http://qa.lifesciencedb.jp/questions/880/tophat%E3%81%A8cufflinks%E3%81%8C%E3%82%A4%E3%83%B3%E3%82%B9%E3%83%88%E3%83%BC%E3%83%AB%E3%81%A7%E3%81%8D%E3%81%AA%E3%81%84<p>こんにちは</p> <p>Tophatとcufflinksがインストールできません。 レベルは初心者なので、わけもわからずやっている状態ですが、 DRY解析教本を読みながらコツコツやっています。 いろいろやってみましたが、どうにもなりませんでした。</p> <p>$brew install tophat Error: No available formula with the name "tophat" ==&gt; Searching for a previously deleted formula (in the last month)... Error: No previously deleted formula found. ==&gt; Searching for similarly named formulae... Error: No similarly named formulae found. ==&gt; Searching taps... ==&gt; Searching taps on GitHub... Error: No formulae found in taps.</p> <p>$ brew install cufflinks Error: No available formula with the name "cufflinks" ==&gt; Searching for a previously deleted formula (in the last month)... Error: No previously deleted formula found. ==&gt; Searching for similarly named formulae... Error: No similarly named formulae found. ==&gt; Searching taps... ==&gt; Searching taps on GitHub... Error: No formulae found in taps.</p> <p>$brew tap brewsci/science ==&gt; Tapping brewsci/science Cloning into '/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science'... remote: Counting objects: 468, done. remote: Compressing objects: 100% (465/465), done. remote: Total 468 (delta 1), reused 153 (delta 1), pack-reused 0 Receiving objects: 100% (468/468), 429.98 KiB | 305.00 KiB/s, done. Resolving deltas: 100% (1/1), done. Error: Invalid formula: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/ome-common.rb uninitialized constant #&lt;class:0x00000001032840c0&gt;::MinimumMacOSRequirement Did you mean? MaximumMacOSRequirement Error: Invalid formula: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/ome-files.rb uninitialized constant #&lt;class:0x00000001023892a0&gt;::MinimumMacOSRequirement Did you mean? MaximumMacOSRequirement Error: Invalid formula: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/ome-xml.rb uninitialized constant #&lt;class:0x00000001022e3a08&gt;::MinimumMacOSRequirement Did you mean? MaximumMacOSRequirement Error: Invalid formula: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/osgearth.rb uninitialized constant #&lt;class:0x0000000103086fe8&gt;::MinimumMacOSRequirement Did you mean? MaximumMacOSRequirement Error: Cannot tap brewsci/science: invalid syntax in tap!</p> <pre><code>$ brew config HOMEBREW_VERSION: 1.7.0 ORIGIN: https://github.com/Homebrew/brew HEAD: 7e8fb9a0f8ab5e841763ec6c7fefa72a8462b594 Last commit: 3 days ago Core tap ORIGIN: https://github.com/Homebrew/homebrew-core Core tap HEAD: ea3fec61c268ccbbe4172a2f1cbfd08760025cf0 Core tap last commit: 51 minutes ago HOMEBREW_PREFIX: /usr/local CPU: quad-core 64-bit skylake Homebrew Ruby: 2.3.7 =&gt; /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.7/bin/ruby Clang: 9.1 build 902 Git: 2.18.0 =&gt; /usr/local/bin/git Curl: 7.54.0 =&gt; /usr/bin/curl Java: 10.0.2, 1.8.0_121 macOS: 10.13.6-x86_64 CLT: 9.4.1.0.1.1528165917 Xcode: 9.4.1 XQuartz: 2.7.11 =&gt; /opt/X11 $ brew list bam eigen ilmbase numpy samtools bedtools fastqc jpeg opencv sqlite blast ffmpeg lame openexr stringtie boost gdbm libidn2 openssl tbb bowtie gettext libpng python wget bowtie2 git libtiff python@2 x264 bwa hisat2 libunistring readline xvid curl htslib lmdb rmtrash xz </code></pre> <p>brewのupdate, upgrade, doctorはしました。問題なかったです。 問題を解決するにあたって何を質問したら良いかもわかっていない状態です。</p> <p>どうぞよろしくお願いします。</p>jaThu, 19 Jul 2018 16:06:11 +0900http://qa.lifesciencedb.jp/questions/880/tophat%E3%81%A8cufflinks%E3%81%8C%E3%82%A4%E3%83%B3%E3%82%B9%E3%83%88%E3%83%BC%E3%83%AB%E3%81%A7%E3%81%8D%E3%81%AA%E3%81%84/881<p>あなたがペーストされたエラーメッセージ</p> <blockquote> <p>No available formula with the name "tophat" </p> </blockquote> <p>にある通り、tophatという名前のフォーミュラが利用できない、ということです。あなたの設定されたHomebrewでは、Tophatが利用できないようです。</p> <p>TopHatのウェブサイト https://ccb.jhu.edu/software/tophat/index.shtml にも</p> <blockquote> <p>Please note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e. spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way.</p> </blockquote> <p>とあるように、別のソフトウェアを利用された方が良いと思います。</p>hubThu, 19 Jul 2018 16:06:11 +0900http://qa.lifesciencedb.jp/questions/880/tophat%E3%81%A8cufflinks%E3%81%8C%E3%82%A4%E3%83%B3%E3%82%B9%E3%83%88%E3%83%BC%E3%83%AB%E3%81%A7%E3%81%8D%E3%81%AA%E3%81%84/881