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-rw-r--r--gnu/packages/bioinformatics.scm162
1 files changed, 40 insertions, 122 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6d21e14360..d37d93047e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12,7 +12,7 @@
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
-;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
@@ -211,8 +211,7 @@ structure of the predicted RNA.")
(snippet
`(begin
;; Delete bundled htslib.
- (delete-file-recursively "c/htslib-1.3.1")
- #t))))
+ (delete-file-recursively "c/htslib-1.3.1")))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; BamM is Python 2 only.
@@ -232,37 +231,22 @@ structure of the predicted RNA.")
;; Use autogen so that 'configure' works.
(substitute* "autogen.sh" (("/bin/sh") sh))
(setenv "CONFIG_SHELL" sh)
- (invoke "./autogen.sh")))
- #t))
- (delete 'build)
- ;; Run tests after installation so compilation only happens once.
- (delete 'check)
- (add-after 'install 'wrap-executable
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (path (getenv "PATH")))
- (wrap-program (string-append out "/bin/bamm")
- `("PATH" ":" prefix (,path))))
- #t))
- (add-after 'wrap-executable 'post-install-check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (setenv "PATH"
- (string-append (assoc-ref outputs "out")
- "/bin:"
- (getenv "PATH")))
- (setenv "PYTHONPATH"
- (string-append
- (assoc-ref outputs "out")
- "/lib/python"
- (string-take (string-take-right
- (assoc-ref inputs "python") 5) 3)
- "/site-packages:"
- (getenv "PYTHONPATH")))
+ (invoke "./autogen.sh")))))
+ (delete 'build) ;the build loops otherwise
+ (replace 'check
+ (lambda _
;; There are 2 errors printed, but they are safe to ignore:
;; 1) [E::hts_open_format] fail to open file ...
;; 2) samtools view: failed to open ...
- (invoke "nosetests")
- #t)))))
+ (invoke "nosetests")))
+ (add-after 'install 'wrap-executable
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (path (getenv "PATH"))
+ (pythonpath (getenv "GUIX_PYTHONPATH")))
+ (wrap-program (string-append out "/bin/bamm")
+ `("PATH" ":" prefix (,path))
+ `("GUIX_PYTHONPATH" ":" prefix (,pythonpath)))))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
@@ -819,9 +803,7 @@ intended to behave exactly the same as the original BWK awk.")
"14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0"))))
(build-system python-build-system)
(arguments
- `(#:modules ((ice-9 ftw)
- (srfi srfi-1)
- (srfi srfi-26)
+ `(#:modules ((srfi srfi-26)
(guix build utils)
(guix build python-build-system))
;; See https://github.com/daler/pybedtools/issues/192
@@ -847,10 +829,7 @@ intended to behave exactly the same as the original BWK awk.")
;; This issue still occurs on python2
(substitute* "pybedtools/test/test_issues.py"
(("def test_issue_303")
- "def _test_issue_303"))
- #t))
- ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
- ;; build system.
+ "def _test_issue_303"))))
;; Force the Cythonization of C++ files to guard against compilation
;; problems.
(add-after 'unpack 'remove-cython-generated-files
@@ -862,30 +841,12 @@ intended to behave exactly the same as the original BWK awk.")
(string-take filename (string-index-right filename #\.)))
(define (cythonized? c/c++-file)
(member (strip-extension c/c++-file) cython-sources))
- (for-each delete-file (filter cythonized? c/c++-files))
- #t)))
+ (for-each delete-file (filter cythonized? c/c++-files)))))
(add-after 'remove-cython-generated-files 'generate-cython-extensions
(lambda _
(invoke "python" "setup.py" "cythonize")))
(replace 'check
(lambda _
- (let* ((cwd (getcwd))
- (build-root-directory (string-append cwd "/build/"))
- (build (string-append
- build-root-directory
- (find (cut string-prefix? "lib" <>)
- (scandir (string-append
- build-root-directory)))))
- (scripts (string-append
- build-root-directory
- (find (cut string-prefix? "scripts" <>)
- (scandir build-root-directory)))))
- (setenv "PYTHONPATH"
- (string-append build ":" (getenv "PYTHONPATH")))
- ;; Executable scripts such as 'intron_exon_reads.py' must be
- ;; available in the PATH.
- (setenv "PATH"
- (string-append scripts ":" (getenv "PATH"))))
;; The tests need to be run from elsewhere...
(mkdir-p "/tmp/test")
(copy-recursively "pybedtools/test" "/tmp/test")
@@ -1942,15 +1903,10 @@ multiple sequence alignments.")
(snippet '(begin
;; Drop bundled htslib. TODO: Also remove samtools
;; and bcftools.
- (delete-file-recursively "htslib")
- #t))))
+ (delete-file-recursively "htslib")))))
(build-system python-build-system)
(arguments
- `(#:modules ((ice-9 ftw)
- (srfi srfi-26)
- (guix build python-build-system)
- (guix build utils))
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(add-before 'build 'set-flags
(lambda* (#:key inputs #:allow-other-keys)
@@ -1960,22 +1916,16 @@ multiple sequence alignments.")
(setenv "HTSLIB_INCLUDE_DIR"
(string-append (assoc-ref inputs "htslib") "/include"))
(setenv "LDFLAGS" "-lncurses")
- (setenv "CFLAGS" "-D_CURSES_LIB=1")
- #t))
+ (setenv "CFLAGS" "-D_CURSES_LIB=1")))
(replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
+ (lambda _
;; This file contains tests that require a connection to the
;; internet.
(delete-file "tests/tabix_test.py")
- ;; FIXME: This test fails
+ ;; FIXME: These tests fail with "AttributeError: 'array.array'
+ ;; object has no attribute 'tostring'".
(delete-file "tests/AlignmentFile_test.py")
- ;; Add first subdirectory of "build" directory to PYTHONPATH.
- (setenv "PYTHONPATH"
- (string-append
- (getenv "PYTHONPATH")
- ":" (getcwd) "/build/"
- (car (scandir "build"
- (negate (cut string-prefix? "." <>))))))
+ (delete-file "tests/AlignedSegment_test.py")
;; Step out of source dir so python does not import from CWD.
(with-directory-excursion "tests"
(setenv "HOME" "/tmp")
@@ -2316,9 +2266,9 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Make sure 'couger' runs with the correct PYTHONPATH.
(let* ((out (assoc-ref outputs "out"))
- (path (getenv "PYTHONPATH")))
+ (path (getenv "GUIX_PYTHONPATH")))
(wrap-program (string-append out "/bin/couger")
- `("PYTHONPATH" ":" prefix (,path))))
+ `("GUIX_PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("python" ,python-2)
@@ -2981,19 +2931,14 @@ data and settings.")
(substitute* "src/plasma/fasta.hpp"
(("#define FASTA_HPP" line)
(string-append line "\n#include <random>")))
- #t))
- ;; FIXME: this is needed because we're using texlive-union, which
- ;; doesn't handle fonts correctly. It expects to be able to generate
- ;; fonts in the home directory.
- (add-before 'build 'setenv-HOME
- (lambda _ (setenv "HOME" "/tmp") #t)))))
+ #t)))))
(inputs
`(("boost" ,boost)
("cairo" ,cairo)
("rmath-standalone" ,rmath-standalone)))
(native-inputs
- `(("texlive" ,(texlive-union (list texlive-fonts-cm
- texlive-fonts-amsfonts
+ `(("texlive" ,(texlive-updmap.cfg (list texlive-cm
+ texlive-amsfonts
texlive-latex-doi
texlive-latex-examplep
@@ -6433,25 +6378,6 @@ complexity samples.")
(base32
"148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx"))))
(build-system python-build-system)
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- ;; Tests must be run after installation, as the "screed" command does
- ;; not exist right after building.
- (delete 'check)
- (add-after 'install 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (setenv "PYTHONPATH"
- (string-append out "/lib/python"
- (string-take (string-take-right
- (assoc-ref inputs "python")
- 5) 3)
- "/site-packages:"
- (getenv "PYTHONPATH")))
- (setenv "PATH" (string-append out "/bin:" (getenv "PATH"))))
- (invoke "python" "setup.py" "test")
- #t)))))
(native-inputs
`(("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)
@@ -11138,7 +11064,7 @@ matplotlib.use('Agg')
" line)))
;; Make sure GESS has all modules in its path
(wrap-script (string-append target "GESS.py")
- `("PYTHONPATH" ":" = (,target ,(getenv "PYTHONPATH"))))
+ `("GUIX_PYTHONPATH" ":" = (,target ,(getenv "GUIX_PYTHONPATH"))))
(mkdir-p bin)
(symlink (string-append target "GESS.py")
(string-append bin "GESS.py"))
@@ -12088,11 +12014,7 @@ variational inference.")
(modify-phases %standard-phases
(replace 'check
(lambda _
- (setenv "PYTHONPATH"
- (string-append (getcwd) ":"
- (getenv "PYTHONPATH")))
- (invoke "pytest" "tests")
- #t)))))
+ (invoke "pytest" "tests"))))))
(propagated-inputs
`(("python-h5py" ,python-h5py)
("python-numpy" ,python-numpy)
@@ -13320,11 +13242,11 @@ conversions, region filtering, FASTA sequence extraction and more.")
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
- (path (getenv "PYTHONPATH")))
+ (path (getenv "GUIX_PYTHONPATH")))
(for-each (lambda (script)
(install-file script bin)
(wrap-program (string-append bin "/" script)
- `("PYTHONPATH" ":" prefix (,path))))
+ `("GUIX_PYTHONPATH" ":" prefix (,path))))
'("cmp_bed.py"
"find_circ.py"
"maxlength.py"
@@ -13369,11 +13291,7 @@ in RNA-seq data.")
(delete-file "scanpy/tests/test_preprocessing.py")
(delete-file "scanpy/tests/test_read_10x.py")
- (setenv "PYTHONPATH"
- (string-append (getcwd) ":"
- (getenv "PYTHONPATH")))
- (invoke "pytest")
- #t)))))
+ (invoke "pytest"))))))
(propagated-inputs
`(("python-anndata" ,python-anndata)
("python-h5py" ,python-h5py)
@@ -14270,10 +14188,10 @@ datasets.")
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
- (path (getenv "PYTHONPATH")))
+ (path (getenv "GUIX_PYTHONPATH")))
(wrap-program (string-append out
"/share/filtlong/scripts/histogram.py")
- `("PYTHONPATH" ":" prefix (,path))))
+ `("GUIX_PYTHONPATH" ":" prefix (,path))))
#t))
(add-before 'check 'patch-tests
(lambda _
@@ -14346,12 +14264,12 @@ choosing which reads pass the filter.")
#t)))
(add-after 'install 'wrap-programs
(lambda* (#:key outputs #:allow-other-keys)
- (let ((pythonpath (getenv "PYTHONPATH"))
+ (let ((pythonpath (getenv "GUIX_PYTHONPATH"))
(perl5lib (getenv "PERL5LIB"))
(scripts (string-append (assoc-ref outputs "out")
"/share/nanopolish/scripts")))
(for-each (lambda (file)
- (wrap-program file `("PYTHONPATH" ":" prefix (,pythonpath))))
+ (wrap-program file `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))
(find-files scripts "\\.py"))
(for-each (lambda (file)
(wrap-script file `("PERL5LIB" ":" prefix (,perl5lib))))
@@ -14568,7 +14486,7 @@ to an artifact/contaminant file.")
`(("openmpi" ,openmpi)
("zlib" ,zlib)))
(native-inputs
- `(("texlive" ,(texlive-union (list texlive-latex-graphics
+ `(("texlive" ,(texlive-updmap.cfg (list texlive-latex-graphics
texlive-latex-hyperref)))))
(home-page "https://www.ebi.ac.uk/~zerbino/velvet/")
(synopsis "Nucleic acid sequence assembler for very short reads")
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-10 12:00:25 +0000