diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 81 |
1 files changed, 50 insertions, 31 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 48edd56854..fdb42562e8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -805,15 +805,16 @@ time.") (define-public crossmap (package (name "crossmap") - (version "0.1.6") + (version "0.2.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" version ".tar.gz")) (sha256 (base32 - "163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp")) - ;; patch has been sent upstream already + "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) + ;; This patch has been sent upstream already and is available + ;; for download from Sourceforge, but it has not been merged. (patches (list (search-patch "crossmap-allow-system-pysam.patch"))) (modules '((guix build utils))) @@ -1838,19 +1839,25 @@ the phenotype as it models the data.") (license license:asl2.0))) (define-public pbtranscript-tofu - (let ((commit "c7bbd5472")) + (let ((commit "8f5467fe6")) (package (name "pbtranscript-tofu") - (version (string-append "0.4.1." commit)) + (version (string-append "2.2.3." commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/PacificBiosciences/cDNA_primer.git") (commit commit))) - (file-name (string-append name "-" version ".tar.gz")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx")))) + "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f")) + (modules '((guix build utils))) + (snippet + '(begin + ;; remove bundled Cython sources + (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz") + #t)))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -1860,34 +1867,29 @@ the phenotype as it models the data.") #:configure-flags '("--single-version-externally-managed" "--record=pbtranscript-tofu.txt") #:phases - (alist-cons-after - 'unpack 'enter-directory-and-clean-up - (lambda _ - (chdir "pbtranscript-tofu/pbtranscript/") - ;; Delete clutter - (delete-file-recursively "dist/") - (delete-file-recursively "build/") - (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/") - (delete-file-recursively "pbtools.pbtranscript.egg-info") - (delete-file "Cython-0.20.1.tar.gz") - (delete-file "setuptools_cython-0.2.1-py2.7.egg") - (delete-file "setuptools_cython-0.2.1.tar.gz") - (delete-file "setup.cfg") - (for-each delete-file - (find-files "." "\\.so$")) - ;; files should be writable for install phase - (for-each (lambda (f) (chmod f #o755)) - (find-files "." "\\.py$"))) - %standard-phases))) + (modify-phases %standard-phases + (add-after 'unpack 'enter-directory + (lambda _ + (chdir "pbtranscript-tofu/pbtranscript/") + #t)) + ;; With setuptools version 18.0 and later this setup.py hack causes + ;; a build error, so we disable it. + (add-after 'enter-directory 'patch-setuppy + (lambda _ + (substitute* "setup.py" + (("if 'setuptools.extension' in sys.modules:") + "if False:")) + #t))))) (inputs - `(("python-cython" ,python2-cython) - ("python-numpy" ,python2-numpy) + `(("python-numpy" ,python2-numpy) ("python-bx-python" ,python2-bx-python) ("python-networkx" ,python2-networkx) ("python-scipy" ,python2-scipy) - ("python-pbcore" ,python2-pbcore))) + ("python-pbcore" ,python2-pbcore) + ("python-h5py" ,python2-h5py))) (native-inputs - `(("python-nose" ,python2-nose) + `(("python-cython" ,python2-cython) + ("python-nose" ,python2-nose) ("python-setuptools" ,python2-setuptools))) (home-page "https://github.com/PacificBiosciences/cDNA_primer") (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") @@ -2703,7 +2705,24 @@ sequences.") (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target - #:make-flags '("-f" "Makefile.Linux") + ;; The CC and CCFLAGS variables are set to contain a lot of x86_64 + ;; optimizations by default, so we override these flags such that x86_64 + ;; flags are only added when the build target is an x86_64 system. + #:make-flags + (list (let ((system ,(or (%current-target-system) + (%current-system))) + (flags '("-ggdb" "-fomit-frame-pointer" + "-ffast-math" "-funroll-loops" + "-fmessage-length=0" + "-O9" "-Wall" "-DMAKE_FOR_EXON" + "-DMAKE_STANDALONE" + "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\"")) + (flags64 '("-mmmx" "-msse" "-msse2" "-msse3"))) + (if (string-prefix? "x86_64" system) + (string-append "CCFLAGS=" (string-join (append flags flags64))) + (string-append "CCFLAGS=" (string-join flags)))) + "-f" "Makefile.Linux" + "CC=gcc ${CCFLAGS}") #:phases (alist-cons-after 'unpack 'enter-dir |