From 946fd9be16138a9c038813d9f3d438d90d55bacd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 11 Jan 2022 14:18:06 +0100
Subject: gnu: stringtie: Update to 2.2.0.

* gnu/packages/bioinformatics.scm (stringtie): Update to 2.2.0.
[source]: Simplify snippet.
[arguments]: Add make-flags; update build phases.
[inputs]: Remove samtools-0.1; add bzip2, htslib-for-stringtie, and
libdeflate.
[license]: Change to Expat license.
---
 gnu/packages/bioinformatics.scm | 40 +++++++++++++++-------------------------
 1 file changed, 15 insertions(+), 25 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2b9a27d44b..169d0c4dd1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7380,22 +7380,25 @@ against local background noises.")
 (define-public stringtie
   (package
     (name "stringtie")
-    (version "1.2.1")
+    (version "2.2.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
                                   "stringtie-" version ".tar.gz"))
               (sha256
                (base32
-                "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
+                "08w3ish4y9kf9acp7k38iwi8ixa6j51m6qyf0vvfj7yz78a3ai3x"))
+              ;; This package bundles an annoying amount of third party source
+              ;; code.
               (modules '((guix build utils)))
               (snippet
-               '(begin
-                  (delete-file-recursively "samtools-0.1.18")
-                  #t))))
+               '(delete-file-recursively "htslib"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no test suite
+       #:make-flags '("LIBDEFLATE=-ldeflate"
+                      "LIBBZ2=-lbz2"
+                      "LIBLZMA=-llzma")
        #:phases
        (modify-phases %standard-phases
          ;; no configure script
@@ -7403,27 +7406,14 @@ against local background noises.")
          (add-before 'build 'use-system-samtools
            (lambda _
              (substitute* "Makefile"
-               (("stringtie: \\$\\{BAM\\}/libbam\\.a")
-                "stringtie: "))
-             (substitute* '("gclib/GBam.h"
-                            "gclib/GBam.cpp")
-               (("#include \"(bam|sam|kstring).h\"" _ header)
-                (string-append "#include <samtools/" header ".h>")))
-             #t))
-         (add-after 'unpack 'remove-duplicate-typedef
-           (lambda _
-             ;; This typedef conflicts with the typedef in
-             ;; glibc-2.25/include/bits/types.h
-             (substitute* "gclib/GThreads.h"
-               (("typedef long long __intmax_t;") ""))
-             #t))
+               ((" -lm") " -lm -lhts")
+               ((" \\$\\{HTSLIB\\}/libhts\\.a") " "))))
          (replace 'install
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
-              (install-file "stringtie" bin)
-              #t))))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+               (install-file "stringtie" bin)))))))
     (inputs
-     (list samtools-0.1 zlib))
+     (list bzip2 htslib-for-stringtie libdeflate zlib))
     (home-page "http://ccb.jhu.edu/software/stringtie/")
     (synopsis "Transcript assembly and quantification for RNA-Seq data")
     (description
@@ -7436,7 +7426,7 @@ other transcript assemblers, but also alignments of longer sequences that have
 been assembled from those reads.  To identify differentially expressed genes
 between experiments, StringTie's output can be processed either by the
 Cuffdiff or Ballgown programs.")
-    (license license:artistic2.0)))
+    (license license:expat)))
 
 (define-public taxtastic
   (package
-- 
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