diff --git a/README.md b/README.md index 158c1f2e..e58570df 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/v2.26.1/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/v2.27.0/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/v2.26.1.tar.gz -tar xzf v2.26.1.tar.gz -cd vsearch-2.26.1 +wget https://github.com/torognes/vsearch/archive/v2.27.0.tar.gz +tar xzf v2.27.0.tar.gz +cd vsearch-2.27.0 ./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/v2.26.1/vsearch-2.26.1-linux-x86_64.tar.gz -tar xzf vsearch-2.26.1-linux-x86_64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.27.0/vsearch-2.27.0-linux-x86_64.tar.gz +tar xzf vsearch-2.27.0-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/v2.26.1/vsearch-2.26.1-linux-ppc64le.tar.gz -tar xzf vsearch-2.26.1-linux-ppc64le.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.27.0/vsearch-2.27.0-linux-ppc64le.tar.gz +tar xzf vsearch-2.27.0-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/v2.26.1/vsearch-2.26.1-linux-aarch64.tar.gz -tar xzf vsearch-2.26.1-linux-aarch64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.27.0/vsearch-2.27.0-linux-aarch64.tar.gz +tar xzf vsearch-2.27.0-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/v2.26.1/vsearch-2.26.1-macos-aarch64.tar.gz -tar xzf vsearch-2.26.1-macos-aarch64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.27.0/vsearch-2.27.0-macos-aarch64.tar.gz +tar xzf vsearch-2.27.0-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/v2.26.1/vsearch-2.26.1-macos-x86_64.tar.gz -tar xzf vsearch-2.26.1-macos-x86_64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.27.0/vsearch-2.27.0-macos-x86_64.tar.gz +tar xzf vsearch-2.27.0-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/v2.26.1/vsearch-2.26.1-win-x86_64.zip +https://github.com/torognes/vsearch/releases/download/v2.27.0/vsearch-2.27.0-win-x86_64.zip ``` -Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.26.1-linux-x86_64` or `vsearch-2.26.1-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-2.27.0-linux-x86_64` or `vsearch-2.27.0-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-2.26.1-win-x86_64`. The vsearch executable is called +called `vsearch-2.27.0-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 @@ -130,10 +130,12 @@ a folder (for instance `C:\Users\\bin`), and add the new folder to the user `Path`: open the `Environment Variables` window by searching for it in the Start menu, `Edit` user variables, add `;C:\Users\\bin` to the end of the `Path` variable, and save -your changes. +your changes. The windows distribution also includes the `libbz2.dll` +and `zlib1.dll` files required for reading compressed input +files. These DLL's have been obtained for mingw-w64 from the MSYS2 +platform. - -**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/v2.26.1/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.26.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases). +**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.27.0/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.27.0/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 5ae8d204..80e8392d 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], [2.26.1], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch]) +AC_INIT([vsearch], [2.27.0], [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 99668be0..3a35c7d1 100644 --- a/man/vsearch.1 +++ b/man/vsearch.1 @@ -1,7 +1,7 @@ .\" import www macros (URL, TAG, MTO) .mso www.tmac .\" ============================================================================ -.TH vsearch 1 "November 25, 2023" "version 2.26.1" "USER COMMANDS" +.TH vsearch 1 "January 19, 2024" "version 2.27.0" "USER COMMANDS" .\" ============================================================================ .SH NAME vsearch \(em a versatile open-source tool for microbiome analysis, @@ -4106,7 +4106,7 @@ Source code and binaries are available at .PP .\" ============================================================================ .SH COPYRIGHT -Copyright (C) 2014-2023, Torbjørn Rognes, Frédéric Mahé and Tomás +Copyright (C) 2014-2024, Torbjørn Rognes, Frédéric Mahé and Tomás Flouri .PP All rights reserved. @@ -4863,6 +4863,15 @@ are used, OTU tables will include samples and OTUs with no matches. .BR v2.26.1\~ "released November 25th, 2023" No real changes, but the previous version was released without proper updates to the source code. +.TP +.BR v2.27.0\~ "released January 19th, 2024" +The usearch_global and search_exact commands now support FASTQ files +as well as FASTA files as input. This version of vsearch includes +clarifications and updates to the manual. Some code has been +refactored. Generic Dockerfiles for major Linux distributions have +been included. Some warnings from compilers and other tools have been +eliminated. The release for Windows will also include DLL's for the +two compression libraries. .LP .\" ============================================================================ .\" TODO: