bioinformatics: Add booster.

* guix-science/packages/bioinformatics.scm (booster): New variable.

1 files changed, 63 insertions, 0 deletions

diff --git a/guix-science/packages/bioinformatics.scm b/guix-science/packages/bioinformatics.scm
index c3f7654..fe6dd01 100644
--- a/guix-science/packages/bioinformatics.scm
+++ b/guix-science/packages/bioinformatics.scm
@@ -2388,6 +2388,69 @@ array-based and next-generation sequence data, and genomic
 annotations.")
    (license license:expat)))
 
+(define-public booster
+  ;; Use latest upstream commit, which fixes a segfault issue.
+  (let ((commit "b9eee3213b6b75a9b066a82ec0558817f898df1b")
+        (revision "0")
+        (version "0.1.2"))
+    (package
+      (name "booster")
+      (version (git-version version revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/evolbioinfo/booster")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1k5n8nqga68q951zd6lnjinpb1rairny5qpvmphhq27gzcg7r1zk"))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'fix-install-path
+              ;; Replace default install path, which is set to $HOME/bin.
+              (lambda _
+                (substitute* "src/Makefile"
+                  (("INSTALL_PATH=.*")
+                   (string-append "INSTALL_PATH="
+                                  #$output "/bin" "\n")))))
+            (add-after 'unpack 'set-version
+              ;; Replace default version, which relies on git.
+              (lambda _
+                (substitute* "src/Makefile"
+                  (("GIT_VERSION :=.*")
+                   (string-append "GIT_VERSION := "
+                                  #$version)))))
+            (delete 'configure)
+            (add-before 'build 'change-source-directory
+              (lambda _
+                (chdir "src")))
+            (delete 'check)
+            (add-after 'install 'check
+              (lambda* (#:key tests? #:allow-other-keys)
+                (when tests?
+                  (let ((booster (string-append #$output "/bin/booster")))
+                    (with-directory-excursion "../examples"
+                      (invoke "gunzip" "ref.nw.gz")
+                      (invoke "gunzip" "boot.nw.gz")
+                      (invoke booster
+                              "-i"
+                              "ref.nw"
+                              "-b"
+                              "boot.nw"
+                              "-i"
+                              "TBE.nw")))))))))
+      (native-inputs (list gzip))
+      (home-page "http://booster.c3bi.pasteur.fr/")
+      (synopsis "BOOtstrap Support by TransfER")
+      (description
+       "This package provides a new way of computing bootstrap supports in large
+phylogenies.")
+      (license license:gpl2))))
+
 (define-public cmaple
   (package
     (name "cmaple")