From 17f39fc7446f3594caf58326933e8f6aa335d137 Mon Sep 17 00:00:00 2001 From: Kdreval Date: Tue, 19 Mar 2024 10:17:23 -0700 Subject: [PATCH] website: add install --- docs/concepts/GAMBLR_family.html | 4 + docs/concepts/glossary.html | 4 + docs/index.html | 4 + docs/install.html | 691 +++++++++++++++++++++++++++++++ docs/install.qmd | 24 ++ docs/search.json | 57 +-- docs/why.html | 4 + 7 files changed, 763 insertions(+), 25 deletions(-) create mode 100644 docs/install.html create mode 100644 docs/install.qmd diff --git a/docs/concepts/GAMBLR_family.html b/docs/concepts/GAMBLR_family.html index fe42869..f5af8bb 100644 --- a/docs/concepts/GAMBLR_family.html +++ b/docs/concepts/GAMBLR_family.html @@ -99,6 +99,10 @@ Getting started
  • diff --git a/docs/concepts/glossary.html b/docs/concepts/glossary.html index add2d16..c8e874c 100644 --- a/docs/concepts/glossary.html +++ b/docs/concepts/glossary.html @@ -96,6 +96,10 @@ Getting started
  • diff --git a/docs/index.html b/docs/index.html index ab390cf..70a4523 100644 --- a/docs/index.html +++ b/docs/index.html @@ -130,6 +130,10 @@ Getting started
  • diff --git a/docs/install.html b/docs/install.html new file mode 100644 index 0000000..db26b6a --- /dev/null +++ b/docs/install.html @@ -0,0 +1,691 @@ + + + + + + + + + +GAMBLR.viz – install + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    +

    Installation

    +

    We recommend installing the package directly from GitHub (requires devtools dependency).

    +
    if (!require("devtools")) install.packages("devtools")
+
+devtools::install_github(
+    "morinlab/GAMBLR.viz",
+    repos = BiocManager::repositories()
+)
    +

    You can confirm successful installation by running a simple info command:

    +
    viz_info() #Prints general info to the console
    + + +
    + + Back to top
    + +
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    +
    +
    +   +
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    + + + + \ No newline at end of file diff --git a/docs/install.qmd b/docs/install.qmd new file mode 100644 index 0000000..e69f7b8 --- /dev/null +++ b/docs/install.qmd @@ -0,0 +1,24 @@ +--- +hide: + - toc + - navigation + - footer +--- + +# Installation + +We recommend installing the package directly from GitHub (requires `devtools` dependency). + +```r +if (!require("devtools")) install.packages("devtools") + +devtools::install_github( + "morinlab/GAMBLR.viz", + repos = BiocManager::repositories() +) +``` + +You can confirm successful installation by running a simple info command: +```r +viz_info() #Prints general info to the console +``` \ No newline at end of file diff --git a/docs/search.json b/docs/search.json index ce5264e..fea321d 100644 --- a/docs/search.json +++ b/docs/search.json @@ -7,32 +7,11 @@ "text": "GAMBLR.viz is the top-most member of the GAMBLR family of packages that is designed to be used outside of GSC and for users who are not members of Morin Lab. It mostly serves the purpose of providing functions for high-level visualizations of genomic data, including simple somatic mutations, structural variations, copy number alterations, and combinations of these data.\nThe GAMBLR family includes:\n\nGAMBLR.data - collection of genomic data for analysis of Mature B-cell neoplasms\nGAMBLR.helpers - a set of low-level functions for data operation\nGAMBLR.utils - higher level set of functions to operate on genomic data\nGAMBLR.viz - this package\nGAMBLR.results - used to access the full data in GAMBL project. Only available for members of the Morin Lab and requires access to GSC, but can also be run locally once properly configured and synced.\n\nThis diagram illustrates in a simplified way the dependency relationship of different packages in the GAMBLR.family:\n\n\n\n\nflowchart LR\n A(\"GAMBLR.data\") --> B(\"GAMBLR.helpers\")\n B --> C(\"GAMBLR.utils\")\n C --> D(\"GAMBLR.viz\")\n D --> E{\"Morin Lab member?\"}\n E -- YES --> F(\"GAMBLR.results\")\n E -- NO --> A\n\n\n\n\n\nAll dependencies should be installed automatically for you, just like with any other R package. If not, please report the issue in the appropriate GitHub repo.\n\n\n\n Back to top" }, { - "objectID": "index.html", - "href": "index.html", - "title": "GAMBLR.viz", + "objectID": "install.html", + "href": "install.html", + "title": "Installation", "section": "", - "text": "Why use GAMBLR.viz?\n \n \n \n How to install?\n \n \n \n How to use?\n \n \n \n Release notes\n \n \n \n GitHub" - }, - { - "objectID": "index.html#install", - "href": "index.html#install", - "title": "GAMBLR.viz", - "section": "Install", - "text": "Install\nWe recommend installing the package directly from GitHub (requires devtools dependency).\ndevtools::install_github(\n \"morinlab/GAMBLR.viz\",\n repos = BiocManager::repositories()\n)\n\n\n\nShow quickstart" - }, - { - "objectID": "index.html#quickstart", - "href": "index.html#quickstart", - "title": "GAMBLR.viz", - "section": "Quickstart", - "text": "Quickstart\nThe quick and easy way to get started is to make sure the devtools dependency is installed, then install the GAMBLR.viz:\n# Verify devtools is installed\nif (!require(\"devtools\")) install.packages(\"devtools\")\n\n# Install GAMBLR.viz\ndevtools::install_github(\n \"morinlab/GAMBLR.viz\",\n repos = BiocManager::repositories()\n)" - }, - { - "objectID": "index.html#installation-for-developers", - "href": "index.html#installation-for-developers", - "title": "GAMBLR.viz", - "section": "Installation for developers", - "text": "Installation for developers\nThe easiest way to obtain and contribute to GAMBLR.viz is to do this via cloning the repository\ncd\ngit clone git@github.com:morinlab/GAMBLR.viz.git\nIn your R editor of choice (which is hopefully VS Code now), set your working directory to the place you just cloned the repo.\nsetwd(\"~/GAMBLR.viz\")\nInstall the package in R by running the following command (requires the devtools package):\ndevtools::install()\nAfter applying your modifications to the code, use the following command to quickly test your changes without directly installing the packaage (requires the devtools dependency):\ndevtools::load_all()\nGAMBLR.viz is a free open-source package, but the Master branch is protected. We welcome contributions (pull request, bug report, feature request, PR review) from all levels of users. All commits must be submitted via pull request on a branch. Please refer to the GitHub documentation for details on how to do pull request." + "text": "Installation\nWe recommend installing the package directly from GitHub (requires devtools dependency).\nif (!require(\"devtools\")) install.packages(\"devtools\")\n\ndevtools::install_github(\n \"morinlab/GAMBLR.viz\",\n repos = BiocManager::repositories()\n)\nYou can confirm successful installation by running a simple info command:\nviz_info() #Prints general info to the console\n\n\n\n\n Back to top" }, { "objectID": "why.html", @@ -76,6 +55,34 @@ "section": "Getting started", "text": "Getting started\nIf you’re interested in trying GAMBLR.viz we recommend the getting started tutorial." }, + { + "objectID": "index.html", + "href": "index.html", + "title": "GAMBLR.viz", + "section": "", + "text": "Why use GAMBLR.viz?\n \n \n \n How to install?\n \n \n \n How to use?\n \n \n \n Release notes\n \n \n \n GitHub" + }, + { + "objectID": "index.html#install", + "href": "index.html#install", + "title": "GAMBLR.viz", + "section": "Install", + "text": "Install\nWe recommend installing the package directly from GitHub (requires devtools dependency).\ndevtools::install_github(\n \"morinlab/GAMBLR.viz\",\n repos = BiocManager::repositories()\n)\n\n\n\nShow quickstart" + }, + { + "objectID": "index.html#quickstart", + "href": "index.html#quickstart", + "title": "GAMBLR.viz", + "section": "Quickstart", + "text": "Quickstart\nThe quick and easy way to get started is to make sure the devtools dependency is installed, then install the GAMBLR.viz:\n# Verify devtools is installed\nif (!require(\"devtools\")) install.packages(\"devtools\")\n\n# Install GAMBLR.viz\ndevtools::install_github(\n \"morinlab/GAMBLR.viz\",\n repos = BiocManager::repositories()\n)" + }, + { + "objectID": "index.html#installation-for-developers", + "href": "index.html#installation-for-developers", + "title": "GAMBLR.viz", + "section": "Installation for developers", + "text": "Installation for developers\nThe easiest way to obtain and contribute to GAMBLR.viz is to do this via cloning the repository\ncd\ngit clone git@github.com:morinlab/GAMBLR.viz.git\nIn your R editor of choice (which is hopefully VS Code now), set your working directory to the place you just cloned the repo.\nsetwd(\"~/GAMBLR.viz\")\nInstall the package in R by running the following command (requires the devtools package):\ndevtools::install()\nAfter applying your modifications to the code, use the following command to quickly test your changes without directly installing the packaage (requires the devtools dependency):\ndevtools::load_all()\nGAMBLR.viz is a free open-source package, but the Master branch is protected. We welcome contributions (pull request, bug report, feature request, PR review) from all levels of users. All commits must be submitted via pull request on a branch. Please refer to the GitHub documentation for details on how to do pull request." + }, { "objectID": "concepts/glossary.html", "href": "concepts/glossary.html", diff --git a/docs/why.html b/docs/why.html index 787f694..dd189ce 100644 --- a/docs/why.html +++ b/docs/why.html @@ -96,6 +96,10 @@ Getting started