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/bioinformatics.scm')

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 @@ (define-public subread
 (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 @@ (define-public stringtie
          (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 @@ (define-public stringtie
 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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