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+# `primal-page`
+
+**Usage**:
+
+```console
+$ primal-page [OPTIONS] COMMAND [ARGS]...
+```
+
+**Options**:
+
+* `--version`
+* `--install-completion`: Install completion for the current shell.
+* `--show-completion`: Show completion for the current shell, to copy it or customize the installation.
+* `--help`: Show this message and exit.
+
+**Commands**:
+
+* `aliases`: Manage aliases
+* `build-index`: Build an index.json file from all schemes...
+* `create`: Create a new scheme in the required format
+* `dev`: Development commands
+* `download`: Download schemes from the index.json
+* `modify`: Modify an existing scheme's metadata...
+* `remove`: Remove a scheme's version from the repo,...
+
+## `primal-page aliases`
+
+Manage aliases
+
+**Usage**:
+
+```console
+$ primal-page aliases [OPTIONS] COMMAND [ARGS]...
+```
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+**Commands**:
+
+* `add`: Add an alias:schemename to the alias file
+* `remove`: Remove an alias from the alias file.
+
+### `primal-page aliases add`
+
+Add an alias:schemename to the alias file
+
+**Usage**:
+
+```console
+$ primal-page aliases add [OPTIONS] ALIASES_FILE ALIAS SCHEMENAME
+```
+
+**Arguments**:
+
+* `ALIASES_FILE`: The path to the alias file to write to  [required]
+* `ALIAS`: The alias to add  [required]
+* `SCHEMENAME`: The schemename the alias refers to  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page aliases remove`
+
+Remove an alias from the alias file. Does nothing if the alias does not exist
+
+**Usage**:
+
+```console
+$ primal-page aliases remove [OPTIONS] ALIASES_FILE ALIAS
+```
+
+**Arguments**:
+
+* `ALIASES_FILE`: The path to the alias file to write to  [required]
+* `ALIAS`: The alias to add  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+## `primal-page build-index`
+
+Build an index.json file from all schemes in the directory
+
+**Usage**:
+
+```console
+$ primal-page build-index [OPTIONS]
+```
+
+**Options**:
+
+* `--gitaccount TEXT`: The name of the github account  [default: quick-lab]
+* `--gitserver TEXT`: The name of the github server  [default: https://github.com/]
+* `--parentdir PATH`: The parent directory  [default: .]
+* `--git-commit-sha TEXT`: The git commit
+* `--force / --no-force`: Force the creation of the index.json  [default: no-force]
+* `--help`: Show this message and exit.
+
+## `primal-page create`
+
+Create a new scheme in the required format
+
+**Usage**:
+
+```console
+$ primal-page create [OPTIONS] SCHEMEPATH
+```
+
+**Arguments**:
+
+* `SCHEMEPATH`: The path to the primerscheme directory  [required]
+
+**Options**:
+
+* `--schemename TEXT`: The name of the scheme  [required]
+* `--ampliconsize INTEGER RANGE`: Amplicon size  [x>=100; required]
+* `--schemeversion TEXT`: Scheme version, default is parsed from config.json  [required]
+* `--species INTEGER`: The species this scheme targets. Please use NCBI taxonomy ids  [required]
+* `--authors TEXT`: Any authors  [required]
+* `--schemestatus [withdrawn|deprecated|autogenerated|draft|tested|validated]`: Scheme status  [default: draft]
+* `--citations TEXT`: Any associated citations. Please use DOI
+* `--primerbed PATH`: Manually specify the primer bed file, default is *primer.bed
+* `--reference PATH`: Manually specify the reference.fasta file, default is *.fasta
+* `--output PATH`: Where to output the scheme  [default: primerschemes]
+* `--configpath PATH`: Where the config.json file is located
+* `--algorithmversion TEXT`: The version of primalscheme or other
+* `--description TEXT`: A description of the scheme
+* `--derivedfrom TEXT`: Which scheme has this scheme been derived from
+* `--primerclass [primerschemes]`: The primer class  [default: primerschemes]
+* `--collection [ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET]`: The collection
+* `--link-protocol TEXT`: Optional link to protocol
+* `--link-validation TEXT`: Optional link to validation data
+* `--links-homepage TEXT`: Optional link to homepage
+* `--link-vendor TEXT`: Optional link to vendors
+* `--link-misc TEXT`: Optional miscellaneous link
+* `--fix / --no-fix`: Attempt to fix the scheme  [default: no-fix]
+* `--help`: Show this message and exit.
+
+## `primal-page download`
+
+Download schemes from the index.json
+
+**Usage**:
+
+```console
+$ primal-page download [OPTIONS] COMMAND [ARGS]...
+```
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+**Commands**:
+
+* `all`: Download all schemes from the index.json
+* `scheme`: Download a scheme from the index.json
+
+### `primal-page download all`
+
+Download all schemes from the index.json
+
+**Usage**:
+
+```console
+$ primal-page download all [OPTIONS]
+```
+
+**Options**:
+
+* `--output PATH`: The directory the primerschemes dir will be created in  [required]
+* `--index-url TEXT`: The URL to the index.json  [default: https://raw.githubusercontent.com/quick-lab/primerschemes/main/index.json]
+* `--help`: Show this message and exit.
+
+### `primal-page download scheme`
+
+Download a scheme from the index.json
+
+**Usage**:
+
+```console
+$ primal-page download scheme [OPTIONS] SCHEMENAME AMPLICONSIZE SCHEMEVERSION
+```
+
+**Arguments**:
+
+* `SCHEMENAME`: The name of the scheme  [required]
+* `AMPLICONSIZE`: Amplicon size  [required]
+* `SCHEMEVERSION`: Scheme version  [required]
+
+**Options**:
+
+* `--output PATH`: The directory the primerschemes dir will be created in  [required]
+* `--index-url TEXT`: The URL to the index.json  [default: https://raw.githubusercontent.com/quick-lab/primerschemes/main/index.json]
+* `--help`: Show this message and exit.
+
+## `primal-page modify`
+
+Modify an existing scheme's metadata (info.json)
+
+**Usage**:
+
+```console
+$ primal-page modify [OPTIONS] COMMAND [ARGS]...
+```
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+**Commands**:
+
+* `add-author`: Append an author to the authors list in...
+* `add-citation`: Append an citation to the authors list in...
+* `add-collection`: Add a Collection to the Collection list in...
+* `add-link`: Add a link to the selected link field to...
+* `change-contactinfo`: Change the contactinfo field in the info.json
+* `change-derivedfrom`: Replaces the derivedfrom in the info.json...
+* `change-description`: Replaces the description in the info.json...
+* `change-license`: Replaces the license in the info.json file
+* `change-primerclass`: Change the primerclass field in the info.json
+* `change-status`: Change the status field in the info.json
+* `regenerate`: Validates the info.json and regenerate the...
+* `remove-author`: Remove an author from the authors list in...
+* `remove-citation`: Remove an citation form the authors list...
+* `remove-collection`: Remove an Collection from the Collection...
+* `remove-link`: Add a link to the selected link field to...
+* `reorder-authors`: Reorder the authors in the info.json file
+
+### `primal-page modify add-author`
+
+Append an author to the authors list in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify add-author [OPTIONS] SCHEMEINFO AUTHOR
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `AUTHOR`: The author to add  [required]
+
+**Options**:
+
+* `--author-index INTEGER`: The 0-based index to insert the author at. Default is the end  [required]
+* `--help`: Show this message and exit.
+
+### `primal-page modify add-citation`
+
+Append an citation to the authors list in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify add-citation [OPTIONS] SCHEMEINFO CITATION
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `CITATION`: The citation to add  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify add-collection`
+
+Add a Collection to the Collection list in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify add-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}`: The Collection to add  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify add-link`
+
+Add a link to the selected link field to the info.json
+
+**Usage**:
+
+```console
+$ primal-page modify add-link [OPTIONS] SCHEMEINFO LINKFIELD LINK
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `LINKFIELD`: The link field to add to. protocols, validation, homepage, vendors, misc  [required]
+* `LINK`: The link to add.  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify change-contactinfo`
+
+Change the contactinfo field in the info.json
+
+**Usage**:
+
+```console
+$ primal-page modify change-contactinfo [OPTIONS] SCHEMEINFO CONTACTINFO
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `CONTACTINFO`: The contact information for this scheme. Use 'None' to remove the contact info  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify change-derivedfrom`
+
+Replaces the derivedfrom in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify change-derivedfrom [OPTIONS] SCHEMEINFO DERIVEDFROM
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `DERIVEDFROM`: The new derivedfrom. Use 'None' to remove the derivedfrom  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify change-description`
+
+Replaces the description in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify change-description [OPTIONS] SCHEMEINFO DESCRIPTION
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `DESCRIPTION`: The new description. Use 'None' to remove the description  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify change-license`
+
+Replaces the license in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify change-license [OPTIONS] SCHEMEINFO LICENSE
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `LICENSE`: The new license. Use 'None' show the work is not licensed (Not recommended)  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify change-primerclass`
+
+Change the primerclass field in the info.json
+
+**Usage**:
+
+```console
+$ primal-page modify change-primerclass [OPTIONS] SCHEMEINFO PRIMERCLASS:{primerschemes}
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `PRIMERCLASS:{primerschemes}`: The primerclass to change to  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify change-status`
+
+Change the status field in the info.json
+
+**Usage**:
+
+```console
+$ primal-page modify change-status [OPTIONS] SCHEMEINFO [SCHEMESTATUS]:[withdrawn|deprecated|autogenerated|draft|tested|validated]
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `[SCHEMESTATUS]:[withdrawn|deprecated|autogenerated|draft|tested|validated]`: The scheme class  [default: draft]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify regenerate`
+
+Validates the info.json and regenerate the README.md
+
+**Usage**:
+
+```console
+$ primal-page modify regenerate [OPTIONS] SCHEMEINFO
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify remove-author`
+
+Remove an author from the authors list in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify remove-author [OPTIONS] SCHEMEINFO AUTHOR
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `AUTHOR`: The author to remove  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify remove-citation`
+
+Remove an citation form the authors list in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify remove-citation [OPTIONS] SCHEMEINFO CITATION
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `CITATION`: The citation to remove  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify remove-collection`
+
+Remove an Collection from the Collection list in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify remove-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}`: The Collection to remove  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify remove-link`
+
+Add a link to the selected link field to the info.json
+
+**Usage**:
+
+```console
+$ primal-page modify remove-link [OPTIONS] SCHEMEINFO LINKFIELD LINK
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `LINKFIELD`: The link field to remove from. protocols, validation, homepage, vendors, misc  [required]
+* `LINK`: The link to remove.  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page modify reorder-authors`
+
+Reorder the authors in the info.json file
+
+**Usage**:
+
+```console
+$ primal-page modify reorder-authors [OPTIONS] SCHEMEINFO [AUTHOR_INDEX]
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+* `[AUTHOR_INDEX]`: The indexes in the new order, separated by spaces. e.g. 1 0 2. Any indexes not provided will be appended to the end
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+## `primal-page remove`
+
+Remove a scheme's version from the repo, will also remove size and schemename directories if empty
+
+**Usage**:
+
+```console
+$ primal-page remove [OPTIONS] SCHEMEINFO
+```
+
+**Arguments**:
+
+* `SCHEMEINFO`: The path to info.json  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
diff --git a/docs/examples.md b/docs/examples.md
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--- /dev/null
+++ b/docs/examples.md
@@ -0,0 +1,45 @@
+# Adding a scheme
+
+> See [primal-page create](cli.md#primal-page-create) full details.
+
+To add a scheme into ```quick-lab/primerschemes```, primal-page is used to create the info.json metadata file and insure all the files are in the correct format. 
+
+## Creating a scheme from primalscheme(1) files
+
+### .primer.bed
+From primalscheme a file should be output called `{scheme-name}.primer.bed`. This file contains all the data needed to produce the primer scheme.
+
+> Old version of primalscheme do not contains the 7th column (PrimerSequence)
+
+![primerbed](assets/primalscheme1bed.png)
+
+
+
+
+## Manual editing of files
+
+Do not do this unless you have to.
+
+If you edit the `info.json` use `primal-page modify regenerate {info.json}` to validate the changes, and regenerate the README.md
+
+If you edit the `primer.bed` or `reference.fasta` use `primal-page dev regenerate {info.json}` to update the hashes in info.json need to be updated.
+
+> If you are editing `primer.bed` or `reference.fasta` something has gone wrong
+
+
+### Modifying cascade graph
+```mermaid
+flowchart TD
+
+info[info.json]
+readme[README.md]
+primer[primer.bed]
+ref[reference.fasta]
+
+
+info -->|Embedded| readme
+
+primer -->|md5 hash| info
+ref -->|md5 hash| info
+
+```
diff --git a/docs/index.md b/docs/index.md
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--- /dev/null
+++ b/docs/index.md
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+# primal-page
+
+![primalpage](assets/primalpage.png)
+
+`primal-page` is a python tool for creating and modifying metadata for primerschemes according to the schema used in [labs](https://labs.primalscheme.com/).
+
+
+
+## Installation
+
+### via pip
+```
+pip install primal-page
+
+# To run
+primal-page
+```
+
+### from source
+```
+git clone https://github.com/ChrisgKent/primal-page.git
+cd primal-page
+poetry build
+
+# To run 
+poetry run primal-page
+```
+
+
+## Overview
+
+### create
+To create the metadata file, use `primal-page create`, which will ask for required data to create the metadata file. For a more details please see [examples](examples.md) page or the [cli](cli.md).
+
+### modify
+
+Once the metadata files are generated, they can be modified with `primal-page modify` and the appropriate option.
+
+>*Do not modify the files manually* [see](examples.md#manual-editing-of-files). 
+
+### aliases
+
+Aliases are a way to provide alternative names for a schemename. For example, the schemename `hbv` (from `hbv/600.v2.1.0`) scheme has the aliases of `hepatitis-b-virus`:`hbv`.  
+
+This is currently used for;
+
+- The searchbar in [labs](https://labs.primalscheme.com). So Searching for `hepatitis` will provide `hbv/600.v2.1.0`
+- Backwards compatibility. The [`ncoV-2019`](https://github.com/artic-network/primer-schemes/tree/master/nCoV-2019) schemes are renamed `artic-sars-cov-2`, so we want to ensure that `ncoV-2019/400/v5.3.2` points to the correct scheme.
+
+
+
+
+
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..d3d13ea
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,20 @@
+site_name: primal-page
+
+repo_url: https://github.com/ChrisgKent/primal-page
+repo_name: primal-page
+
+site_url: https://chrisgkent.github.io/primal-page/
+theme:
+  name: material
+
+nav:
+  - Overview: index.md
+  - Command Line Interface: cli.md
+  - Examples: examples.md
+
+markdown_extensions:
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format