From 1a29fc3ff95a6e5155607893a45e39ba75c1b806 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:43:28 +0100 Subject: gnu: pigx-rnaseq: Use pandoc-1. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78754793a5..3672241aac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12720,8 +12720,8 @@ 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/") -- cgit v1.2.3 From fd757a8f21252044f8180ed69de1cd82ef1857f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:44:32 +0100 Subject: gnu: pigx-chipseq: Use pandoc-1. * gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3672241aac..59cd1bdee8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12778,8 +12778,8 @@ expression report comparing samples in an easily configurable manner.") ("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) -- cgit v1.2.3 From 9dcb4d22a4ed004db02f4443b697caf5f29531e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:44:55 +0100 Subject: gnu: pigx-bsseq: Use pandoc-1. * gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 59cd1bdee8..1c9965ac10 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12845,8 +12845,8 @@ 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) -- cgit v1.2.3 From 2915221bcba0ee152b9d1910ec2462f2d5ebf8e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:45:17 +0100 Subject: gnu: pigx-scrnaseq: Use pandoc-1. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1c9965ac10..91f5d617eb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12903,8 +12903,8 @@ 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) -- cgit v1.2.3 From 32b7ccf9b4c490613395d5f8ad06334c797e47e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:45:40 +0100 Subject: gnu: pigx-chipseq: Update to 0.0.8. * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8. [inputs]: Add python-magic, python-xlrd, and trim-galore. [arguments]: Disable tests. --- gnu/packages/bioinformatics.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 91f5d617eb..80f1437f22 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12737,7 +12737,7 @@ 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/" @@ -12745,10 +12745,11 @@ 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. @@ -12773,8 +12774,11 @@ 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) -- cgit v1.2.3 From d93a1c276b85944198da8395b2d46e06d8a24665 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 11:51:35 +0100 Subject: gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1. * gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 80f1437f22..c6f9b8f347 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8434,7 +8434,7 @@ 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) -- cgit v1.2.3 From d8f08c85adc18c103e99a706db98e046a5c1c94b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 16:55:08 +0100 Subject: gnu: pigx: Update to 0.0.2. * gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c6f9b8f347..1e1f0e5dad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12948,7 +12948,7 @@ 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/" @@ -12956,7 +12956,7 @@ based methods.") "/pigx-" version ".tar.gz")) (sha256 (base32 - "1nxb2hbp40yg3j7n56k4dhsd2fl1j8g0wpiiln56prqzljwnlgmf")))) + "0sb708sl42h3s5z872jb1w70bbqplwapnsc1wm27zcsvi7li4gw8")))) (build-system gnu-build-system) (inputs `(("python" ,python) -- cgit v1.2.3 From 51237011bfa1da1374fbd84581e337d6b54a5fc9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 20:39:53 +0100 Subject: gnu: pigx-scrnaseq: Update to 0.0.3. * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3. [inputs]: Add coreutils and perl. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e1f0e5dad..a6dcc63bf3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12871,7 +12871,7 @@ 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/" @@ -12879,7 +12879,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "03gwp83823ji59y6nvyz89i4yd3faaqpc3791qia71i91470vfsg")))) + "12qdq0nj1wdkyighdxj6924bmbpd1a0b3gam6w64l4hiqrv5sijz")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -12898,7 +12898,9 @@ 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) -- cgit v1.2.3 From 096589035ed154b6ecb4619ca8cdde208be1b8da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 20:53:27 +0100 Subject: gnu: bismark: Fix references to gunzip. * gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to gunzip executable. [inputs]: Add gzip. --- gnu/packages/bioinformatics.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a6dcc63bf3..af994c6a89 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11514,7 +11514,7 @@ 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") @@ -11537,7 +11537,16 @@ 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 -- cgit v1.2.3 From 9dbdc830f6fbf95127d2845603ca8b23a4e40982 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 21:03:07 +0100 Subject: gnu: pigx-bsseq: Update to 0.0.7. * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7. [inputs]: Add coreutils, sed, and grep. --- gnu/packages/bioinformatics.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index af994c6a89..c1f9e66a53 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12816,7 +12816,7 @@ 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/" @@ -12824,7 +12824,7 @@ in an easily configurable manner.") "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp")))) + "0pw797gxx6x1n56lyrvglj7q5hqq4ylfqkvlcrzq1z3j5lxcyl69")))) (build-system gnu-build-system) (arguments `(#:phases @@ -12848,7 +12848,10 @@ 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) -- cgit v1.2.3