | Example test-cmds.txt
133 |
134 | mytool -v
135 | mytool -h
136 |
137 | Test the container recipe where your Dockerfile is:
138 |
139 | docker build .
140 |
141 | If ok, commit and push your changes to your fork and ask for a pull request to our repository.
142 |
143 | #### 2.4.3 Use a BioContainer
144 |
145 | When a container is deployed and the developer closes the issue in GitHub, the user `(henrik)` receives a notification that the container is ready.
146 | The user can then use [docker](http://www.docker.com) or [rkt](https://coreos.com/rkt/docs/latest/) to pull or fetch the corresponding container.
147 |
148 |
149 | ## 3. Developing containers
150 | -----------------------
151 |
152 | ### 3.1. How to build BioContainers
153 |
154 | There are two different ways to build a container.
155 |
156 | * Go to the GitHub repository with the recipe of the software you want, clone it, and build it yourself on your machine.
157 | * Use the docker daemon to search for a ready-to-use version of the containerized software you want.
158 |
159 | Inside the central repository there is a list of softwares with docker recipes, there you can find more information about how to work with them.
160 |
161 | ### 3.2. What do I need to develop?
162 |
163 | BioContainers are based on Linux systems, so you will need a computer with Linux installed, you also will need the `docker` or `rkt` daemon and the software you want to containerize.
164 |
165 | ### 3.3. How to create a Docker based Biocontainer?
166 |
167 | Having all in hands now you need to create a Dockerfile. Dockerfiles are simple recipes to instruct the daemon on how to set an appropriate OS and how to download, manage, install and give access to the software inside.
168 |
169 | You can check the [Docker](https://docs.docker.com/reference/builder/) documentation for more information.
170 |
171 | Once the container is ready you can get in touch with us so we can make the appropriate arrangements to make your container available to everyone in the community by giving an automated build system.
172 |
173 | ### 3.3. How to create a rkt based Biocontainer?
174 |
175 | Having all in hands now you need to create a rkt. rkt containers are simple recipes to instruct the daemon on how to set an appropriate OS and how to download, manage, install and give access to the software inside.
176 |
177 | You can check the [rkt](https://github.com/coreos/rkt/blob/master/Documentation/getting-started-guide.md) documentation for more information.
178 |
179 | Once the container is ready you can get in touch with us so we can make the appropriate arrangements to make your container available to everyone in the community by giving an automated build system.
180 |
181 |
182 | ## 4. Support
183 | ----------
184 |
185 | ### 4.1. Get involved
186 |
187 | Whether you want to make your own software available to others as a container, to just use them on your pipelines and analysis or just give opinions, you are most welcome. This is a community-driven project, that means everyone has a voice.
188 |
189 | Here are some general ideas:
190 |
191 | * Browse our list of containers
192 | * Propose your own ideas or software
193 | * Interact with other if you think there is something missing.
194 |
195 |
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/container-specs.md:
--------------------------------------------------------------------------------
1 | Container Specifications
2 | ========================
3 |
4 | Each container should provide a well-defined metadata header that allows the final users to test, deploy and get support around the container.
5 | We explain here the containers metadata, their meaning and use in BioContainers:
6 |
7 |
8 |
9 | | Field | Description | Optional | Example |
10 | |----------------|------------ |------------------------------------------------------|-----------|
11 | | LABEL base_image | The original image where the software has been built | **Mandatory** | base_image=" biodckr/biodocker" |
12 | | LABEL version | Version of the tool's Dockerfile | **Mandatory** | version="2" |
13 | | LABEL software.version | Version of the software or tool | **Mandatory** | software.version="2015020" |
14 | | LABEL software | Name of the software or tool | **Mandatory** | software="Comet" |
15 | | LABEL about.summary | A short description of the software or tool. | **Mandatory** | about.summary="Peptide" identification|
16 | | LABEL about.home | The original software website. | **Mandatory** | about.home="http://comet-ms.sourceforge.net/" |
17 | | LABEL about.documentation | URL(s) containing information about software | _Optional_ | about.documentation="http://comet-ms.sourceforge.net/" |
18 | | LABEL about.license | SPDX license specification. If not in the SPDX list, specify URL in license_file> | **Mandatory** | about.license="SPDX:Apache-2.0" |
19 | | LABEL about.license_file | License path location in the container or url (according to license requirements) | _Optional_ | |
20 | | LABEL about.tags | Tags about the software that enable to find and classify the software tool.| _Optional_ | about.tags="proteomics, mass spectrometry, biocontainers" |
21 | | LABEL maintainer | The developer in charge of the container/software | **Mandatory** | maintainer="Yasset Perez-Riverol