Minor changes to manual and recent news

BenLangmead · bac283e83c654920adb05cc8aad1288748f63479 · ch4rr0 committed Jun 12, 2017 · Jun 12, 2017 · bac283e
1 parent 7c25602
commit bac283e83c654920adb05cc8aad1288748f63479
Unified Split

Showing with 62 additions and 59 deletions.

+1 −3 MANUAL

+1 −3 MANUAL.markdown

+7 −3 NEWS

+1 −1 doc/manual.html

+1 −1 doc/website/manual.ssi

+45 −0 doc/website/old_news.ssi

+5 −47 doc/website/recent_news.ssi

+1 −1 doc/website/rhsidebar.ssi
diff --git a/MANUAL b/MANUAL
@@ -86,9 +86,7 @@ systems.
 If TBB is not available, then use the `NO_TBB=1` option.  On Linux or
 Mac OS X, this requires the pthreads library, which is installed by
 default.  On Windows, native Windows threads will be used, which require
-no special libraries. Bowtie binaries that are *not* built with TBB are
-referred to as legacy. Pre-built packages for such builds will include
-"legacy" in the filename e.g. `bowtie-1.2-linux-x86_64.zip`.
+no special libraries.
 
 [MinGW]:    http://www.mingw.org/
 [TDM's MinGW Build]: http://www.tdragon.net/recentgcc/
diff --git a/MANUAL.markdown b/MANUAL.markdown
@@ -91,9 +91,7 @@ systems.
 If TBB is not available, then use the `NO_TBB=1` option.  On Linux or
 Mac OS X, this requires the pthreads library, which is installed by
 default.  On Windows, native Windows threads will be used, which require
-no special libraries. Bowtie binaries that are *not* built with TBB are
-referred to as legacy. Pre-built packages for such builds will include
-"legacy" in the filename e.g. `bowtie-1.2-linux-x86_64.zip`.
+no special libraries.
 
 [MinGW]:    http://www.mingw.org/
 [TDM's MinGW Build]: http://www.tdragon.net/recentgcc/
diff --git a/NEWS b/NEWS
@@ -26,13 +26,17 @@ subscribe to our mailing list:
 Version Release History
 =======================
 
-Version 1.2.1 - Jun 06, 2017
-Please note that Bowtie will be switching to the Artistic 2.0 license in the next release.
+Version 1.2.1 - Jun 11, 2017
+- Please note that Bowtie will be switching to the Artistic 2.0 license in the next release.
+- Pre-build binaries now include statically linked TBB and zlib libraries no longer requiring
+  these libraries to be pre-installed
 
+    * Fixed an issue which caused Bowtie to hang during parallell index
+      building when running an optimized binary
     * Deprecated --refout option.  It will be fully removed in the next
       release
     * Added parallel index building with the bowtie2-build --threads
-      option
+      option (credit to Aidan Reilly - https://github.com/aidanreilly8)
     * Added native support for gzipped read files.  The wrapper
       script is no longer responsible for this, which simplifies the wrapper
       and improves speed and thread scaling.
diff --git a/doc/manual.html b/doc/manual.html
@@ -81,7 +81,7 @@ <h2 id="building-from-source">Building from source</h2>
 <p>Building Bowtie from source requires a GNU-like environment that includes GCC, GNU Make and other basics. It should be possible to build Bowtie on a vanilla Linux or Mac installation. Bowtie can also be built on Windows using <a href="http://www.mingw.org/">MinGW</a>. We recommend <a href="http://www.tdragon.net/recentgcc/">TDM's MinGW Build</a>. You also must also have <a href="http://www.mingw.org/wiki/msys">MSYS</a> installed.</p>
 <p>To build Bowtie, extract the sources, change to the extracted directory, and run GNU <code>make</code> (usually with the command <code>make</code>, but sometimes with <code>gmake</code>) with no arguments. If building with <a href="http://www.mingw.org/">MinGW</a>, run <code>make</code> from the <a href="http://www.mingw.org/wiki/msys">MSYS</a> command line.</p>
 <p>To build Bowtie including support for the <code>bowtie</code> <a href="#bowtie-options-p"><code>-p</code></a> and <code>bowtie-build</code> <a href="#bowtie-build-options-threads"><code>--threads</code></a> multithreading options, we recommend that you first install the <a href="https://www.threadingbuildingblocks.org">Thread Building Blocks library</a>, also known as TBB, the default threading library. TBB is installed by default on many operating systems.</p>
-<p>If TBB is not available, then use the <code>NO_TBB=1</code> option. On Linux or Mac OS X, this requires the pthreads library, which is installed by default. On Windows, native Windows threads will be used, which require no special libraries. Bowtie binaries that are <em>not</em> built with TBB are referred to as legacy. Pre-built packages for such builds will include &quot;legacy&quot; in the filename e.g. <code>bowtie-1.2-linux-x86_64.zip</code>.</p>
+<p>If TBB is not available, then use the <code>NO_TBB=1</code> option. On Linux or Mac OS X, this requires the pthreads library, which is installed by default. On Windows, native Windows threads will be used, which require no special libraries.</p>
 <h1 id="the-bowtie-aligner">The <code>bowtie</code> aligner</h1>
 <p><code>bowtie</code> takes an index and a set of reads as input and outputs a list of alignments. Alignments are selected according to a combination of the <a href="#bowtie-options-v"><code>-v</code></a>/<a href="#bowtie-options-n"><code>-n</code></a>/<a href="#bowtie-options-e"><code>-e</code></a>/<a href="#bowtie-options-l"><code>-l</code></a> options (plus the <a href="#bowtie-options-I"><code>-I</code></a>/<a href="#bowtie-options-X"><code>-X</code></a>/<a href="#bowtie-options-fr"><code>--fr</code></a>/<a href="#bowtie-options-fr"><code>--rf</code></a>/ <a href="#bowtie-options-fr"><code>--ff</code></a> options for paired-end alignment), which define which alignments are legal, and the <a href="#bowtie-options-k"><code>-k</code></a>/<a href="#bowtie-options-a"><code>-a</code></a>/<a href="#bowtie-options-m"><code>-m</code></a>/<a href="#bowtie-options-m"><code>-M</code></a>/<a href="#bowtie-options-best"><code>--best</code></a>/<a href="#bowtie-options-strata"><code>--strata</code></a> options which define which and how many legal alignments should be reported.</p>
 <p>By default, Bowtie enforces an alignment policy similar to <a href="http://maq.sf.net">Maq</a>'s default quality-aware policy (<a href="#bowtie-options-n"><code>-n</code></a> 2 <a href="#bowtie-options-l"><code>-l</code></a> 28 <a href="#bowtie-options-e"><code>-e</code></a> 70). See <a href="#the--n-alignment-mode">the -n alignment mode</a> section of the manual for details about this mode. But Bowtie can also enforce a simpler end-to-end k-difference policy (e.g. with <a href="#bowtie-options-v"><code>-v</code></a> 2). See <a href="#the--v-alignment-mode">the -v alignment mode</a> section of the manual for details about that mode. <a href="#the--n-alignment-mode">The -n alignment mode</a> and <a href="#the--v-alignment-mode">the -v alignment mode</a> are mutually exclusive.</p>
diff --git a/doc/website/manual.ssi b/doc/website/manual.ssi
@@ -72,7 +72,7 @@
 <p>Building Bowtie from source requires a GNU-like environment that includes GCC, GNU Make and other basics. It should be possible to build Bowtie on a vanilla Linux or Mac installation. Bowtie can also be built on Windows using <a href="http://www.mingw.org/">MinGW</a>. We recommend <a href="http://www.tdragon.net/recentgcc/">TDM's MinGW Build</a>. You also must also have <a href="http://www.mingw.org/wiki/msys">MSYS</a> installed.</p>
 <p>To build Bowtie, extract the sources, change to the extracted directory, and run GNU <code>make</code> (usually with the command <code>make</code>, but sometimes with <code>gmake</code>) with no arguments. If building with <a href="http://www.mingw.org/">MinGW</a>, run <code>make</code> from the <a href="http://www.mingw.org/wiki/msys">MSYS</a> command line.</p>
 <p>To build Bowtie including support for the <code>bowtie</code> <a href="#bowtie-options-p"><code>-p</code></a> and <code>bowtie-build</code> <a href="#bowtie-build-options-threads"><code>--threads</code></a> multithreading options, we recommend that you first install the <a href="https://www.threadingbuildingblocks.org">Thread Building Blocks library</a>, also known as TBB, the default threading library. TBB is installed by default on many operating systems.</p>
-<p>If TBB is not available, then use the <code>NO_TBB=1</code> option. On Linux or Mac OS X, this requires the pthreads library, which is installed by default. On Windows, native Windows threads will be used, which require no special libraries. Bowtie binaries that are <em>not</em> built with TBB are referred to as legacy. Pre-built packages for such builds will include &quot;legacy&quot; in the filename e.g. <code>bowtie-1.2-linux-x86_64.zip</code>.</p>
+<p>If TBB is not available, then use the <code>NO_TBB=1</code> option. On Linux or Mac OS X, this requires the pthreads library, which is installed by default. On Windows, native Windows threads will be used, which require no special libraries.</p>
 <h1 id="the-bowtie-aligner">The <code>bowtie</code> aligner</h1>
 <p><code>bowtie</code> takes an index and a set of reads as input and outputs a list of alignments. Alignments are selected according to a combination of the <a href="#bowtie-options-v"><code>-v</code></a>/<a href="#bowtie-options-n"><code>-n</code></a>/<a href="#bowtie-options-e"><code>-e</code></a>/<a href="#bowtie-options-l"><code>-l</code></a> options (plus the <a href="#bowtie-options-I"><code>-I</code></a>/<a href="#bowtie-options-X"><code>-X</code></a>/<a href="#bowtie-options-fr"><code>--fr</code></a>/<a href="#bowtie-options-fr"><code>--rf</code></a>/ <a href="#bowtie-options-fr"><code>--ff</code></a> options for paired-end alignment), which define which alignments are legal, and the <a href="#bowtie-options-k"><code>-k</code></a>/<a href="#bowtie-options-a"><code>-a</code></a>/<a href="#bowtie-options-m"><code>-m</code></a>/<a href="#bowtie-options-m"><code>-M</code></a>/<a href="#bowtie-options-best"><code>--best</code></a>/<a href="#bowtie-options-strata"><code>--strata</code></a> options which define which and how many legal alignments should be reported.</p>
 <p>By default, Bowtie enforces an alignment policy similar to <a href="http://maq.sf.net">Maq</a>'s default quality-aware policy (<a href="#bowtie-options-n"><code>-n</code></a> 2 <a href="#bowtie-options-l"><code>-l</code></a> 28 <a href="#bowtie-options-e"><code>-e</code></a> 70). See <a href="#the--n-alignment-mode">the -n alignment mode</a> section of the manual for details about this mode. But Bowtie can also enforce a simpler end-to-end k-difference policy (e.g. with <a href="#bowtie-options-v"><code>-v</code></a> 2). See <a href="#the--v-alignment-mode">the -v alignment mode</a> section of the manual for details about that mode. <a href="#the--n-alignment-mode">The -n alignment mode</a> and <a href="#the--v-alignment-mode">the -v alignment mode</a> are mutually exclusive.</p>
diff --git a/doc/website/old_news.ssi b/doc/website/old_news.ssi
@@ -1,3 +1,48 @@
+<h2>1.0.0 release - 4/9/13</h2>
+<ul>
+ <li>Finally, a 64-bit Windows binary!</li>
+ <li>Due to general performance improvements spinlocking 
+     is now used by default. The <tt>EXTRA_FLAGS=-DNO_SPINLOCK</tt> may be 
+     used to reverse this during compilation.</li>
+ <li>Fixed some race conditions.</li>
+ <li>CygWin builds now use pthreads library.</li>
+ <li>Changed MinGW to optionally use pthread library on Win32 platforms.</li>
+ <li>Changed the Windows build to use native Windows threads by default.</li>
+ <li>Renamed <tt>COPYING</tt> to <tt>LICENSE</tt> to be more GitHub-friendly.</li>
+ <li>Tokenizer no longer has limit of 10,000 tokens, which was a
+     problem for users trying to index a very large number of FASTA
+     files.</li>
+ <li>Removed references to no-longer-implemented <tt>--cutoff</tt> option for
+     bowtie-build</li>
+</ul>
+
+<h2>0.12.9 release - 12/16/12</h2>
+<ul>
+ <li>Fixed a bug whereby read names would not be truncated at first
+     whitespace character in unmapped or maxed-out SAM records.</li>
+ <li>Fixed errors and warnings when compiling with <tt>clang++</tt>.</li>
+ <li>Fixed most errors and warnings when compiling with recent versions
+     of <tt>g++</tt>, though you may need to add <tt>EXTRA_FLAGS=-Wno-enum-compare</tt>
+     to avoid all warnings.</li>
+</ul>
+
+<h2>0.12.8 release - 5/6/12</h2>
+<ul>
+   <li>Fixed a bug that would sometimes cause an immediate segmentation
+     fault in
+     <tt><a href="manual.shtml#bowtie-options-sam">--sam</a></tt>
+     mode.</li>
+   <li>Fixed <tt>make_galGal3.sh</tt> script to not omit chromosome 25.</li>
+   <li>Removed <tt>-B</tt> option from usage message for <tt>bowtie-build</tt>; that option
+     is not implemented.</li>
+   <li>Fixed issue that could cause Bowtie not to compile when
+     <tt>BOWTIE_PTHREADS</tt> is left undefined and <tt>pthreads.h</tt> is not present.</li>
+   <li>Elaborated documentation for
+     <tt><a href="">-B/--offbase</a></tt> option to indicate that
+     it only affects offsets in the default output mode, not in SAM
+     mode.</li>
+</ul>
+
 <h2><a href="bowtie2">Bowtie 2</a> beta released - 10/16/2011</h2>
 <ul>
   <li><a href="bowtie2">Bowtie 2</a> 2.0.0-beta2 is available now.</li>
diff --git a/doc/website/recent_news.ssi b/doc/website/recent_news.ssi
@@ -1,8 +1,10 @@
-<h2>1.2.1 - 06/06/2017<h2>
-<p>Please note that Bowtie will be switching to the Artistic 2.0 license in the next release.</p>
+<h2>1.2.1 - 06/12/2017<h2>
+<p>Please note that Bowtie will be switching to the Artistic 2.0 license in the next release.<br/>
+Pre-build binaries now include statically linked TBB and zlib libraries no longer requiring</p>
 <ul>
+    <li>Fixed an issue which caused Bowtie to hang during parallell index building when running an optimized binary</li>
     <li>Deprecated <tt>--refout</tt> option.  It will be fully removed in the next release</li>
-    <li>Added parallel index building with the bowtie2-build <tt><a href="manual.shtml#bowtie-build-options-threads">--threads</a></tt> option</li>
+    <li>Added parallel index building with the bowtie2-build <tt><a href="manual.shtml#bowtie-build-options-threads">--threads</a></tt> option (credit to <a href="https://github.com/aidanreilly8">Aidan Reilly</a>)</li>
     <li>Added native support for gzipped read files.  The wrapper script is no longer responsible for this, which simplifies the wrapper and improves speed and thread scaling.</li>
     <li>Added support for interleaved paired-end FASTQ inputs (<tt><a href="manual.shtml#command-line">--interleaved</a></tt>)</li>
     <li>Fixed issue where first character of some read names was omitted from SAM output when using tabbed input formats</li>
@@ -74,47 +76,3 @@
  <li>Bowtie source now lives in a <a href="https://github.com/BenLangmead/bowtie">public GitHub repository</a>.</li>
 </ul>
 
-
-<h2>1.0.0 release - 4/9/13</h2>
-<ul>
- <li>Finally, a 64-bit Windows binary!</li>
- <li>Due to general performance improvements spinlocking 
-     is now used by default. The <tt>EXTRA_FLAGS=-DNO_SPINLOCK</tt> may be 
-     used to reverse this during compilation.</li>
- <li>Fixed some race conditions.</li>
- <li>CygWin builds now use pthreads library.</li>
- <li>Changed MinGW to optionally use pthread library on Win32 platforms.</li>
- <li>Changed the Windows build to use native Windows threads by default.</li>
- <li>Renamed <tt>COPYING</tt> to <tt>LICENSE</tt> to be more GitHub-friendly.</li>
- <li>Tokenizer no longer has limit of 10,000 tokens, which was a
-     problem for users trying to index a very large number of FASTA
-     files.</li>
- <li>Removed references to no-longer-implemented <tt>--cutoff</tt> option for
-     bowtie-build</li>
-</ul>
-<h2>0.12.9 release - 12/16/12</h2>
-<ul>
- <li>Fixed a bug whereby read names would not be truncated at first
-     whitespace character in unmapped or maxed-out SAM records.</li>
- <li>Fixed errors and warnings when compiling with <tt>clang++</tt>.</li>
- <li>Fixed most errors and warnings when compiling with recent versions
-     of <tt>g++</tt>, though you may need to add <tt>EXTRA_FLAGS=-Wno-enum-compare</tt>
-     to avoid all warnings.</li>
-</ul>
-
-<h2>0.12.8 release - 5/6/12</h2>
-<ul>
-   <li>Fixed a bug that would sometimes cause an immediate segmentation
-     fault in
-     <tt><a href="manual.shtml#bowtie-options-sam">--sam</a></tt>
-     mode.</li>
-   <li>Fixed <tt>make_galGal3.sh</tt> script to not omit chromosome 25.</li>
-   <li>Removed <tt>-B</tt> option from usage message for <tt>bowtie-build</tt>; that option
-     is not implemented.</li>
-   <li>Fixed issue that could cause Bowtie not to compile when
-     <tt>BOWTIE_PTHREADS</tt> is left undefined and <tt>pthreads.h</tt> is not present.</li>
-   <li>Elaborated documentation for
-     <tt><a href="">-B/--offbase</a></tt> option to indicate that
-     it only affects offsets in the default output mode, not in SAM
-     mode.</li>
-</ul>
diff --git a/doc/website/rhsidebar.ssi b/doc/website/rhsidebar.ssi
@@ -21,7 +21,7 @@
             <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2">Bowtie 1.2.1</a>
           </td>
           <td align="right">
-            06/06/17
+            06/12/17
           </td>
         </tr>
         <tr>