v0.5.0

wwood · Aug 28, 2020 · 2e8d49c · 2e8d49c
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diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "coverm"
-version = "0.4.0"
+version = "0.5.0"
 authors = ["Ben Woodcroft <[email protected]>"]
 license = "GPL-3.0"
 description = "Read coverage calculator for metagenomics"
@@ -19,17 +19,18 @@ rust-htslib = { version="0.32.*", default-features = false }
 clap = "2.*"
 log = "0.4.*"
 env_logger = "0.7.*"
-nix = "0.17.*"
+nix = "0.18.*"
 tempdir = "0.3.*"
 tempfile = "3.*"
 ansi_term = "0.12"
 lazy_static = "1.4.0"
 rand = "0.7.*"
 serde = "1.0"
-version-compare = "0.0.10"
-bird_tool_utils = {git = "https://github.com/wwood/bird_tool_utils", rev = "3b16f11ed421ae74c1a140f3894da02584bcb5b5"}
-galah = {git = "https://github.com/wwood/galah", rev = "e55f48cf4c9f23a1f362df6f05be518895f2b480"}
-man = {git = "https://github.com/wwood/man", rev = "6aed86ec55ab6c867b391658586a597770c6dcb1"}
+version-compare = "0.0.11"
+bird_tool_utils = "0.2.0"
+galah = "0.2.0"
+bird_tool_utils-man = "0.4.0"
+roff = "0.1.*"
 
 [dev-dependencies]
 assert_cli = "0.6.*"

diff --git a/README.md b/README.md
@@ -17,10 +17,9 @@
 CoverM aims to be a configurable, easy to use and fast DNA read coverage and
 relative abundance calculator focused on metagenomics applications.
 
-CoverM calculates coverage of genomes/MAGs (`coverm genome`) or individual
-contigs (`coverm contig`). Calculating coverage by read mapping, its input can
-either be BAM files sorted by reference, or raw reads and reference FASTA
-sequences.
+CoverM calculates coverage of genomes/MAGs `coverm genome` ([help](https://wwood.github.io/coverm/coverm-genome.html)) or individual
+contigs `coverm contig` ([help](https://wwood.github.io/coverm/coverm-contig.html)). Calculating coverage by read mapping, its input can
+either be BAM files sorted by reference, or raw reads and reference genomes in various formats.
 
 ## Installation
 
@@ -97,27 +96,16 @@ coverm shell-completion --shell bash --output-file /dev/stdout >>~/.bash_complet
 In both cases, to take effect, the terminal will likely need to be restarted. To test, type `coverm gen` and it should complete after pressing the TAB key.
 
 ## Usage
-```
-Mapping coverage analysis for metagenomics
-
-Usage: coverm <subcommand> ...
-
-Main subcommands:
-	contig	Calculate coverage of contigs
-	genome	Calculate coverage of genomes
 
-Less used utility subcommands:
-	make	Generate BAM files through alignment
-	filter	Remove (or only keep) alignments with insufficient identity
-	cluster	Dereplicate and cluster genomes
-	shell-completion
-		Generate shell completion scripts
-
-Other options:
-	-V, --version	Print version information
-```
+CoverM operates in several modes. Detailed usage information is given at the links below, or alternatively by using the `-h` or `--full-help` flags for each mode:
+* [genome](https://wwood.github.com/coverm/coverm-genome.html) - Calculate coverage of genomes
+* [contig](https://wwood.github.com/coverm/coverm-contig.html) - Calculate coverage of contigs
 
-For more detailed usage see `coverm <command> -h` or `coverm <command> --full-help`.
+There are several utility modes as well:
+* [make](https://wwood.github.com/coverm/coverm-make.html) - Generate BAM files through alignment
+* [filter](https://wwood.github.com/coverm/coverm-filter.html) - Remove (or only keep) alignments with insufficient identity
+* [cluster](https://wwood.github.com/coverm/coverm-cluster.html) - Dereplicate and cluster genomes
+* shell-completion - Generate shell completion scripts
 
 ## Calculation methods
 

diff --git a/docs/coverm-cluster.html b/docs/coverm-cluster.html
diff --git a/docs/coverm-contig.html b/docs/coverm-contig.html
diff --git a/docs/coverm-filter.html b/docs/coverm-filter.html
diff --git a/docs/coverm-genome.html b/docs/coverm-genome.html
diff --git a/docs/coverm-make.html b/docs/coverm-make.html
diff --git a/prelude b/prelude
@@ -0,0 +1,10 @@
+---
+title: "coverm SUBCOMMAND usage"
+author: "Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology"
+date: "`r Sys.Date()` (`r system('cargo run -- --version',intern=T)`)"
+output:
+  prettydoc::html_pretty:
+    theme: leonids
+    highlight: github
+    toc: true
+---
diff --git a/release.sh b/release.sh
@@ -2,26 +2,27 @@
 
 set -o pipefail
 
-export LIBCLANG_PATH=~/.guix-profile/lib
+echo "Building normally .."
+cargo build --release
 
 export VERSION=`cargo run -- --version |awk '{print $2}'`
 
 # For minimap header fix binary
-export PATH=target/debug:$PATH
+export PATH=target/release:$PATH
 
 echo "Found version $VERSION .."
 
-echo "Building normally .."
-cargo build --release
+
 
 echo "Testing release version .."
 cargo test --release
 
 echo "Building musl static binary .."
-cargo build --target x86_64-unknown-linux-musl --release
+# Use cross not cargo here so htslib is OK - see https://github.com/rust-bio/rust-htslib
+cross build --target x86_64-unknown-linux-musl --release
 
 echo "Making static dist .."
-mkdir dist/coverm-x86_64-unknown-linux-musl-$VERSION
+mkdir -p dist/coverm-x86_64-unknown-linux-musl-$VERSION
 cp \
  target/x86_64-unknown-linux-musl/release/coverm \
  target/x86_64-unknown-linux-musl/release/remove_minimap2_duplicated_headers \
@@ -31,4 +32,15 @@ cd dist
 tar czf coverm-x86_64-unknown-linux-musl-$VERSION.tar.gz coverm-x86_64-unknown-linux-musl-$VERSION
 cd ..
 
-echo "Now make sure git is up to date, and run LIBCLANG_PATH=~/.guix-profile/lib cargo publish"
+echo "Building HTML versions of man pages .."
+for SUBCOMMAND in genome cluster contig filter make
+do
+    echo "Documenting $SUBCOMMAND .."
+    cargo run -- $SUBCOMMAND --full-help-roff |pandoc - -t markdown -f man |sed 's/\\\[/[/g; s/\\\]/]/g' |cat <(sed s/SUBCOMMAND/$SUBCOMMAND/ prelude) - >docs/coverm-$SUBCOMMAND.Rmd
+    echo "library(prettydoc); setwd('docs'); rmarkdown::render('coverm-$SUBCOMMAND.Rmd','prettydoc::html_pretty','coverm-$SUBCOMMAND.html')" |R --no-save
+    rm docs/coverm-$SUBCOMMAND.Rmd
+    echo "Finished documenting $SUBCOMMAND"
+done
+
+
+echo "Now make sure git is up to date, the documentation HTML has been properly generated and run cargo publish"
diff --git a/src/bin/coverm.rs b/src/bin/coverm.rs
@@ -630,7 +630,11 @@ fn main() {
             ); // Where write the completions to
         }
         Some("cluster") => {
-            galah::cluster_argument_parsing::run_cluster_subcommand(&matches);
+            galah::cluster_argument_parsing::run_cluster_subcommand(
+                &matches,
+                "coverm",
+                crate_version!(),
+            );
         }
         _ => {
             app.print_help().unwrap();