diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2021-11-29 17:01:43 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-11-30 16:46:17 +0100 |
| commit | 173a2998d9facce29386788d25bcc08781386f60 (patch) | |
| tree | e3c3bad049f901c677725e461d508cefcead778f | |
| parent | d95a982cdd898790d247f013440f08a448265e3f (diff) | |
| download | guix-173a2998d9facce29386788d25bcc08781386f60.tar.gz guix-173a2998d9facce29386788d25bcc08781386f60.zip | |
gnu: r-umi4cpackage: Embed references to perl and bowtie2.
* gnu/packages/bioinformatics.scm (r-umi4cpackage)[arguments]: Add build
phases to patch calls of bowtie2 and perl.
[inputs]: Add perl and bowtie.
[synopsis]: Remove trailing period.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 17 |
1 files changed, 16 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 67335daead..dffd59d863 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7812,12 +7812,27 @@ single cell ATAC-seq sequencing data.") (base32 "0bjzamdw2lcfhlbzc0vdva87c3wwnij8jsvnrpx4wyyxvpcz13m5")))) (properties `((upstream-name . "umi4cPackage"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-references + (lambda _ + (substitute* "inst/conf/paths.conf" + (("TG3C\\.bowtie2_bin=.*") + (string-append "TG3C.bowtie2_bin=" + (which "bowtie2") "\n"))) + (substitute* "inst/perl/map3c/TG3C/import3C.pl" + (("\"perl") + (string-append "\"" (which "perl"))))))))) + (inputs + `(("perl" ,perl) + ("bowtie" ,bowtie))) (propagated-inputs `(("r-misha" ,r-misha) ("r-zoo" ,r-zoo))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tanaylab/umi4cpackage") - (synopsis "Processing and analysis of UMI-4C contact profiles.") + (synopsis "Processing and analysis of UMI-4C contact profiles") (description "This is a package that lets you process UMI-4C data from scratch to produce nice plots.") (license license:expat)))) |