seqan 2.4.0(new formula) #549
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Formula/seqan.rb
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| desc "C++ library of sequence algorithms and data structures" | ||
| homepage "https://www.seqan.de/" | ||
| # doi "10.1186/1471-2105-9-11" | ||
| # tag "bioinformatics" |
Formula/seqan.rb
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| # doi "10.1186/1471-2105-9-11" | ||
| # tag "bioinformatics" | ||
| # doi "https://doi.org/10.1016/j.jbiotec.2017.07.017" | ||
| # tag "Journal of Biotechnology" |
Formula/seqan.rb
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| class Seqan < Formula | ||
| desc "C++ library of sequence algorithms and data structures" | ||
| homepage "https://www.seqan.de/" | ||
| # doi "10.1186/1471-2105-9-11" |
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Please use brew tap brewsci/base and then…
$ brew cite --ruby 10.1186/1471-2105-9-11
# cite D_ring_2008: "https://doi.org/10.1186/1471-2105-9-11"| # doi "10.1186/1471-2105-9-11" | |
| # cite D_ring_2008: "https://doi.org/10.1186/1471-2105-9-11" |
Formula/seqan.rb
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| homepage "https://www.seqan.de/" | ||
| # doi "10.1186/1471-2105-9-11" | ||
| # tag "bioinformatics" | ||
| # doi "https://doi.org/10.1016/j.jbiotec.2017.07.017" |
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Same as above use brew cite --ruby 10.1016/j.jbiotec.2017.07.017
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Please move these # cite comments below head.
Formula/seqan.rb
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| # tag "bioinformatics" | ||
| # doi "https://doi.org/10.1016/j.jbiotec.2017.07.017" | ||
| # tag "Journal of Biotechnology" | ||
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Formula/seqan.rb
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| head "https://github.com/seqan/seqan.git" | ||
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| # seqan-library installs only header files. | ||
| bottle :unneeded |
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Please remove these three lines 12-14.
Formula/seqan.rb
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| test do | ||
| # seqan-library installs only header files, so we test if version.h exists and has the right version number. | ||
| system "test -e filename", include/"seqan/version.h" |
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| system "test -e filename", include/"seqan/version.h" | |
| assert_predicate include/"seqan/version.h", :exist? |
Formula/seqan.rb
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| test do | ||
| # seqan-library installs only header files, so we test if version.h exists and has the right version number. | ||
| system "test -e filename", include/"seqan/version.h" | ||
| system "grep \"SEQAN_VERSION_MAJOR 2\"", include/"seqan/version.h" |
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Please do not include the version number in the test.
| system "grep \"SEQAN_VERSION_MAJOR 2\"", include/"seqan/version.h" | |
| assert_match "SEQAN_VERSION_MAJOR", include/"seqan/version.h" |
Formula/seqan.rb
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| system "test -e filename", include/"seqan/version.h" | ||
| system "grep \"SEQAN_VERSION_MAJOR 2\"", include/"seqan/version.h" | ||
| system "grep \"SEQAN_VERSION_MINOR 4\"", include/"seqan/version.h" | ||
| system "grep \"SEQAN_VERSION_PATCH 0\"", include/"seqan/version.h" |
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Please delete these two lines 32 and 33.
Try… rm -rf /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby
rm -rf /usr/local/Homebrew/Library/Homebrew/vendor/bundle
brew style hello |
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@sjackman I did a complete fresh install of homebrew and I could get audit to work this way. I also adapted the test as you suggested, though I needed to read in the version file, otherwise the assertion failed as the pattern was matched against the path name and not the file content. Please let me know, if this needs to be revised some how. I am very new to ruby 😅. And many thanks for the quick response and review. 👍 |
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Merged. Thank you for contribution to Brewsci/bio, @rrahn ! 🏆 |
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@sjackman you are welcome and many thanks for the quick support. |
brew install --build-from-source FORMULA, whereFORMULAis the name of the formula you're submitting?brew audit --strict FORMULA(after doingbrew install FORMULA)?Note
Currently brew audit fails: the related issue is documented here: Homebrew/brew#5561; all suggested solutions did not work for me, but I copied the formula from the science repo and made small adaptions. Any suggestions on getting audit to work is very appreciated.