2.2.6 Release

BenLangmead · Jul 22, 2015 · d108044 · d108044
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diff --git a/MANUAL b/MANUAL
@@ -160,12 +160,16 @@ execution times on SMP architectures where this is possible. On POSIX
 platforms (like linux, Mac OS, etc) it needs the pthread library. Although
 it is possible to use pthread library on non-POSIX platform like Windows, due
 to performance reasons bowtie 2 will try to use Windows native multithreading
-if possible.
+if possible. We recommend that you first install the [Threading Building Blocks library],
+also known as TBB, and then build using `make WITH_TBB=1`. TBB comes installed
+by default on many popular linux distros. If TBB is not available, then simply omit 
+the `WITH_TBB=1` option.
 
 [MinGW]:    http://www.mingw.org/
 [MSYS]:     http://www.mingw.org/wiki/msys
 [pthreads]: http://sourceware.org/pthreads-win32/
 [GnuWin32]: http://gnuwin32.sf.net/packages/coreutils.htm
+[Threading Building Blocks library]: https://www.threadingbuildingblocks.org
 [Download]: https://sourceforge.net/projects/bowtie-bio/files/bowtie2/
 [sourceforge site]: https://sourceforge.net/projects/bowtie-bio/files/bowtie2/
 [Xcode]:    http://developer.apple.com/xcode/

diff --git a/NEWS b/NEWS
@@ -16,6 +16,19 @@ Please report any issues using the Sourceforge bug tracker:
 Version Release History
 =======================
 
+Version 2.2.6 - Jul 22, 2015
+   * Switched to a stable sort to avoid some potential reproducibility confusions.
+   * Added 'install' target for *nix platforms.
+   * Added the Intel TBB option which provides in most situations a better performance
+     output. TBB is not present by default in the current build but can be added 
+     by compiling the source code with WITH_TBB=1 option.
+   * Fixed a bug that caused seed lenght to be dependent of the -L and -N parameters order.
+   * Fixed a bug that caused --local followed by -N to reset seed lenght to 22 which is
+     actually the default value for global.
+   * Enable compilation on FreeBDS and clang, although gmake port is still required.
+   * Fixed an issue that made bowtie2 compilation process to fail on Snow Leopard.
+
+
 Version 2.2.5 - Mar 9, 2015
    * Fixed some situations where incorrectly we could detect a Mavericks platform.
    * Fixed some manual issues including some HTML bad formating.

diff --git a/doc/manual.html b/doc/manual.html
@@ -125,7 +125,7 @@ <h1 id="obtaining-bowtie-2">Obtaining Bowtie 2</h1>
 <h2 id="building-from-source">Building from source</h2>
 <p>Building Bowtie 2 from source requires a GNU-like environment with GCC, GNU Make and other basics. It should be possible to build Bowtie 2 on most vanilla Linux installations or on a Mac installation with <a href="http://developer.apple.com/xcode/">Xcode</a> installed. Bowtie 2 can also be built on Windows using a 64-bit MinGW distribution and MSYS. In order to simplify the MinGW setup it might be worth investigating popular MinGW personal builds since these are coming already prepared with most of the toolchains needed.</p>
 <p>First, download the source package from the <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/">sourceforge site</a>. Make sure you're getting the source package; the file downloaded should end in <code>-source.zip</code>. Unzip the file, change to the unzipped directory, and build the Bowtie 2 tools by running GNU <code>make</code> (usually with the command <code>make</code>, but sometimes with <code>gmake</code>) with no arguments. If building with MinGW, run <code>make</code> from the MSYS environment.</p>
-<p>Bowtie 2 is using the multithreading software model in order to speed up execution times on SMP architectures where this is possible. On POSIX platforms (like linux, Mac OS, etc) it needs the pthread library. Although it is possible to use pthread library on non-POSIX platform like Windows, due to performance reasons bowtie 2 will try to use Windows native multithreading if possible.</p>
+<p>Bowtie 2 is using the multithreading software model in order to speed up execution times on SMP architectures where this is possible. On POSIX platforms (like linux, Mac OS, etc) it needs the pthread library. Although it is possible to use pthread library on non-POSIX platform like Windows, due to performance reasons bowtie 2 will try to use Windows native multithreading if possible. We recommend that you first install the <a href="https://www.threadingbuildingblocks.org">Threading Building Blocks library</a>, also known as TBB, and then build using <code>make WITH_TBB=1</code>. TBB comes installed by default on many popular linux distros. If TBB is not available, then simply omit the <code>WITH_TBB=1</code> option.</p>
 <h2 id="adding-to-path">Adding to PATH</h2>
 <p>By adding your new Bowtie 2 directory to your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH environment variable</a>, you ensure that whenever you run <code>bowtie2</code>, <code>bowtie2-build</code> or <code>bowtie2-inspect</code> from the command line, you will get the version you just installed without having to specify the entire path. This is recommended for most users. To do this, follow your operating system's instructions for adding the directory to your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH</a>.</p>
 <p>If you would like to install Bowtie 2 by copying the Bowtie 2 executable files to an existing directory in your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH</a>, make sure that you copy all the executables, including <code>bowtie2</code>, <code>bowtie2-align-s</code>, <code>bowtie2-align-l</code>, <code>bowtie2-build</code>, <code>bowtie2-build-s</code>, <code>bowtie2-build-l</code>, <code>bowtie2-inspect</code>, <code>bowtie2-inspect-s</code> and <code>bowtie2-inspect-l</code>.</p>
@@ -510,7 +510,7 @@ <h4 id="alignment-options">Alignment options</h4>
 <pre><code>-L &lt;int&gt;</code></pre>
 </td><td>
 
-<p>Sets the length of the seed substrings to align during <a href="#multiseed-heuristic">multiseed alignment</a>. Smaller values make alignment slower but more senstive. Default: the <a href="#bowtie2-options-sensitive"><code>--sensitive</code></a> preset is used by default, which sets <code>-L</code> to 22 in <a href="#bowtie2-options-end-to-end"><code>--end-to-end</code></a> mode and to 20 in <a href="#bowtie2-options-local"><code>--local</code></a> mode.</p>
+<p>Sets the length of the seed substrings to align during <a href="#multiseed-heuristic">multiseed alignment</a>. Smaller values make alignment slower but more senstive. Default: the <a href="#bowtie2-options-sensitive"><code>--sensitive</code></a> preset is used by default, which sets <code>-L</code> to 20 both in <a href="#bowtie2-options-end-to-end"><code>--end-to-end</code></a> mode and in <a href="#bowtie2-options-local"><code>--local</code></a> mode.</p>
 </td></tr>
 <tr><td id="bowtie2-options-i">
 
@@ -527,7 +527,7 @@ <h4 id="alignment-options">Alignment options</h4>
 Seed 3 rc:             ATGATAGCGT
 Seed 4 fw:                   TCATGCATAA
 Seed 4 rc:                   TTATGCATGA</code></pre>
-<p>Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying <code>-i S,1,2.5</code> sets the interval function <code>f</code> to <code>f(x) = 1 + 2.5 * sqrt(x)</code>, where x is the read length. See also: <a href="#setting-function-options">setting function options</a>. If the function returns a result less than 1, it is rounded up to 1. Default: the <a href="#bowtie2-options-sensitive"><code>--sensitive</code></a> preset is used by default, which sets <code>-i</code> to <code>S,1,1.15</code> in <a href="#bowtie2-options-end-to-end"><code>--end-to-end</code></a> mode and to <code>-i S,1,0.75</code> in <a href="#bowtie2-options-local"><code>--local</code></a> mode.</p>
+<p>Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying <code>-i S,1,2.5</code> sets the interval function <code>f</code> to <code>f(x) = 1 + 2.5 * sqrt(x)</code>, where x is the read length. See also: <a href="#setting-function-options">setting function options</a>. If the function returns a result less than 1, it is rounded up to 1. Default: the <a href="#bowtie2-options-sensitive"><code>--sensitive</code></a> preset is used by default, which sets <code>-i</code> to <code>S,1,1.15</code> in <a href="#bowtie2-options-end-to-end"><code>--end-to-end</code></a> mode to <code>-i S,1,0.75</code> in <a href="#bowtie2-options-local"><code>--local</code></a> mode.</p>
 </td></tr>
 <tr><td id="bowtie2-options-n-ceil">
 

diff --git a/doc/website/manual.ssi b/doc/website/manual.ssi
@@ -1,5 +1,5 @@
 <h1>Table of Contents</h1>
-<p>&nbsp;Version <b>2.2.5</b></p>
+<p>&nbsp;Version <b>2.2.6</b></p>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml">
 <head>
@@ -125,7 +125,7 @@
 <h2 id="building-from-source">Building from source</h2>
 <p>Building Bowtie 2 from source requires a GNU-like environment with GCC, GNU Make and other basics. It should be possible to build Bowtie 2 on most vanilla Linux installations or on a Mac installation with <a href="http://developer.apple.com/xcode/">Xcode</a> installed. Bowtie 2 can also be built on Windows using a 64-bit MinGW distribution and MSYS. In order to simplify the MinGW setup it might be worth investigating popular MinGW personal builds since these are coming already prepared with most of the toolchains needed.</p>
 <p>First, download the source package from the <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/">sourceforge site</a>. Make sure you're getting the source package; the file downloaded should end in <code>-source.zip</code>. Unzip the file, change to the unzipped directory, and build the Bowtie 2 tools by running GNU <code>make</code> (usually with the command <code>make</code>, but sometimes with <code>gmake</code>) with no arguments. If building with MinGW, run <code>make</code> from the MSYS environment.</p>
-<p>Bowtie 2 is using the multithreading software model in order to speed up execution times on SMP architectures where this is possible. On POSIX platforms (like linux, Mac OS, etc) it needs the pthread library. Although it is possible to use pthread library on non-POSIX platform like Windows, due to performance reasons bowtie 2 will try to use Windows native multithreading if possible.</p>
+<p>Bowtie 2 is using the multithreading software model in order to speed up execution times on SMP architectures where this is possible. On POSIX platforms (like linux, Mac OS, etc) it needs the pthread library. Although it is possible to use pthread library on non-POSIX platform like Windows, due to performance reasons bowtie 2 will try to use Windows native multithreading if possible. We recommend that you first install the <a href="https://www.threadingbuildingblocks.org">Threading Building Blocks library</a>, also known as TBB, and then build using <code>make WITH_TBB=1</code>. TBB comes installed by default on many popular linux distros. If TBB is not available, then simply omit the <code>WITH_TBB=1</code> option.</p>
 <h2 id="adding-to-path">Adding to PATH</h2>
 <p>By adding your new Bowtie 2 directory to your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH environment variable</a>, you ensure that whenever you run <code>bowtie2</code>, <code>bowtie2-build</code> or <code>bowtie2-inspect</code> from the command line, you will get the version you just installed without having to specify the entire path. This is recommended for most users. To do this, follow your operating system's instructions for adding the directory to your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH</a>.</p>
 <p>If you would like to install Bowtie 2 by copying the Bowtie 2 executable files to an existing directory in your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH</a>, make sure that you copy all the executables, including <code>bowtie2</code>, <code>bowtie2-align-s</code>, <code>bowtie2-align-l</code>, <code>bowtie2-build</code>, <code>bowtie2-build-s</code>, <code>bowtie2-build-l</code>, <code>bowtie2-inspect</code>, <code>bowtie2-inspect-s</code> and <code>bowtie2-inspect-l</code>.</p>
@@ -510,7 +510,7 @@ Reference: GCAGATTATATGAGTCAGCTACGATATTGTTTGGGGTGACACATTACGCGTCTTTGAC</code></pr
 <pre><code>-L &lt;int&gt;</code></pre>
 </td><td>
 
-<p>Sets the length of the seed substrings to align during <a href="#multiseed-heuristic">multiseed alignment</a>. Smaller values make alignment slower but more senstive. Default: the <a href="#bowtie2-options-sensitive"><code>--sensitive</code></a> preset is used by default, which sets <code>-L</code> to 22 in <a href="#bowtie2-options-end-to-end"><code>--end-to-end</code></a> mode and to 20 in <a href="#bowtie2-options-local"><code>--local</code></a> mode.</p>
+<p>Sets the length of the seed substrings to align during <a href="#multiseed-heuristic">multiseed alignment</a>. Smaller values make alignment slower but more senstive. Default: the <a href="#bowtie2-options-sensitive"><code>--sensitive</code></a> preset is used by default, which sets <code>-L</code> to 20 both in <a href="#bowtie2-options-end-to-end"><code>--end-to-end</code></a> mode and in <a href="#bowtie2-options-local"><code>--local</code></a> mode.</p>
 </td></tr>
 <tr><td id="bowtie2-options-i">
 
@@ -527,7 +527,7 @@ Seed 3 fw:             ACGCTATCAT
 Seed 3 rc:             ATGATAGCGT
 Seed 4 fw:                   TCATGCATAA
 Seed 4 rc:                   TTATGCATGA</code></pre>
-<p>Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying <code>-i S,1,2.5</code> sets the interval function <code>f</code> to <code>f(x) = 1 + 2.5 * sqrt(x)</code>, where x is the read length. See also: <a href="#setting-function-options">setting function options</a>. If the function returns a result less than 1, it is rounded up to 1. Default: the <a href="#bowtie2-options-sensitive"><code>--sensitive</code></a> preset is used by default, which sets <code>-i</code> to <code>S,1,1.15</code> in <a href="#bowtie2-options-end-to-end"><code>--end-to-end</code></a> mode and to <code>-i S,1,0.75</code> in <a href="#bowtie2-options-local"><code>--local</code></a> mode.</p>
+<p>Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying <code>-i S,1,2.5</code> sets the interval function <code>f</code> to <code>f(x) = 1 + 2.5 * sqrt(x)</code>, where x is the read length. See also: <a href="#setting-function-options">setting function options</a>. If the function returns a result less than 1, it is rounded up to 1. Default: the <a href="#bowtie2-options-sensitive"><code>--sensitive</code></a> preset is used by default, which sets <code>-i</code> to <code>S,1,1.15</code> in <a href="#bowtie2-options-end-to-end"><code>--end-to-end</code></a> mode to <code>-i S,1,0.75</code> in <a href="#bowtie2-options-local"><code>--local</code></a> mode.</p>
 </td></tr>
 <tr><td id="bowtie2-options-n-ceil">
 
@@ -1330,3 +1330,4 @@ r7  16  gi|9626243|ref|NC_001416.1| 4692    42  143M    *   0   0   TCAGCCGGACGC
 <p>Then to view the variants, run:</p>
 <pre><code>bcftools view eg2.raw.bcf</code></pre>
 <p>See the official SAMtools guide to <a href="http://samtools.sourceforge.net/mpileup.shtml">Calling SNPs/INDELs with SAMtools/BCFtools</a> for more details and variations on this process.</p>
+
diff --git a/doc/website/recent_news.ssi b/doc/website/recent_news.ssi
@@ -1,3 +1,14 @@
+<h2>Version 2.2.6 - Jul 22, 2015</h2>
+<ul>
+   <li>Switched to a stable sort to avoid some potential reproducibility confusions.</li>
+   <li>Added 'install' target for *nix platforms.</li>
+   <li>Added the Intel TBB option which provides in most situations a better performance output. TBB is not present by default in the current build but can be added by compiling the source code with WITH_TBB=1 option.</li>
+   <li>Fixed a bug that caused seed lenght to be dependent of the -L and -N parameters order.</li>
+   <li>Fixed a bug that caused --local followed by -N to reset seed lenght to 22 which is actually the default value for global.</li>
+   <li>Enable compilation on FreeBDS and clang, although gmake port is still required.</li>
+   <li>Fixed an issue that made bowtie2 compilation process to fail on Snow Leopard.</li>
+</ul>
+
 <h2>Version 2.2.5 - Mar 9, 2015</h2>
 <ul>
    <li>Fixed some situations where incorrectly we could detect a Mavericks platform.</li>

diff --git a/doc/website/rhsidebar.ssi b/doc/website/rhsidebar.ssi
@@ -15,10 +15,10 @@
      <table width="100%">
       <tr>
       <td>
-        <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5">Bowtie2 2.2.5</a>
+        <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6">Bowtie2 2.2.6</a>
       </td>
       <td align="right">
-        3/9/15&nbsp;
+        7/22/15&nbsp;
       </td>
       </tr>
       <tr>