Merge branch 'master' of https://github.com/DesmondWillowbrook/Librarian

cli/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "cli"
-version = "1.2.0"
+version = "1.3.0"
 edition = "2018"
 authors = ["Kartavya Vashishtha <[email protected]>"]
 description = "A tool to predict the sequencing library type from the base composition of a supplied FastQ file. Uncompresses .gz files when reading."

cli/README.md

@@ -3,7 +3,7 @@
 Queries the Babraham server (or your own!) with supplied FASTQ files and downloads plots.
 
 ```
-Librarian CLI 1.2.0
+Librarian CLI 1.3.0
 A tool to predict the sequencing library type from the base composition of a supplied FastQ file. Uncompresses .gz files
 when reading.
 
@@ -19,10 +19,14 @@ FLAGS:
             installed, along with the `scripts` folder. See
             https://github.com/DesmondWillowbrook/Librarian/blob/master/cli/README.md for more details.
             
-            This cannot be set together with `api`.
+            This cannot be set together with `--api`.
     -q, --quiet      
             Suppresses all output except errors
 
+        --raw        
+            Only output the librarian_heatmap.txt file used by MultiQC, and don't output any plots.
+            
+            This option requires `local` to be set.
     -V, --version    
             Prints version information
 
@@ -32,7 +36,7 @@ OPTIONS:
             Specifies query URL to send prediction request to. Defaults to Babraham Bioinformatic's server. Passed
             argument is given precedence over environment variable.
             
-            If --local is set, this argument is ignored. [env: LIBRARIAN_API_URL=]  [default:
+            This cannot be set together with `--local`. [env: LIBRARIAN_API_URL=]  [default:
             https://www.bioinformatics.babraham.ac.uk/librarian/api/plot_comp]
     -o, --output-dir <output-dir>    
             Output directory (eg. `output_dir/`) [default: ]
@@ -49,7 +53,9 @@ CLI binaries can be found in the [Github Releases](https://github.com/DesmondWil
 
 The released binaries are statically linked with `musl`, so there shouldn't be too much in the way of system requirements for the CLI except running Linux.
 
-Running with the `--local` option **requires additional dependencies** to be installed. Refer to the [server README's Runtime Dependencies section](../server/README.md#runtime-dependencies) for a list of the other dependencies. (The CLI tar file includes a copy of the `scripts` folder beside the binary)
+Running with the `--local` option **requires additional dependencies** to be installed. Refer to the [server README's *Runtime Dependencies* section](../server/README.md#runtime-dependencies) for a list of the other dependencies. (The CLI tar file includes a copy of the `scripts` folder beside the binary)
+
+You might find it useful to refer to [the CLI dockerfile](../local-cli.dockerfile) for a list of dependencies.
 
 ## Install from source
 Requires a recent version of the [Rust](https://rust-lang.org) toolchain. 

cli/src/bin/librarian.rs

@@ -36,7 +36,7 @@ struct Cli {
     /// Defaults to Babraham Bioinformatic's server.
     /// Passed argument is given precedence over environment variable.
     /// 
-    /// If --local is set, this argument is ignored.
+    /// This cannot be set together with `--local`.
     /// 
     #[structopt(long, env = "LIBRARIAN_API_URL", default_value = "https://www.bioinformatics.babraham.ac.uk/librarian/api/plot_comp")]
     pub api: String,
@@ -45,7 +45,7 @@ struct Cli {
     /// Requires Rscript and other dependencies to be installed, along with the `scripts` folder.
     /// See https://github.com/DesmondWillowbrook/Librarian/blob/master/cli/README.md for more details. 
     /// 
-    /// This cannot be set together with `api`.
+    /// This cannot be set together with `--api`.
     /// 
     #[structopt(short, long, conflicts_with("api"))]
     pub local: bool,

docs/cli

@@ -0,0 +1 @@
+../cli

docs/installation.md

@@ -3,3 +3,9 @@ hide:
   - footer
 ---
 
+<!--if you edit this, make sure you also edit -->
+## CLI installation
+View [CLI installation](cli/README.md#installation) for more details.
+
+## Server installation
+View [Server installation](server/README.md#installation) for more details.

docs/server

@@ -0,0 +1 @@
+../server

Dockerfile → local-cli.dockerfile

@@ -39,8 +39,9 @@ LABEL org.opencontainers.image.source https://github.com/DesmondWillowbrook/Libr
 ENTRYPOINT ["./librarian", "--local", "--raw", "--output-dir", "/app/out/"]
 
 # example command to run this image:
-# docker run -v  \ 
-# ~/Babraham_Projects/Librarian/frontend/example_inputs/example_inputs/:/app/in # volume mapping from host to container
+# docker run  \ 
+# -v $(pwd):/app/in # volume mapping from host to container
+# -v $(pwd)/out:/app/out # volume mapping from host to container
 # -e RUST_LOG='trace' # set the log level to trace
 # -t desmondwillowbrook/librarian-server # image name
 # /app/in/RNA.example.fastq # path of file relative to mapped volume

server/README.md

@@ -1,34 +1,27 @@
 # Server
 Serves the webpages in `frontend/dist` along with running backend services.
 
-## Setup:
+## Installation
 
-```bash
-docker pull docker.io/desmondwillowbrook/librarian-server
-docker run -dp 8186:8186 desmondwillowbrook/librarian-server
-```
-
-### Non-Docker setup
-
-#### Build dependencies
+### Build dependencies
 - [`npm`](https://www.npmjs.com/get-npm)
 - [`Rust (with Cargo)`](https://www.rust-lang.org/) 
 - [`wasm-pack`](https://rustwasm.github.io/wasm-pack/installer/)
 
-#### Runtime dependencies
+### Runtime dependencies
 The `scripts` folder included with the binary should be in the same directory as the binary. `Rscript` should be present in $PATH.
 
 ```bash
 apt-get install -y r-base-core r-base-dev libssl-dev libcurl4-openssl-dev libxml2-dev
 Rscript -e 'install.packages(c("tidyverse", "umap", "ggrastr", "pins", "rmarkdown"))'
 ```
 
-#### Building from source
+### Building from source
 
 ```bash
 git clone https://github.com/DesmondWillowbrook/Librarian.git
 cd Librarian
-./run.sh
+./run-server.sh
 ```
 
 Alternatively, in case you haven't made any changes to the frontend, you can just run the server binary without rebuilding the frontend website.