From e6e7db33c2b640e16ded8d69c63ad5c46589e3b6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Torbj=C3=B8rn=20Rognes?= Date: Fri, 7 Jul 2023 13:11:45 +0200 Subject: [PATCH] VSEARCH 2.23.0: Numerous fixes and documentation updates --- README.md | 36 ++++++++++++++++++------------------ configure.ac | 2 +- man/vsearch.1 | 14 +++++++++++++- 3 files changed, 32 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 5044caa2..2f1d8a4d 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ Most of the nucleotide based commands and options in USEARCH version 7 are suppo ## Getting Help -If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch_manual.pdf), please visit the [VSEARCH Web Forum](https://groups.google.com/forum/#!forum/vsearch-forum) to post a question or start a discussion. +If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch_manual.pdf), please visit the [VSEARCH Web Forum](https://groups.google.com/forum/#!forum/vsearch-forum) to post a question or start a discussion. ## Example @@ -50,9 +50,9 @@ In the example below, VSEARCH will identify sequences in the file database.fsa t **Source distribution** To download the source distribution from a [release](https://github.com/torognes/vsearch/releases) and build the executable and the documentation, use the following commands: ``` -wget https://github.com/torognes/vsearch/archive/v2.22.1.tar.gz -tar xzf v2.22.1.tar.gz -cd vsearch-2.22.1 +wget https://github.com/torognes/vsearch/archive/v2.23.0.tar.gz +tar xzf v2.23.0.tar.gz +cd vsearch-2.23.0 ./autogen.sh ./configure CFLAGS="-O3" CXXFLAGS="-O3" make @@ -81,48 +81,48 @@ Binary distributions are provided for x86-64 systems running GNU/Linux, macOS (v Download the appropriate executable for your system using the following commands if you are using a Linux x86_64 system: ```sh -wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-linux-x86_64.tar.gz -tar xzf vsearch-2.22.1-linux-x86_64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-linux-x86_64.tar.gz +tar xzf vsearch-2.23.0-linux-x86_64.tar.gz ``` Or these commands if you are using a Linux ppc64le system: ```sh -wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-linux-ppc64le.tar.gz -tar xzf vsearch-2.22.1-linux-ppc64le.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-linux-ppc64le.tar.gz +tar xzf vsearch-2.23.0-linux-ppc64le.tar.gz ``` Or these commands if you are using a Linux aarch64 (arm64) system: ```sh -wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-linux-aarch64.tar.gz -tar xzf vsearch-2.22.1-linux-aarch64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-linux-aarch64.tar.gz +tar xzf vsearch-2.23.0-linux-aarch64.tar.gz ``` Or these commands if you are using a Mac with an Apple Silicon CPU: ```sh -wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-macos-aarch64.tar.gz -tar xzf vsearch-2.22.1-macos-aarch64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-macos-aarch64.tar.gz +tar xzf vsearch-2.23.0-macos-aarch64.tar.gz ``` Or these commands if you are using a Mac with an Intel CPU: ```sh -wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-macos-x86_64.tar.gz -tar xzf vsearch-2.22.1-macos-x86_64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-macos-x86_64.tar.gz +tar xzf vsearch-2.23.0-macos-x86_64.tar.gz ``` Or if you are using Windows, download and extract (unzip) the contents of this file: ``` -https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-win-x86_64.zip +https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-win-x86_64.zip ``` -Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.22.1-linux-x86_64` or `vsearch-2.22.1-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`. Versions with statically compiled libraries are available for Linux systems. These have "-static" in their name, and could be used on systems that do not have all the necessary libraries installed. +Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.23.0-linux-x86_64` or `vsearch-2.23.0-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`. Versions with statically compiled libraries are available for Linux systems. These have "-static" in their name, and could be used on systems that do not have all the necessary libraries installed. **Windows**: You will now have the binary distribution in a folder -called `vsearch-2.22.1-win-x86_64`. The vsearch executable is called +called `vsearch-2.23.0-win-x86_64`. The vsearch executable is called `vsearch.exe`. The manual in PDF format is called `vsearch_manual.pdf`. If you want to be able to call `vsearch.exe` from any command prompt window, you can put the vsearch executable in @@ -133,7 +133,7 @@ searching for it in the Start menu, `Edit` user variables, add your changes. -**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases). +**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases). ## Packages, plugins, and wrappers diff --git a/configure.ac b/configure.ac index d0b2e5d1..ef2e0a0c 100644 --- a/configure.ac +++ b/configure.ac @@ -2,7 +2,7 @@ # Process this file with autoconf to produce a configure script. AC_PREREQ([2.63]) -AC_INIT([vsearch], [2.22.1], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch]) +AC_INIT([vsearch], [2.23.0], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch]) AC_CANONICAL_TARGET AM_INIT_AUTOMAKE([subdir-objects]) AC_LANG([C++]) diff --git a/man/vsearch.1 b/man/vsearch.1 index f5354a2b..cf4eb2fa 100644 --- a/man/vsearch.1 +++ b/man/vsearch.1 @@ -1,5 +1,5 @@ .\" ============================================================================ -.TH vsearch 1 "September 19, 2022" "version 2.22.1" "USER COMMANDS" +.TH vsearch 1 "July 7, 2023" "version 2.23.0" "USER COMMANDS" .\" ============================================================================ .SH NAME vsearch \(em a versatile open-source tool for microbiome analysis, @@ -4810,6 +4810,18 @@ Add the derep_smallmem command for dereplication using little memory. .TP .BR v2.22.1\~ "released September 19th, 2022" Fix compiler warning. +.TP +.BR v2.23.0\~ "released July 7th, 2023" +Update documentation. Add citation file. Modernize and improve +code. Fix several minor bugs. Fix compilation with GCC 13. Print stats +after fastq_mergepairs to log file instead of stderr. Handle sizein +option correctly with dbmatched option for usearch_global. Allow +maxseqlength option for makeudb_usearch. Fix memory allocation problem +with chimera detection. Add lengthout and xlength options. Increase +precision for eeout option. Add warning about sintax algorithm, random +seed and multiple threads. Refactor chimera detection code. Add +undocumented experimental long_chimeras_denovo command. Fix segfault +with clustering. Add more references. .LP .\" ============================================================================ .\" TODO: