diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 26 insertions, 18 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 89f1ac36ea..956257d7bb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -4206,8 +4207,15 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (modify-phases %standard-phases (add-after 'unpack 'set-cc (lambda _ (setenv "CC" "gcc") #t)) - ;; FIXME: This fails with "permission denied". - (delete 'reset-gzip-timestamps)))) + + (add-before 'reset-gzip-timestamps 'make-files-writable + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure .gz files are writable so that the + ;; 'reset-gzip-timestamps' phase can do its work. + (let ((out (assoc-ref outputs "out"))) + (for-each make-file-writable + (find-files out "\\.gz$")) + #t)))))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) @@ -7450,13 +7458,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.26.5") + (version "3.26.6") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m")))) + "17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7517,13 +7525,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.40.2") + (version "3.40.6") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7")))) + "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7650,13 +7658,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.40.1") + (version "2.40.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx")))) + "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7811,13 +7819,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci")))) + "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7875,13 +7883,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.44.0") + (version "1.44.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd")))) + "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s")))) (build-system r-build-system) (arguments `(#:phases @@ -7922,13 +7930,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.36.3") + (version "1.36.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3")))) + "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8346,13 +8354,13 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl")))) + "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -9410,14 +9418,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3")))) + "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs |