diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 32 |
1 files changed, 7 insertions, 25 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 9e63a26..bb11987 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -15,6 +15,7 @@ #:use-module (guix build-system trivial) #:use-module (guix build-system waf) #:use-module (gnu packages) + #:use-module (gn packages java) #:use-module (gn packages python) #:use-module (gn packages twint) #:use-module (gnu packages algebra) @@ -2060,20 +2061,12 @@ cases include: #t))) (add-after 'fix-build 'insert-rtg-tools (lambda* (#:key inputs #:allow-other-keys) - (let ((rtg-tools (assoc-ref inputs "rtg-tools"))) - (mkdir "external/libexec") - (invoke "unzip" "-j" rtg-tools - "rtg-tools-3.12.1/rtg" - "rtg-tools-3.12.1/RTG.jar" - "rtg-tools-3.12.1/README.txt" - "rtg-tools-3.12.1/LICENSE.txt" - "rtg-tools-3.12.1/third-party/gzipfix.jar" - "-d" "external/libexec/rtg-tools-install") - (mkdir "external/libexec/rtg-tools-install/third-party") - (rename-file "external/libexec/rtg-tools-install/gzipfix.jar" - "external/libexec/rtg-tools-install/third-party/gzipfix.jar") + (let ((rtg-tools (assoc-ref inputs "rtg-tools")) + (dest "external/libexec/rtg-tools-install")) + (mkdir-p dest) + (copy-recursively rtg-tools dest) (copy-file "external/rtg.cfg" - "external/libexec/rtg-tools-install/rtg.cfg") + (string-append dest "/rtg.cfg")) #t))) (replace 'configure (lambda* (#:key outputs (configure-flags '()) (out-of-source? #t) @@ -2155,18 +2148,6 @@ cases include: ,(string-append samtools "/bin"))))) (find-files (string-append out "/bin") "\\.py$")) #t)))))) - (native-inputs - `(("rtg-tools" - ;; When updating this package also update the insert-rtg-tools phase. - ;; This bundled software is bsd-2 licensed. - ,(origin - (method url-fetch) - (uri (string-append "https://github.com/RealTimeGenomics/rtg-tools" - "/releases/download/3.12.1" - "/rtg-tools-3.12.1-nojre.zip")) - (sha256 - (base32 "1an4axkrj28br09xpj9g0a6k5hrx1cx4wcldrryvj6a0ljqqrz2y")))) - ("unzip" ,unzip))) (inputs `(("bcftools" ,bcftools) ("boost" ,boost-static) ; has to be boost-static @@ -2179,6 +2160,7 @@ cases include: ("python2-pandas" ,python2-pandas) ("python2-pysam" ,python2-pysam) ("python2-scipy" ,python2-scipy) + ("rtg-tools" ,rtg-tools) ("samtools" ,samtools) ("zlib" ,zlib))) (home-page "https://github.com/Illumina/hap.py") |