make site static for now

_site.yml

@@ -4,8 +4,6 @@ navbar:
   left:
   - text: Download
     href: search.html
-  - text: BLAST
-    href: blast.html
   - text: Protocols
     href: protocols.html
   - text: About
@@ -23,5 +21,5 @@ output:
     css: styles.css
     lib_dir: site_libs
     self_contained: no
-output_dir: website
+output_dir: docs
 

docs/data/.gitignore

@@ -0,0 +1 @@
+releases.csv

docs/data/README.md

@@ -0,0 +1 @@
+This folder contains the archived copies of the rps10 database and blast databases made from them.

docs/data/blast_databases/.gitignore

@@ -0,0 +1 @@
+release_*

docs/data/blast_databases/README.md

@@ -0,0 +1 @@
+This is where blast databases for the rsp10 locus are stored.

docs/data/releases/.gitignore

@@ -0,0 +1 @@
+release_*

docs/data/releases/README.md

@@ -0,0 +1 @@
+This is where releases will be automatically added nightly when the google drive releases spreadsheet is updated.

docs/notes/database_format_and_update_ideas.Rmd

@@ -0,0 +1,47 @@
+---
+output:
+  pdf_document: default
+  html_document: default
+  word_document: default
+---
+
+## Google Drive folder structure
+
+* **OomcyeteDB database**
+  * **database_releases**: A folder containing the spreadsheet files for each release. Once a file is added here it should not be edited.
+  * **rps10_database.ods**: A file with the current working version of the oomcyete database. 
+  * **releases.ods**: A file with information on the releases of the oomycete database. Adding a line to this file causes an update.
+  * **maintenance_guide.odt**: A guide to updating and maintaining the database.
+
+## Proposed format
+
+The database is composed of two spreadsheet files: 
+
+* **rps10_database.ods**: A spreadsheet file named with two sheets: 
+  1. **sequence_data**: A table with one row per sequence and associated information, including a taxonomic ID (e.g., ncbi taxid)
+    * *name*: The name of the organism as originally described when entered in the database, including the genus, species, and any sub-species level information.
+    * *genbank_id*: The GenBank accession number for the sequence. This can be left blank for sequences without an accession.
+    * *taxon_id*: The taxon ID for the sequence. For sequences with a GenBank accession, this should be the NCBI taxon ID associated with the accession. For sequences without a GenBank accession, a OomyceteDB-specific taxon identifier starting with "oodb_tax_" is required and there must be an entry in the "taxon_data" sheet corresponding to this ID.  This can be left blank for sequences with a GenBank accession and it will be filled in automatically when the validation script is run.
+    * *public*: A column with TRUE/FALSE, determining whether the sequence will appear in the new releases.
+    * *auto_update*: A column with TRUE/FALSE, determining whether the validation script can modify data in this row (e.g. add/update NCBI taxon ID for entries with a GenBank accession)
+    * *source*: The source of the sequence and taxonomic identification.
+    * *sequence*: The sequence, in capital letters representing nucleotides and valid IUPAC.
+    * *notes*: Any miscellaneous notes regarding the sequence.
+  2. **taxon_data**: A table with one row per unique taxonomic ID and a full classification
+    * *taxon_id*: A unique taxon ID, either an NCBI taxon id or a OomyceteDB-specific taxon identifier starting with "oodb_tax_".
+    * *auto_update*: A column with TRUE/FALSE, determining whether the validation script should update the classification with the current NCBI taxonomy information.
+    * *classification*: The full NCBI taxonomic classification, with ranks separated by ";". For OomyceteDB-specific taxon IDs, this should be added manually.
+    * *notes*: Any notes regarding the taxonomic classification.
+* **releases.ods**: A table with one row per release
+  * *release_number*: Unique release number starting from 1 and incrementing.
+  * *release_date*: The date of the release in YYYY-MM-DD format
+  * *source_file*: The name of the spreadsheet file in the "database_releases" folder corresponding to the release
+  * *public*: A column with TRUE/FALSE, determining whether the release should be made public.
+  * *release_notes*: Any miscellaneous notes regard the release. Should include what had changed since the last release.
+
+## Update procedure
+
+1. Between releases, the **rps10_database.ods** file is manually edited. 
+2. Before a release, a validation script is run to check that the database is in the correct format and that fills in missing data and updates taxonomic data that might have changed on GenBank.
+3. A line is added to the release.ods file
+4. During the next night, the release is automatically added to the server using a cron job.

docs/shiny_apps/blast/.gitignore

@@ -0,0 +1 @@
+blast