Instructions for releasing a new version of Bowtie
==================================================

Author: BTL
Date: 12/15/2012

1. Check that the code compiles with no issues, including with very recent
   versions of g++, and with clang on a Mac.
   - To compile with clang on the Mac: "make clean ; make CPP=clang++ allall"
   - Note: B/c of some of the SeqAn code, I have never been able to get bowtie
     to compile without warnings on very recent versions of g++.  I get a
     bunch of warning that can be suppressed with -Wno-enum-compare, but that
     flag isn't recognized by all g++ versions and could itself cause an error
     in versions where it's not supported.

2. Check that all the simple tests pass:
   perl scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build

3. Check that random tests pass:
   sh scripts/test/random_bowtie_tests_p.sh

4. Check that performance, sensitivity and accuracy are not substantially
   changed.  (Need infrastructure for this!)

5. Update VERSION with new version number

6. Update NEWS and doc/website/recent_news.ssi
   - In both cases, add a section at the top describing the new release, along
     with bullet points describing improvements and changes in that release.
   - For recent_news.ssi, hyperlink concepts or command-line options so that
     they point into the manual.
   - Make sure to update the version numbers mentioned in the paragraph at the
     beginning of the NEWS file.
   - Potentially move an entry or two from the bottom of
     doc/website/recent_news.ssi to the top of doc/website/old_news.ssi if it
	 gets too long.

7. Update the manual
   - In Bowtie root directory, do "make doc" (you'll have to have 'pandoc'
     installed).  The output will be stored both in MANUAL and doc/manual.html.
   - In doc/manual.html, highlight and copy everything from <div id="TOC"> down
     to but not including </body>.  Then paste it in the corresponding part of
	 doc/website/manual.ssi.
   - Update the version number at the top of doc/website/manual.ssi.

8. Upload updated webpages
   - In doc/website directory, do "sh push.sh"

9. Make source archive: "make bowtie-src.zip"

10. Make Mac OS X 32-bit and 64-bit binaries.
   - On a computer with Mac OS X 10.6, run "make BITS=32 bowtie-bin.zip".  Then
     rename and upload.
   - On a computer with Mac OS X 10.6, run "make BITS=64 bowtie-bin.zip".  Then
     rename and upload.

11. Make Linux 32-bit and 64-bit binaries.
   - On a Linux machine, run "make BITS=32 bowtie-bin.zip".  Then rename and
     upload.
   - On a Linux machine, run "make BITS=64 bowtie-bin.zip".  Then rename and
     upload.

X. Make an SVN tag for the new version
