diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/sambamba.scm | 46 |
1 files changed, 26 insertions, 20 deletions
diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm index 261e325..c2759fa 100644 --- a/gn/packages/sambamba.scm +++ b/gn/packages/sambamba.scm @@ -19,10 +19,10 @@ #:use-module (srfi srfi-1)) (define-public sambamba - (let ((commit "52ab1eff7070cd3dafad94a15c9fd6e243a45a4d")) + (let ((commit "7cff06533b539a99b4e0db681fb573214d63aae2")) (package (name "sambamba") - (version (string-append "0.6.6-" (string-take commit 7))) + (version (string-append "0.6.7-pre1-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -31,7 +31,7 @@ (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "16nfvmipa1gj7f8c9lqhh5yffdmaic1pzcrm9281dqwywl9w8hsg")))) + "11k2xqgmbvxwki569439kvzf2b0cqy2x21kbgjijwvpqk9j8czx4")))) (build-system gnu-build-system) (outputs '("out" ; disable all checks for speed "debug")) @@ -52,37 +52,35 @@ ("which" ,which) ("htslib-src" ,(origin - (method url-fetch) - (uri "https://github.com/lomereiter/htslib/archive/2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5.tar.gz") - ;;(uri "https://github.com/samtools/htslib/archive/1.3.tar.gz") - (file-name "htslib-0.2.0-rc10-271-g2f3c3ea-dirty.tar.gz") + (method git-fetch) + (uri (git-reference + (url "https://github.com/pjotrp/htslib.git") + (commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))) + (file-name (string-append "htslib-src-" (string-take commit 7) "-checkout")) (sha256 - (base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w")))) - ;;(base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9")) - ;;(patches (list (search-patch "htslib-add-cram_to_bam.patch"))))) + (base32 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) ("biod-src" ,(origin (method git-fetch) (uri (git-reference - (url "https://github.com/pjotrp/BioD.git") - (commit "b7f1db860d212ee5fb6f9adfb36c6e783aaeb6f5"))) + (url "https://github.com/biod/BioD.git") + (commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))) (file-name (string-append "biod-src-" (string-take commit 7) "-checkout")) (sha256 - (base32 "01xkdjdn9lb2b4b5ykzhnrk2rjikagav8b3fyac3zafcfq600cr4")))) + (base32 "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")))) ("dlang-undeaD-src" ,(origin (method git-fetch) (uri (git-reference (url "https://github.com/dlang/undeaD.git") - (commit "610234f159132f91046d4fb893889fb8ee14cd2f"))) + (commit "92803d25c88657e945511f0976a0c79d8da46e89"))) (file-name (string-append "dlang-undeaD-src-" (string-take commit 7) "-checkout")) (sha256 - (base32 "12zxsgvka4a82ghp2gaviph6kz13jzjb5pbc8v6i3rmcnifzpbrl")))))) + (base32 "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))))) (arguments `(#:phases (modify-phases %standard-phases (delete 'configure) - (delete 'check) (add-after 'unpack 'patch-pileup-d (lambda* (#:key inputs #:allow-other-keys) (substitute* "sambamba/pileup.d" @@ -94,9 +92,8 @@ ;; The current build compiles htslib statically into the ;; executable. On top of that, we need to patch the latest ;; version of htslib to have it working with Sambamba. - (and (with-directory-excursion "htslib" - (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src") - "--strip-components=1"))) + (and + (copy-recursively (assoc-ref inputs "htslib-src") "htslib") (copy-recursively (assoc-ref inputs "dlang-undeaD-src") "undeaD") (copy-recursively (assoc-ref inputs "biod-src") "BioD")))) (replace @@ -104,7 +101,16 @@ (lambda* (#:key inputs outputs make-flags #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (debug-out (assoc-ref outputs "debug"))) - (zero? (system* "make" "-f" "Makefile.guix" "guix" + (zero? (system* "make" "-f" "Makefile.guix" "guix" "-j" "8" + (string-append "LDC_LIB_PATH=" + (assoc-ref inputs "ldc") + "/lib")))))) + (replace + 'check + (lambda* (#:key inputs outputs make-flags #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (debug-out (assoc-ref outputs "debug"))) + (zero? (system* "make" "-f" "Makefile.guix" "check" (string-append "LDC_LIB_PATH=" (assoc-ref inputs "ldc") "/lib")))))) |