diff options
| author | pjotrp | 2017-02-24 16:03:16 +0000 |
|---|---|---|
| committer | pjotrp | 2017-02-24 16:03:16 +0000 |
| commit | 2bef484b005f1fd18173ecde3da34bf9e67587f2 (patch) | |
| tree | 7e035889d7e0090c6f29c79f12dd0ce9c5332f00 | |
| parent | ac594bf9c0e2a95e9cd96a7e1d68c39a2ae7f82e (diff) | |
| download | guix-bioinformatics-2bef484b005f1fd18173ecde3da34bf9e67587f2.tar.gz | |
sambamba: now links in samtools and bcftools
| -rw-r--r-- | gn/packages/sambamba.scm | 26 |
1 files changed, 18 insertions, 8 deletions
diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm index 46cf0e7..221aeb6 100644 --- a/gn/packages/sambamba.scm +++ b/gn/packages/sambamba.scm @@ -8,6 +8,7 @@ #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (gnu packages base) + #:use-module (gnu packages bioinformatics) ; for samtools in sambamba #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages perl) @@ -18,10 +19,10 @@ #:use-module (srfi srfi-1)) (define-public sambamba - (let ((commit "6ae174bcb50d3a8f1b6dd10de9c68bbc4770e56a")) + (let ((commit "54778aea4c054702d34740d229bbf03e5b907482")) (package (name "sambamba") - (version (string-append "0.6.6-pre3-" (string-take commit 7))) + (version (string-append "0.6.6-pre4-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -30,19 +31,23 @@ (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1m26i8icllclynqia4yi2mp7zfs2zajllva6bzxn188fhlyjwzqr")))) + "131311h0ccz3r74yvw20f96pc86s760cvvnzgxin0kks7wgixmmz")))) (build-system gnu-build-system) (outputs '("out" "debug")) + (inputs + `(("samtools" ,samtools) ; for pileup + ("bcftools" ,bcftools) ; for pileup + ("lz4" ,lz4) + ("zlib" ,zlib) + )) (native-inputs `(("ldc" ,ldc) - ("lz4" ,lz4) ("shunit2" ,shunit2) - ("zlib" ,zlib) ("coreutils" ,coreutils) ; for env - ("perl" ,perl) ; Needed for htslib - ("ruby" ,ruby) ; Needed for htslib - ("python" ,python-2) ; Needed for htslib + ("perl" ,perl) ; Needed for building htslib + ("ruby" ,ruby) ; Needed for building htslib + ("python" ,python-2) ; Needed for building htslib and sambamba ("gcc" ,gcc) ("which" ,which) ("htslib-src" @@ -78,6 +83,11 @@ (modify-phases %standard-phases (delete 'configure) (delete 'check) + (add-after 'unpack 'patch-pileup-d + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "sambamba/pileup.d" + (("string samtoolsBin = null;") (string-append "string samtoolsBin = \"" (which "samtools") "\";")) + (("string bcftoolsBin = null;") (string-append "string bcftoolsBin = \"" (which "bcftools") "\";"))))) (add-after 'unpack 'unpack-htslib-sources (lambda* (#:key inputs #:allow-other-keys) ;; The current build compiles htslib statically into the |