diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 61 |
1 files changed, 13 insertions, 48 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1ffac1a0ca..c53a2920ac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3145,6 +3145,11 @@ data and settings.") `(#:tests? #f ; there are no tests #:phases (modify-phases %standard-phases + (add-before 'build 'set-force-source-date + ;; for reproducible dates, texlive needs this to respect respect + ;; SOURCE_DATE_EPOCH + (lambda _ + (setenv "FORCE_SOURCE_DATE" "1"))) (add-after 'unpack 'fix-latex-errors (lambda _ (with-fluids ((%default-port-encoding #f)) @@ -10526,7 +10531,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.53") + (version "0.1.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -10534,25 +10539,12 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h")) - (patches (search-patches "pigx-chipseq-no-citeproc.patch")))) + "008n6drj9q5av86xihxlj4py2c9p3c5z5ld89c3bksrp77zxiy67")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; parts of the tests rely on access to the network #:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - ;; This was fixed in commit - ;; 0b1c9f7f2e4d0ff601f1de95ab8b2953f4d5dbc7, but there is no - ;; release with this fix. - (call-with-output-file "VERSION" - (lambda (port) (display ,version port))) - ;; See https://github.com/BIMSBbioinfo/pigx_chipseq/issues/176 - (substitute* "m4/ax_r_package.m4" - (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") - "if(system.file(package=\"PKG\") == \"\")")) - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) @@ -10606,7 +10598,7 @@ expression report comparing samples in an easily configurable manner.") bedtools kentutils)) (native-inputs - (list autoconf automake python-pytest)) + (list python-pytest)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for ChIP sequencing experiments") (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak @@ -10621,7 +10613,7 @@ in an easily configurable manner.") (define-public pigx-bsseq (package (name "pigx-bsseq") - (version "0.1.6") + (version "0.1.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" @@ -10629,8 +10621,7 @@ in an easily configurable manner.") "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "1dipikph0xdr8fp0h1flpafcrg60y4aabljg8fl1v92j3gxdggmw")) - (patches (search-patches "pigx-bsseq-no-citeproc.patch")))) + "1hfiignq3410dbl6f67vc6zr69abknpcgxixx475dspky2jb5lyn")))) (build-system gnu-build-system) (arguments `(;; TODO: tests currently require 12+GB of RAM. See @@ -10638,18 +10629,6 @@ in an easily configurable manner.") #:tests? #f #:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - ;; This was fixed in commit - ;; d56ac732524da659afbbb0972f7a87fa178ae58e, but there is no - ;; release with this fix. - (call-with-output-file "VERSION" - (lambda (port) (display ,version port))) - ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/181 - (substitute* "m4/ax_r_package.m4" - (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") - "if(system.file(package=\"PKG\") == \"\")")) - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))) @@ -10661,7 +10640,7 @@ in an easily configurable manner.") (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - (list tzdata automake autoconf)) + (list tzdata)) (inputs (list coreutils sed @@ -10705,7 +10684,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "1.1.8") + (version "1.1.9") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -10713,23 +10692,11 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885")))) + "0adx7877c3lhlrzfid76i8bc829wcmzvrm0jx47gyid8mxqb7vqs")))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - ;; This was fixed in commit - ;; c4ac067438ae9312b5786a72e2bfb3d795e3ec8a, but there is no - ;; release with this fix. - (call-with-output-file "VERSION" - (lambda (port) (display ,version port))) - ;; https://github.com/BIMSBbioinfo/pigx_scrnaseq/issues/59 - (substitute* "m4/ax_r_package.m4" - (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") - "if(system.file(package=\"PKG\") == \"\")")) - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-additional-environment-variables (lambda _ ;; Needed because of loompy @@ -10778,8 +10745,6 @@ methylation and segmentation.") r-singlecellexperiment r-stringr r-yaml)) - (native-inputs - (list autoconf automake)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") (description |