summaryrefslogtreecommitdiff
path: root/topics
AgeCommit message (Collapse)Author
2022-08-22Use ${HOME} for documentation.Frederick Muriuki Muriithi
2022-08-19Documentation: Setup small databaseFrederick Muriuki Muriithi
2022-08-19Documentation: Setup new user, and their default database.Frederick Muriuki Muriithi
2022-08-19Documentation: Setting up local mariadb server for development.Frederick Muriuki Muriithi
2022-08-17Use pre-formatted text blocks for source codeFrederick Muriuki Muriithi
2022-08-17Topic: Queries (On preventing SQL Injection).Frederick Muriuki Muriithi
2022-08-17Installing GN2 on a new machinePjotr Prins
2022-07-19Rescue quality control issues from topics.Arun Isaac
2022-07-19Rescue testing issue from topics.Arun Isaac
2022-07-18Add 'Annotations' sectionFrederick Muriuki Muriithi
2022-07-18Add section on Platforms, Groups, Studies and Datasets.Frederick Muriuki Muriithi
2022-07-06Document how to update penguin2 mariadb to the production database.Arun Isaac
* topics/systems/mariadb/mariadb.gmi (Update MariaDB on penguin2 to the latest production database): New section.
2022-07-05Describe how to extract TS data from a provided datasetBonfaceKilz
* topics/data-uploads/datasets.gmi: New file.
2022-07-01Rescue issues lost in the topics/systems/mariadb directory.Arun Isaac
2022-07-01Move issues lost inside the topics directory.Arun Isaac
2022-06-24virtuoso: Document first time upload failure with large files.Arun Isaac
* topics/systems/virtuoso.gmi (Loading data into virtuoso): Document first time upload failure with large files.
2022-06-22genotype-database: Fold long code lines.Arun Isaac
* topics/genotype-database.gmi (Database Layout): Fold long code lines.
2022-06-22genotype-database: Use '*' as list bullets.Arun Isaac
* topics/genotype-database.gmi [Database layout]: Use '*' as list bullets instead of '-'.
2022-06-21genotype-database: Document design and database layout.Arun Isaac
* topics/genotype-database.gmi (Database layout): New section.
2022-06-21genotype-database: Document reading the entire matrix.Arun Isaac
* topics/genotype-database.gmi: Document reading the entire matrix using the genodb.nparray function.
2022-06-15virtuoso: Document hack to get PID of container shepherd.Arun Isaac
* topics/systems/virtuoso.gmi (Running virtuoso)[Running virtuoso in a guix system container]: Document hack to get PID of container shepherd.
2022-06-15virtuoso: Use /run/current-system/... path to bash in container.Arun Isaac
* topics/systems/virtuoso.gmi (Running virtuoso)[Running virtuoso in a guix system container]: Use /run/current-system/... path to bash in container.
2022-06-15virtuoso: Enter all namespaces with `nsenter -a'.Arun Isaac
* topics/systems/virtuoso.gmi (Running virtuoso)[Running virtuoso in a guix system container]: Enter all namespaces with `nsenter -a'.
2022-06-14topics: virtuoso: Fix wrong grammarBonfaceKilz
2022-06-14topics: virtuoso: Note that conductor interface isn't supportedBonfaceKilz
2022-06-14topics: virtuoso: Note that "/dev/sdX" is non-consequentialBonfaceKilz
2022-06-14topics: virtuoso: Add extra docs on how to run sparql using web UIBonfaceKilz
* topics/systems/virtuoso.gmi (Running SPARQL Queries using isql): Add more detailed section of how to access SPARQL using both the web interface and sqli.
2022-06-14topics: virtuoso: Document how to inspect a system-containerBonfaceKilz
* topics/systems/virtuoso.gmi (Running virtuoso in a guix system container): Demonstrate, using `nsenter`, how one would inspect a system container.
2022-06-14topics: virtuoso: Document how to run sparql queries using isqlBonfaceKilz
* topics/systems/virtuoso.gmi (Running Queries using isql): Document how to use isql to run sparql queries using a guix shell.
2022-06-14virtuoso: Remove unnecessary root file system definition.Arun Isaac
* topics/systems/virtuoso.gmi (Running virtuoso): Remove unnecessary root file system definition.
2022-06-14guix-profiles: Use public path to guix-bioinformatics channel.Arun Isaac
An "Arun-specific path" was accidentally added in an earlier commit.
2022-06-14topics: Explain use of Guix profiles for development.Arun Isaac
* topics/guix-profiles.gmi: New file.
2022-06-09topics: genotype-database: Use new functional interface.Arun Isaac
* topics/genotype-database.gmi: Use new functional interface.
2022-06-08topics: genotype-database: Document reading columns.Arun Isaac
* topics/genotype-database.gmi: Document reading columns in Python.
2022-06-07topics: virtuoso: Fix misspelling of "Protocol".Arun Isaac
* topics/systems/virtuoso.gmi (Loading data into virtuoso): Fix misspelling of "Protocol" changing "Protocal" to "Protocol".
2022-06-03topics: Document genotype databases.Arun Isaac
* topics/genotype-database.gmi: New file.
2022-05-26Move post on debugging with pudb into it's TopicsBonfaceKilz
2022-05-16New Issue: Remove extra pcorrs optionsFrederick Muriuki Muriithi
2022-05-06Added link; minor text editsPjotr Prins
2022-05-06List developer links.Arun Isaac
* topics/links.gmi: New file. * index.skb: Link to it.
2022-05-05topics: Move virtuoso passwords documentation.Arun Isaac
* topics/systems/virtuoso.gmi (Virtuoso users and setting their passwords): Rename to ... (Set passwords for virtuoso users): ... this, and move to after "Running virtuoso".
2022-05-05topics: Simplify virtuoso introduction.Arun Isaac
* topics/systems/virtuoso.gmi: Simplify introduction.
2022-05-05topics: Document minimal virtuoso configuration.Arun Isaac
* topics/systems/virtuoso.gmi (Running virtuoso): Document manually running virtuoso on the command-line with a minimal configuration. (Virtuoso.ini): Delete section.
2022-05-05topics: Document RDF validation, virtuoso graph loading and deletion.Arun Isaac
* topics/systems/virtuoso.gmi (Loading data into virtuoso): Document RDF validation, virtuoso graph loading and deletion.
2022-04-29topics: Fix graph name in virtuoso upload.Arun Isaac
* topics/systems/virtuoso.gmi (SPARQL 1.1 Graph Store HTTP Protocol): Fix graph name.
2022-04-29topics: Document loading data into virtuoso.Arun Isaac
* topics/systems/virtuoso.gmi (Loading data into virtuoso): Organize into new section.
2022-04-29topics: Group running virtuoso into section.Arun Isaac
* topics/systems/virtuoso.gmi (Running virtuoso): Group running virtuoso into section.
2022-04-29topics: Remove blank lines in virtuoso topic.Arun Isaac
* topics/systems/virtuoso.gmi: Remove unnecessary blank lines.
2022-04-29topics: Switch to guix shell in virtuoso topic.Arun Isaac
* topics/systems/virtuoso.gmi: Switch from guix environment to guix shell.
2022-04-29topics: Document virtuoso user configuration.Arun Isaac
* topics/systems/virtuoso.gmi (Virtuoso users and setting their passwords): New section.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-10 12:48:33 +0000