diff --git a/MANUAL b/MANUAL index 41f3a83..e3e1860 100644 --- 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 index 651505c..44a6272 100644 --- 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 index e85e2eb..884111d 100644 --- 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 index 0ed9adc..d8cd85b 100644 --- a/doc/manual.html +++ b/doc/manual.html @@ -81,7 +81,7 @@

Building from source

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 MinGW. We recommend TDM's MinGW Build. You also must also have MSYS installed.

To build Bowtie, extract the sources, change to the extracted directory, and run GNU make (usually with the command make, but sometimes with gmake) with no arguments. If building with MinGW, run make from the MSYS command line.

To build Bowtie including support for the bowtie -p and bowtie-build --threads multithreading options, we recommend that you first install the Thread Building Blocks library, also known as TBB, the default threading library. TBB is installed by default on many operating 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.

+

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.

The bowtie aligner

bowtie 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 -v/-n/-e/-l options (plus the -I/-X/--fr/--rf/ --ff options for paired-end alignment), which define which alignments are legal, and the -k/-a/-m/-M/--best/--strata options which define which and how many legal alignments should be reported.

By default, Bowtie enforces an alignment policy similar to Maq's default quality-aware policy (-n 2 -l 28 -e 70). See the -n alignment mode 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 -v 2). See the -v alignment mode section of the manual for details about that mode. The -n alignment mode and the -v alignment mode are mutually exclusive.

diff --git a/doc/website/manual.ssi b/doc/website/manual.ssi index 92a1ef9..ec2e19c 100644 --- a/doc/website/manual.ssi +++ b/doc/website/manual.ssi @@ -72,7 +72,7 @@

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 MinGW. We recommend TDM's MinGW Build. You also must also have MSYS installed.

To build Bowtie, extract the sources, change to the extracted directory, and run GNU make (usually with the command make, but sometimes with gmake) with no arguments. If building with MinGW, run make from the MSYS command line.

To build Bowtie including support for the bowtie -p and bowtie-build --threads multithreading options, we recommend that you first install the Thread Building Blocks library, also known as TBB, the default threading library. TBB is installed by default on many operating 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.

+

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.

The bowtie aligner

bowtie 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 -v/-n/-e/-l options (plus the -I/-X/--fr/--rf/ --ff options for paired-end alignment), which define which alignments are legal, and the -k/-a/-m/-M/--best/--strata options which define which and how many legal alignments should be reported.

By default, Bowtie enforces an alignment policy similar to Maq's default quality-aware policy (-n 2 -l 28 -e 70). See the -n alignment mode 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 -v 2). See the -v alignment mode section of the manual for details about that mode. The -n alignment mode and the -v alignment mode are mutually exclusive.

diff --git a/doc/website/old_news.ssi b/doc/website/old_news.ssi index 199a836..119cc99 100644 --- a/doc/website/old_news.ssi +++ b/doc/website/old_news.ssi @@ -1,3 +1,48 @@ +

1.0.0 release - 4/9/13

+ + +

0.12.9 release - 12/16/12

+ + +

0.12.8 release - 5/6/12

+ +

Bowtie 2 beta released - 10/16/2011