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author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-11-20 11:14:48 +0100 |
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committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-11-20 15:22:06 +0100 |
commit | b49c5a58dcbc6f10ebeaef7ccb3d24ff59695db8 (patch) | |
tree | 039c972816bd20a731bd54cc2c197968c9e46efb /gnu/packages/bioinformatics.scm | |
parent | c6a24d6e92c730d03dcfcde231fd6e7dece908ca (diff) | |
download | guix-b49c5a58dcbc6f10ebeaef7ccb3d24ff59695db8.tar guix-b49c5a58dcbc6f10ebeaef7ccb3d24ff59695db8.tar.gz |
gnu: preseq: Update to 2.0.
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
file.
* gnu-system.am (dist_patch_DATA): Remove them.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 43 |
1 files changed, 18 insertions, 25 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4ae1ad0470..35cec1edfb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2590,46 +2590,39 @@ structures, classes for genomic regions, mapped sequencing reads, etc.") (define-public preseq (package (name "preseq") - (version "1.0.2") + (version "2.0") (source (origin (method url-fetch) - (uri - (string-append "http://smithlabresearch.org/downloads/preseq-" - version ".tar.bz2")) + (uri (string-append "https://github.com/smithlabcode/" + "preseq/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc")) - (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch") - (search-patch "preseq-1.0.2-link-with-libbam.patch"))) + (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) (modules '((guix build utils))) (snippet ;; Remove bundled samtools. - '(delete-file-recursively "preseq-master/samtools")))) + '(delete-file-recursively "samtools")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target #:phases (modify-phases %standard-phases - (add-after - 'unpack 'enter-dir - (lambda _ - (chdir "preseq-master") - #t)) - (add-after - 'enter-dir 'use-samtools-headers - (lambda _ - (substitute* '("smithlab_cpp/SAM.cpp" - "smithlab_cpp/SAM.hpp") - (("sam.h") "samtools/sam.h")) - #t)) (delete 'configure)) - #:make-flags (list (string-append "PREFIX=" - (assoc-ref %outputs "out")) - (string-append "LIBBAM=" - (assoc-ref %build-inputs "samtools") - "/lib/libbam.a")))) + #:make-flags + (list (string-append "PREFIX=" + (assoc-ref %outputs "out")) + (string-append "LIBBAM=" + (assoc-ref %build-inputs "samtools") + "/lib/libbam.a") + (string-append "SMITHLAB_CPP=" + (assoc-ref %build-inputs "smithlab-cpp") + "/lib") + "PROGS=preseq" + "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) (inputs `(("gsl" ,gsl) ("samtools" ,samtools-0.1) + ("smithlab-cpp" ,smithlab-cpp) ("zlib" ,zlib))) (home-page "http://smithlabresearch.org/software/preseq/") (synopsis "Program for analyzing library complexity") |