Subject: [bug#55424] [PATCH 023/602] gnu: Remove bamm.

From: Maxim Cournoyer <[email-masked]>
Date: Sun, 15 May 2022 00:36:50 -0400

* gnu/packages/bioinformatics.scm (bamm): Delete variable.
---
 gnu/packages/bioinformatics.scm | 79 ---------------------------------
 1 file changed, 79 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9d4fcbb188..5f637fe29a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -210,85 +210,6 @@ (define-public aragorn
 structure of the predicted RNA.")
     (license license:gpl2)))
 
-(define-public bamm
-  (package
-    (name "bamm")
-    (version "1.7.3")
-    (source (origin
-              (method git-fetch)
-              ;; BamM is not available on pypi.
-              (uri (git-reference
-                    (url "https://github.com/Ecogenomics/BamM")
-                    (commit version)
-                    (recursive? #t)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5"))
-              (modules '((guix build utils)))
-              (snippet
-               `(begin
-                  ;; Delete bundled htslib.
-                  (delete-file-recursively "c/htslib-1.3.1")))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2 ; BamM is Python 2 only.
-       ;; Do not use bundled libhts.  Do use the bundled libcfu because it has
-       ;; been modified from its original form.
-       #:configure-flags
-       ,#~(let ((htslib #$(this-package-input "htslib")))
-            (list "--with-libhts-lib" (string-append htslib "/lib")
-                  "--with-libhts-inc" (string-append htslib "/include/htslib")))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (with-directory-excursion "c"
-               (let ((sh (which "sh")))
-                 (for-each make-file-writable (find-files "." ".*"))
-                 ;; Use autogen so that 'configure' works.
-                 (substitute* "autogen.sh" (("/bin/sh") sh))
-                 (setenv "CONFIG_SHELL" sh)
-                 (invoke "./autogen.sh")))))
-         (delete 'build)                ;the build loops otherwise
-         (replace 'check
-           (lambda _
-             ;; There are 2 errors printed, but they are safe to ignore:
-             ;; 1) [E::hts_open_format] fail to open file ...
-             ;; 2) samtools view: failed to open ...
-             (invoke "nosetests")))
-         (add-after 'install 'wrap-executable
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((out  (assoc-ref outputs "out"))
-                    (path (getenv "PATH"))
-                    (pythonpath (getenv "GUIX_PYTHONPATH")))
-               (wrap-program (string-append out "/bin/bamm")
-                 `("PATH" ":" prefix (,path))
-                 `("GUIX_PYTHONPATH" ":" prefix (,pythonpath)))))))))
-    (native-inputs
-     (list autoconf
-           automake
-           libtool
-           zlib
-           python2-nose
-           python2-pysam))
-    (inputs
-     (list htslib-1.3 ; At least one test fails on htslib-1.4+.
-           samtools
-           bwa
-           grep
-           sed
-           coreutils))
-    (propagated-inputs
-     (list python2-numpy))
-    (home-page "https://ecogenomics.github.io/BamM/")
-    (synopsis "Metagenomics-focused BAM file manipulator")
-    (description
-     "BamM is a C library, wrapped in python, to efficiently generate and
-parse BAM files, specifically for the analysis of metagenomic data.  For
-instance, it implements several methods to assess contig-wise read coverage.")
-    (license license:lgpl3+)))
-
 (define-public bamtools
   (package
     (name "bamtools")
-- 
2.36.0