update for v1.4.0

docs/faq.md

@@ -39,8 +39,8 @@ for more details on usage.
 **I ran `git clone [email protected]:huishenlab/biscuit.git`, but when trying to compile the executable, I get an error
 message.**
 
-> First, make sure you included `--recursive` when running `git clone`. If that does not solve your problem, make sure
-you have `zlib` and `ncurses` installed.
+> After version 1.4.0, make sure you `zlib`, `ncurses`, and `pthread` installed. If prior to version 1.4.0, make sure
+you included `--recursive` when running `git clone`.
 
 ## Quality Control Related Questions
 

docs/releases.md

@@ -14,8 +14,12 @@ details regarding each release, see the "Find it on GitHub" link under each rele
 
   - *Publication still in progress*
 
-  - **Version 1.3.0**
+  - **Version 1.4.0**
     - *Latest Release*
+    - Released: 8 January 2024
+    - [Find it on GitHub](https://github.com/huishenlab/biscuit/releases/tag/v1.4.0.20240108)
+
+  - **Version 1.3.0**
     - Released: 27 October 2023
     - [Find it on GitHub](https://github.com/huishenlab/biscuit/releases/tag/v1.3.0.20231027)
 

docs/subcommands/biscuit_version.md

@@ -7,13 +7,12 @@ permalink: /biscuit_version/
 
 # biscuit version
 ```bash
-BISCUIT Version: 1.3.0
+BISCUIT Version: 1.4.0
 
 Using:
-	htslib version: zwdzwd/htslib at commit f29fa32
-	klib   version: zwdzwd/klib   at commit ca862f8
-	sgsl   version: zwdzwd/sgsl   at commit a0ddc77
-	utils  version: zwdzwd/utils  at commit 332459b
+	htslib : version 1.18
+	sgsl   : huishenlab/sgsl  at commit 6533277
+	utils  : huishenlab/utils at commit 5f4aeab
 
 Libraries found at: https://github.com/huishenlab/biscuit/tree/master/lib
 ```

docs/subcommands/subcommand_help.md

@@ -7,12 +7,12 @@ permalink: docs/subcommands
 
 # BISCUIT Subcommands
 
-Usage for all BISCUIT subcommands as of BISCUIT version 1.3.0.
+Usage for all BISCUIT subcommands as of BISCUIT version 1.4.0 (printed with either `biscuit` or `biscuit help`).
 
 ```bash
 
 Program: BISCUIT (BISulfite-seq CUI Toolkit)
-Version: 1.3.0
+Version: 1.4.0
 Contact: Jacob Morrison <[email protected]>
 
 Usage: biscuit <command> [options]
@@ -41,6 +41,7 @@ Command:
 
  -- Other
     version      Print BISCUIT and library versions
+    help         Print usage and exit
     qc           Generate QC files from BAM
     bc           Extract barcodes from FASTQ files
 

index.md

@@ -118,25 +118,46 @@ These commands work on both macOS and Linux.
 
 ### Download Source Code and Compile
 
-The source code for BISCUIT can be downloaded using either `git` or `curl`. Compilation requires that `zlib` and
-`ncurses` are installed.
+#### Version 1.4.0 and Newer
 
-Using `git`,
+As of version 1.4.0, BISCUIT uses a CMake-based build system. Regardless of whether you use `git` or `curl` to download
+the source code, you will `cmake` (minimum version 3.21), `zlib`, `ncurses`, `pthread`, and `curl` installed to build
+BISCUIT.
+
+The source can be retrieved with either of these two commands:
 ```bash
-git clone --recursive [email protected]:huishenlab/biscuit.git
+# git
+git clone [email protected]:huishenlab/biscuit.git
 cd biscuit
-make
+
+# curl
+curl -OL $(curl -s https://api.github.com/repos/huishenlab/biscuit/releases/latest |
+    grep browser_download_url | grep release-source.zip | cut -d '"' -f 4)
+unzip release-source.zip
+cd biscuit-release
 ```
-Note, after v0.2.0, if downloading via `git`, make sure to use the `--recursive` flag to get the submodules. If an SSH
-key has not been set up, and you receive a "permission denied" error, replace the first line with
+
+After retrieving the source code (regardless of retrieval method), building BISCUIT proceeds as follows:
 ```bash
-git clone --recursive https://github.com/huishenlab/biscuit.git
+mkdir build && cd build
+cmake -DCMAKE_INSTALL_PREFIX=../ ../
+make && make install
 ```
+This will create a directory called `bin` in top level directory of BISCUIT where the `biscuit` binary and the QC, asset
+creator, and strand-flipping scripts can be found. You can also specify a different directory to install your files
+(replace `-DCMAKE_INSTALL_PREFIX=../` with `-DCMAKE_INSTALL_PREFIX=/path/to/your/other/location`). If you don't include
+the `-DCMAKE_INSTALL_PREFIX` option, you can specify the install location via:
+`cmake --install --prefix /path/to/your/install/location`. If you don't run the install commands, the BISCUIT binary
+can be found in `build/src/biscuit` (relative to the top level directory of BISCUIT) and the scripts can be found in the
+`scripts/` directory.
+
+#### Version 1.3.0 and Earlier
+
+The source code for BISCUIT version 1.3.0 and earlier can be downloaded from the
+[GitHub releases page](https://github.com/huishenlab/biscuit/releases), specifically the `release-source.zip` file.
+Compilation requires that `zlib` and `ncurses` are installed.
 
-Using `curl`,
 ```bash
-curl -OL $(curl -s https://api.github.com/repos/huishenlab/biscuit/releases/latest |
-    grep browser_download_url | grep release-source.zip | cut -d '"' -f 4)
 unzip release-source.zip
 cd biscuit-release
 make