mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-12-24 21:38:07 -05:00
gnu: sambamba: Update to 0.6.7-10-g223fa20.
* gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git. [arguments]: Disable parallel build; rename build phase "place-biod" to "place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase "unbundle-prerequisites". [native-inputs]: Add python2-minimal; update biod sources; add undead sources.
This commit is contained in:
parent
262ee8eae2
commit
482959ffa4
1 changed files with 36 additions and 15 deletions
|
@ -10999,34 +10999,41 @@ (define htslib-for-sambamba
|
|||
(define-public sambamba
|
||||
(package
|
||||
(name "sambamba")
|
||||
(version "0.6.5")
|
||||
(version "0.6.7-10-g223fa20")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/lomereiter/sambamba/"
|
||||
"archive/v" version ".tar.gz"))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/lomereiter/sambamba.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy"))))
|
||||
"1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; there is no test target
|
||||
#:make-flags
|
||||
'("D_COMPILER=ldc2"
|
||||
;; Override "--compiler" flag only.
|
||||
"D_FLAGS=--compiler=ldc2 -IBioD -g -d"
|
||||
"sambamba-ldmd2-64")
|
||||
`(#:tests? #f ; there is no test target
|
||||
#:parallel-build? #f ; not supported
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure)
|
||||
(add-after 'unpack 'place-biod
|
||||
(add-after 'unpack 'fix-ldc-version
|
||||
(lambda _
|
||||
(substitute* "gen_ldc_version_info.py"
|
||||
(("/usr/bin/env.*") (which "python")))
|
||||
(substitute* "Makefile"
|
||||
(("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
|
||||
#t))
|
||||
(add-after 'unpack 'place-biod-and-undead
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(copy-recursively (assoc-ref inputs "biod") "BioD")
|
||||
(copy-recursively (assoc-ref inputs "undead") "undeaD")
|
||||
#t))
|
||||
(add-after 'unpack 'unbundle-prerequisites
|
||||
(lambda _
|
||||
(substitute* "Makefile"
|
||||
(("htslib/libhts.a lz4/lib/liblz4.a")
|
||||
"-L-lhts -L-llz4")
|
||||
((" htslib-static lz4-static") ""))
|
||||
#t))
|
||||
(replace 'install
|
||||
|
@ -11039,8 +11046,9 @@ (define-public sambamba
|
|||
(native-inputs
|
||||
`(("ldc" ,ldc)
|
||||
("rdmd" ,rdmd)
|
||||
("python" ,python2-minimal)
|
||||
("biod"
|
||||
,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))
|
||||
,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
|
@ -11051,7 +11059,20 @@ (define-public sambamba
|
|||
"-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))))
|
||||
"1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")))))
|
||||
("undead"
|
||||
,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89"))
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/dlang/undeaD.git")
|
||||
(commit commit)))
|
||||
(file-name (string-append "undead-"
|
||||
(string-take commit 9)
|
||||
"-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))))))
|
||||
(inputs
|
||||
`(("lz4" ,lz4)
|
||||
("htslib" ,htslib-for-sambamba)))
|
||||
|
|
Loading…
Reference in a new issue