diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 |
1 files changed, 29 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35c5c4aff1..f4eeecb985 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -97,6 +97,7 @@ #:use-module (gnu packages golang-build) #:use-module (gnu packages golang-check) #:use-module (gnu packages golang-compression) + #:use-module (gnu packages golang-xyz) #:use-module (gnu packages glib) #:use-module (gnu packages graph) #:use-module (gnu packages graphics) @@ -4617,7 +4618,7 @@ interval trees with associated meta-data. It is primarily used by the (define-public python-deeptools (package (name "python-deeptools") - (version "3.4.3") + (version "3.5.5") (source (origin (method git-fetch) (uri (git-reference @@ -4626,8 +4627,23 @@ interval trees with associated meta-data. It is primarily used by the (file-name (git-file-name name version)) (sha256 (base32 - "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl")))) - (build-system python-build-system) + "0mgcs03amrd5157drbm6ikdg0m0szrn9xbflariz2zrrnqpsai6s")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-test + (lambda _ + (substitute* "deeptools/test/test_tools.py" + (("e_ver = _p") + "e_ver = \".\" + _p + \"-real\"")) + (substitute* "deeptools/multiBigwigSummary.py" + (("version='multiBigwigSummary") + "version='%(prog)s")) + (substitute* "deeptools/plotCoverage.py" + (("version='plotCoverage") + "version='%(prog)s"))))))) (native-inputs (list python-mock python-nose)) (propagated-inputs @@ -4639,7 +4655,7 @@ interval trees with associated meta-data. It is primarily used by the python-pysam python-scipy python-deeptoolsintervals - python-plotly-2.4.1)) + python-plotly)) (home-page "https://pypi.org/project/deepTools/") (synopsis "Useful tools for exploring deep sequencing data") (description "This package addresses the challenge of handling large amounts @@ -5837,7 +5853,7 @@ of nucleic acid binding proteins.") (find-files "../bin" ".*")) #t)))))) (inputs - (list gsl lapack openblas perl + (list gsl openblas perl `(,gfortran "lib"))) (home-page "https://github.com/DReichLab/EIG") (synopsis "Tools for population genetics") @@ -8669,7 +8685,9 @@ predicts the locations of structural units in the sequences.") (substitute* "Makefile" (("INSTALLDIR=.*") (string-append - "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n"))))) + "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")) + (("-llapack -lblas") + "-lopenblas")))) (add-before 'install 'make-install-directory ;; The install directory is not created during 'make install'. (lambda* (#:key outputs #:allow-other-keys) @@ -9654,8 +9672,8 @@ accessed/downloaded on demand across HTTP.") (arguments `(#:tests? #f ;no "check" target #:make-flags ,#~(list (string-append "LIB_LAPACK=" - #$(this-package-input "lapack") - "/lib/liblapack.so") + #$(this-package-input "openblas") + "/lib/libopenblas.so") "WITH_LAPACK=1" "FORCE_DYNAMIC=1" ;; disable phoning home @@ -9670,7 +9688,7 @@ accessed/downloaded on demand across HTTP.") "/bin/"))) (install-file "plink" bin))))))) (inputs - (list zlib lapack)) + (list zlib openblas)) (native-inputs (list unzip gcc-8)) (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") @@ -9705,7 +9723,7 @@ subsequent visualization, annotation and storage of results.") (list #:tests? #false ;TEST_EXTRACT_CHR doesn't produce expected files #:make-flags - #~(list "BLASFLAGS=-llapack -lopenblas" + #~(list "BLASFLAGS=-lopenblas" "NO_SSE42=1" "NO_AVX2=1" "STATIC_ZSTD=" @@ -9732,7 +9750,7 @@ subsequent visualization, annotation and storage of results.") (string-append (assoc-ref outputs "out") "/bin"))))))) (inputs - (list lapack openblas zlib `(,zstd "lib"))) + (list openblas zlib `(,zstd "lib"))) (native-inputs (list diffutils plink python simde)) ; for tests (home-page "https://www.cog-genomics.org/plink/") |