diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 60 |
1 files changed, 39 insertions, 21 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 426618147f..31ca5b2521 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8448,7 +8448,7 @@ paired-end data.") ("r-testthat" ,r-testthat) ;; During vignette building knitr checks that "pandoc-citeproc" ;; is in the PATH. - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1))) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-biomart" ,r-biomart) @@ -11521,7 +11521,7 @@ Browser.") (delete 'configure) (delete 'build) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key inputs outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin")) (docdir (string-append (assoc-ref outputs "out") @@ -11544,7 +11544,16 @@ Browser.") scripts) (for-each (lambda (file) (install-file file docdir)) docs) + ;; Fix references to gunzip + (substitute* (map (lambda (file) + (string-append bin "/" file)) + scripts) + (("\"gunzip -c") + (string-append "\"" (assoc-ref inputs "gzip") + "/bin/gunzip -c"))) #t)))))) + (inputs + `(("gzip" ,gzip))) (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/") (synopsis "Map bisulfite treated sequence reads and analyze methylation") (description "Bismark is a program to map bisulfite treated sequencing @@ -12729,8 +12738,8 @@ once. This package provides tools to perform Drop-seq analyses.") ("r-rtracklayer" ,r-rtracklayer) ("r-rjson" ,r-rjson) ("salmon" ,salmon) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("ghc-pandoc" ,ghc-pandoc-1) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml))) (home-page "http://bioinformatics.mdc-berlin.de/pigx/") @@ -12746,7 +12755,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.2") + (version "0.0.8") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12754,10 +12763,11 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "1jliwhifnjgl9x0z730bzpxswi2s84fyg5y8cagbyzpw509452f5")))) + "1plw0bz0b7flj0g9irbn8n520005lmajkiq5flpizzapsl0a0r9g")))) (build-system gnu-build-system) (arguments - `(#:phases + `(#:tests? #f ; parts of the tests rely on access to the network + #:phases (modify-phases %standard-phases (add-after 'install 'wrap-executable ;; Make sure the executable finds all R modules. @@ -12782,13 +12792,16 @@ expression report comparing samples in an easily configurable manner.") ("r-ggplot2" ,r-ggplot2) ("r-plotly" ,r-plotly) ("python-wrapper" ,python-wrapper) + ("python-magic" ,python-magic) ("python-pyyaml" ,python-pyyaml) + ("python-xlrd" ,python-xlrd) ("snakemake" ,snakemake) + ("trim-galore" ,trim-galore) ("macs" ,macs) ("multiqc" ,multiqc) ("perl" ,perl) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("ghc-pandoc" ,ghc-pandoc-1) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) @@ -12812,7 +12825,7 @@ in an easily configurable manner.") (define-public pigx-bsseq (package (name "pigx-bsseq") - (version "0.0.5") + (version "0.0.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" @@ -12820,7 +12833,7 @@ in an easily configurable manner.") "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp")))) + "0pw797gxx6x1n56lyrvglj7q5hqq4ylfqkvlcrzq1z3j5lxcyl69")))) (build-system gnu-build-system) (arguments `(#:phases @@ -12844,7 +12857,10 @@ in an easily configurable manner.") (native-inputs `(("tzdata" ,tzdata))) (inputs - `(("r-minimal" ,r-minimal) + `(("coreutils" ,coreutils) + ("sed" ,sed) + ("grep" ,grep) + ("r-minimal" ,r-minimal) ("r-annotationhub" ,r-annotationhub) ("r-dt" ,r-dt) ("r-genomation" ,r-genomation) @@ -12854,8 +12870,8 @@ in an easily configurable manner.") ("r-bookdown" ,r-bookdown) ("r-ggplot2" ,r-ggplot2) ("r-ggbio" ,r-ggbio) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("ghc-pandoc" ,ghc-pandoc-1) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("snakemake" ,snakemake) @@ -12876,7 +12892,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "0.0.2") + (version "0.0.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -12884,7 +12900,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "03gwp83823ji59y6nvyz89i4yd3faaqpc3791qia71i91470vfsg")))) + "12qdq0nj1wdkyighdxj6924bmbpd1a0b3gam6w64l4hiqrv5sijz")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -12903,7 +12919,9 @@ methylation and segmentation.") `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) #t))))) (inputs - `(("dropseq-tools" ,dropseq-tools) + `(("coreutils" ,coreutils) + ("perl" ,perl) + ("dropseq-tools" ,dropseq-tools) ("fastqc" ,fastqc) ("java-picard" ,java-picard) ("java" ,icedtea-8) @@ -12912,8 +12930,8 @@ methylation and segmentation.") ("python-pandas" ,python-pandas) ("python-numpy" ,python-numpy) ("python-loompy" ,python-loompy) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("ghc-pandoc" ,ghc-pandoc-1) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("snakemake" ,snakemake) ("star" ,star) ("r-minimal" ,r-minimal) @@ -12953,7 +12971,7 @@ based methods.") (define-public pigx (package (name "pigx") - (version "0.0.1") + (version "0.0.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx/" @@ -12961,7 +12979,7 @@ based methods.") "/pigx-" version ".tar.gz")) (sha256 (base32 - "1nxb2hbp40yg3j7n56k4dhsd2fl1j8g0wpiiln56prqzljwnlgmf")))) + "0sb708sl42h3s5z872jb1w70bbqplwapnsc1wm27zcsvi7li4gw8")))) (build-system gnu-build-system) (inputs `(("python" ,python) |