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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
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