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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 91 |
1 files changed, 91 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f879ad01d7..a27807f57f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9780,6 +9780,97 @@ sequences).") "https://mafft.cbrc.jp/alignment/software/license.txt" "BSD-3 with different formatting")))) +(define-public mageck + (package + (name "mageck") + (version "0.5.9.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/mageck/" + (version-major+minor version) + "/mageck-" version ".tar.gz")) + (sha256 + (base32 + "0fnry7d3ngiw0jarvmwd3pxy5vvsf931m4aifz6mjfd6dl1ihsmh")))) + (build-system pyproject-build-system) + (arguments + (list + #:modules '((guix build pyproject-build-system) + (guix build utils) + (srfi srfi-1) + (ice-9 match)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-python3 + (lambda _ + (substitute* "bin/mageck" + (("python2") "python")))) + (add-after 'unpack 'numpy-compatibility + (lambda _ + (substitute* "mageck/cnv_normalization.py" + (("np.float") "float")))) + ;; The build system declares executables both in "scripts" and + ;; "data", which all are supposed to end up in #$output/bin. The + ;; pyproject-build-system gets confused by this, though, so we have + ;; to manually install the mageck executable after the 'install + ;; phase. + (add-after 'unpack 'patch-build-system + (lambda _ + (substitute* "setup.py" + (("scripts=\\['bin/mageck'\\],") "")))) + (add-after 'install 'install-mageck + (lambda _ + (install-file "bin/mageck" (string-append #$output "/bin")))) + (add-after 'install-mageck 'make-excutable + (lambda _ + (for-each (lambda (file) (chmod file #o555)) + (find-files (string-append #$output "/bin"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (let ((tests '(("demo1" "run.sh") + ("demo2" "runmageck.sh") + ("demo3" "run.sh") + ("demo4" "run.sh")))) + (setenv "PATH" + (string-append #$output "/bin:" + (getenv "PATH"))) + (for-each (match-lambda + ((dir script) + (with-directory-excursion (string-append "demo/" dir) + (invoke "bash" script)))) + tests)))))))) + (inputs + (list python-numpy + python-scipy + python-matplotlib + python-statsmodels + python-pyqt + r-minimal + r-xtable + r-gplots)) + (home-page "https://sourceforge.net/projects/mageck/") + (synopsis "Model-based analysis of genome-wide CRISPR-Cas9 Knockout") + (description + "Model-based Analysis of Genome-wide CRISPR-Cas9 +Knockout (MAGeCK) is a computational tool to identify important genes +from the recent genome-scale CRISPR-Cas9 knockout screens +technology. Its features include: + +@enumerate +@item Simple, easy to use pipeline to screen genes in Genome-wide + CRISPR-Cas9 Knockout experiments; +@item High sensitivity and low false discovery rate; +@item Fully utilize the screening data by performing both positive and + negative screening in one dataset; +@item Provide statistical evaluation in genes, sgRNAs and pathways; +@item Require as few as 2 samples; +@item Identify cell-type specific targets; +@item A set of visualization features that generate publication + standard figures. +@end enumerate\n") + (license license:bsd-3))) + (define-public mash (package (name "mash") |