diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 56 |
1 files changed, 27 insertions, 29 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0960329f44..8ed871003a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -43,6 +43,7 @@ (method url-fetch) (uri (string-append "https://github.com/bedops/bedops/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "0wmg6j0icimlrnsidaxrzf3hfgjvlkkcwvpdg7n4gg7hdv2m9ni5")))) @@ -100,6 +101,7 @@ computational cluster.") (method url-fetch) (uri (string-append "https://github.com/arq5x/bedtools2/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl")))) @@ -182,6 +184,7 @@ Python.") (method url-fetch) (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn")) @@ -378,35 +381,30 @@ Illumina, Roche 454, and the SOLiD platform.") '() '("POPCNT_CAPABILITY=0"))) #:phases - (alist-replace - 'unpack - (lambda* (#:key source #:allow-other-keys) - (and (zero? (system* "unzip" source)) - (chdir "hisat-0.1.4-beta"))) - (alist-cons-after - 'unpack 'patch-sources - (lambda _ - ;; XXX Cannot use snippet because zip files are not supported - (substitute* "Makefile" - (("^CC = .*$") "CC = gcc") - (("^CPP = .*$") "CPP = g++") - ;; replace BUILD_HOST and BUILD_TIME for deterministic build - (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") - (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) - (substitute* '("hisat-build" "hisat-inspect") - (("/usr/bin/env") (which "env")))) - (alist-replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (mkdir-p bin) - (for-each - (lambda (file) - (copy-file file (string-append bin file))) - (find-files - "." - "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))) - (alist-delete 'configure %standard-phases)))))) + (alist-cons-after + 'unpack 'patch-sources + (lambda _ + ;; XXX Cannot use snippet because zip files are not supported + (substitute* "Makefile" + (("^CC = .*$") "CC = gcc") + (("^CPP = .*$") "CPP = g++") + ;; replace BUILD_HOST and BUILD_TIME for deterministic build + (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) + (substitute* '("hisat-build" "hisat-inspect") + (("/usr/bin/env") (which "env")))) + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (mkdir-p bin) + (for-each + (lambda (file) + (copy-file file (string-append bin file))) + (find-files + "." + "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))) + (alist-delete 'configure %standard-phases))))) (native-inputs `(("unzip" ,unzip))) (inputs |