diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 52 |
1 files changed, 30 insertions, 22 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index bb5c0fd..628e656 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -426,9 +426,10 @@ association studies (GWAS).") (method url-fetch) (uri (string-append "https://github.com/lomereiter/sambamba/archive/v" - version "tar.gz")) + version ".tar.gz")) + (file-name (string-append "sambamba-" version ".tar.gz")) (sha256 - (base32 "")))) + (base32 "152zbg4m10ikr7xgk20c0nwqwrqvydmpc73p2c1fqmbhpk0l0ws6")))) (build-system gnu-build-system) (inputs `(("ldc" ,ldc) @@ -443,15 +444,13 @@ association studies (GWAS).") ("lz4" ,lz4) ("gcc" ,gcc) ("htslib-src" - (let ((version "0.2.0-rc10")) - ,(origin - (method url-fetch) - (uri (string-append - "https://github.com/lomereiter/htslib/archive/" - version ".tar.gz")) - (file-name (string-append "htslib-" version ".tar.gz")) + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz")) + (file-name (string-append "htslib-0.2.0-rc10.tar.gz")) (sha256 - (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))) + (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs")))) ("biod-src" ,(origin (method git-fetch) @@ -462,17 +461,26 @@ association studies (GWAS).") (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")) (file-name "biod"))))) (arguments - `(#:make-flags "sambamba-ldmd2-64" ; This target is used for releases. - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'unpack-htslib-sources - (lambda* (#:key inputs #:allow-other-keys) - (with-directory-excursion "htslib" - (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src") - "--strip-components=1"))))) - (add-after 'unpack 'move-biod-sources - '()))) ; TODO: Figure out how to move or symlink the BioD sources to the right place. + '(#:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'unpack-htslib-sources + (lambda* (#:key inputs #:allow-other-keys) + ;; Unfortunately, the current build compiles htslib statically + ;; into the executable. Instead of patching the build files + ;; for Guix, this should be resolved on Sambamba upstream. For + ;; now, just extract the source code to the desired directory. + (and (with-directory-excursion "htslib" + (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src") + "--strip-components=1"))) + (zero? (system* "cp" "-R" (assoc-ref inputs "biod-src") "BioD"))))) + ;; Building a production-quality executable is done with a + ;; non-default make target. Adding it with #:make-flags breaks + ;; building tests. Therefore, the default make got replaced by this. + (replace + 'build + (lambda* (#:key (make-flags '()) #:allow-other-keys) + (zero? (system* "make" "sambamba-ldmd2-64" make-flags))))))) (home-page "https://github.com/lomereiter/sambamba") (synopsis "A tool for working with SAM and BAM files written in D.") (description @@ -481,4 +489,4 @@ library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.") - (license license:gpl2+)))) + (license license:gpl2+))) |