guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 788513d4e0d93deeee1d07bf361a40a0180ad1ea
Author: Andreas Enge <[email protected]>
AuthorDate: Thu Oct 23 21:08:49 2025 +0200
gnu: Remove samtools-1.2.
* gnu/packages/bioinformatics.scm (samtools-1.2): Delete variable.
Change-Id: I38effe41c32349b5b72754da07fe6696d2f21669
---
gnu/packages/bioinformatics.scm | 57 -----------------------------------------
1 file changed, 57 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6d1e58334f..fe1bf8807a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11318,63 +11318,6 @@ viewer.")
(inputs
(list htslib-1.10 ncurses perl python zlib))))
-(define-public samtools-1.2
- (package (inherit samtools)
- (name "samtools")
- (version "1.2")
- (source
- (origin
- (method url-fetch)
- (uri
- (string-append "mirror://sourceforge/samtools/samtools/"
- version "/samtools-" version ".tar.bz2"))
- (sha256
- (base32
- "1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2"))
- (modules '((guix build utils)))
- (snippet
- ;; Delete bundled htslib and Windows binaries
- '(for-each delete-file-recursively (list "win32" "htslib-1.2.1")))))
- (arguments
- `(#:make-flags
- ,#~(list (string-append "prefix=" #$output)
- (string-append "BGZIP="
- #$(this-package-input "htslib")
- "/bin/bgzip")
- (string-append "HTSLIB="
- #$(this-package-input "htslib")
- "/lib/libhts.so")
- (string-append "HTSDIR="
- #$(this-package-input "htslib")
- "/include"))
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-makefile-curses
- (lambda _
- (substitute* "Makefile"
- (("-lcurses") "-lncurses")
- (("include \\$\\(HTSDIR.*") ""))))
- (add-after 'unpack 'patch-tests
- (lambda _
- (substitute* "test/test.pl"
- ;; The test script calls out to /bin/bash
- (("/bin/bash") (which "bash"))
- ;; There are two failing tests upstream relating to the "stats"
- ;; subcommand in test_usage_subcommand ("did not have Usage"
- ;; and "usage did not mention samtools stats"), so we disable
- ;; them.
- (("(test_usage_subcommand\\(.*\\);)" cmd)
- (string-append "unless ($subcommand eq 'stats') {" cmd "};")))
- ;; This test fails because the grep output doesn't look as
- ;; expected; it is correct, though.
- (substitute* "test/mpileup/mpileup.reg"
- (("P 52.out.*") ""))))
- (delete 'configure))))
- (native-inputs
- (list grep gawk pkg-config))
- (inputs
- (list htslib-for-samtools-1.2 ncurses perl python zlib))))
-
(define-public samtools-0.1
;; This is the most recent version of the 0.1 line of samtools. The input
;; and output formats differ greatly from that used and produced by samtools
