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@@ -6,9 +6,9 @@ Large files are only retrieved on demand thanks to *git annex*, decorrelating na |
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Git ommix also stores a representation of the provenance of each of those entities using the PROV ontology. |
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Git ommix allows querying the repository structure, implementing multiple useful operations. These operations can apply to the whole patient's history or be constrained to one or multiple specific objects (sample/data/result/diagnosis) |
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- list the objects contributing to the target (the data contributing to a result or to a diagnosis, samples contributing to diagnosiss) |
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- list the objects contributing to the target (the data contributing to a result or to a diagnosis, samples contributing to diagnosis) |
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- get the most recent version of the target |
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- get the PROV-O prevenance of the target, as turtle triplets or as a visual graph |
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- get the PROV-O provenance of the target, as turtle triplets or as a visual graph |
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- display a timeline of diagnoses |
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- execute any sparQL query on a repo |
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@@ -18,9 +18,19 @@ Git ommix allows querying the repository structure, implementing multiple useful |
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GitOmmix is implemented as a bash script. |
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It relies mostly on *git*, but also uses: |
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- git annex (https://git-annex.branchable.com/) to handle large files |
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- rapper (https://librdf.org/raptor/rapper.html) to manage RDF stores |
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- graphviz (https://graphviz.org/) to generate visual representations |
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- git annex (https://git-annex.branchable.com/) to handle large files (10.20230926) |
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- rapper (https://librdf.org/raptor/rapper.html) to manage RDF stores (2.0.15) |
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- roqet (https://librdf.org/rasqal/roqet.html) to query RDF stores (0.9.33) |
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- graphviz (https://graphviz.org/) to generate visual representations (2.42.2) |
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- bash-completion (https://github.com/scop/bash-completion/) to benefit from autocompletions in bash (2.11) |
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Git ommix has been tested on ubuntu 22.04.3 LTS (Jammy). |
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Install *raptor2-utils* and *rasqal-utils* to get rapper and roqet. |
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Bash-completion should already be installed, and *graphviz* can also be found on the official repos. |
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However, the version of *git-annex* provided by ubuntu is too old (8) and version 10 should be installed. |
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The latest version can be obtained from this repo : http://neuro.debian.net/pkgs/git-annex-standalone.html |
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OSX users can find all the required dependencies on *homebrew*. |
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** Installation |
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