diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 25 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f1a73bca7e..8c140a1d24 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4168,7 +4168,7 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (define-public khmer (package (name "khmer") - (version "2.1.2") + (version "3.0.0a3") (source (origin (method git-fetch) @@ -4178,8 +4178,7 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (file-name (git-file-name name version)) (sha256 (base32 - "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m")) - (patches (search-patches "khmer-use-libraries.patch")) + "01l4jczglkl7yfhgvzx8j0df7k54bk1r8sli9ll16i1mis0d8f37")) (modules '((guix build utils))) (snippet '(begin @@ -4192,6 +4191,12 @@ command, or queried for specific k-mers with @code{jellyfish query}.") ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html (delete-file-recursively "third-party/zlib") (delete-file-recursively "third-party/bzip2") + (delete-file-recursively "third-party/seqan") + (substitute* "setup.cfg" + (("# libraries = z,bz2") + "libraries = z,bz2") + (("include:third-party/zlib:third-party/bzip2") + "include:")) #t)))) (build-system python-build-system) (arguments @@ -4208,6 +4213,7 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (inputs `(("zlib" ,zlib) ("bzip2" ,bzip2) + ("seqan" ,seqan-1) ("python-screed" ,python-screed) ("python-bz2file" ,python-bz2file))) (home-page "https://khmer.readthedocs.org/") @@ -6954,14 +6960,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.18.1") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1k57zyzagd7g7wl38l3cn9csylykxcllbfvyq7dz8pvihgkn0ssi")))) + "18s5vpmw766pm64w7bwwfgpsv9yzhwclf0ya1rpqz8qslw7bbdjf")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -7461,13 +7467,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.26.4") + (version "3.26.5") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "013glavk6a1wpyq3q35k343bdp6rf27w30q59i4kf47rp3i37g15")))) + "0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7661,13 +7667,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.40.0") + (version "2.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1i457s91bn7n60bzw3zk4h64xgmawlrr6bq4z4cb7jlm04hdq8qm")))) + "1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7853,13 +7859,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "13zw7bb1adgph9bf9b9y725nr0320b80y70p2yqf3bjb2klfxf55")))) + "0s3q97q4pgj5jwn4g95al44rahrwsncsf45v01v4071msx3xmjxq")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7933,13 +7939,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.36.1") + (version "1.36.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "02psq3jfgghdydwbydb1j792lvfg44l5npb44mx8d54ckr8658dd")))) + "0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8556,13 +8562,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.12.1") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1nq8v1sgkm2ssmvr2z3qw0zsk7zy0dzb95g1mfs8fkpjqh3nqq5s")))) + "070nx0blvvfhsnkbb5j899wy7dgalrh4xfcciir9l2xl67lna1zf")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") @@ -10687,14 +10693,14 @@ memory usage and processing time is minimized.") (define-public r-phangorn (package (name "r-phangorn") - (version "2.5.3") + (version "2.5.5") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 - "1bv86yfk5r015s7ij6v4zz7bagwrw9m13yfs5853drxb19d5h1m3")))) + "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -12742,7 +12748,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "0.0.7") + (version "0.0.8") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -12750,7 +12756,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "131zarirv16w8653m0d66jgjnwqfsxqc0hix0rypssz4d83bl51j")))) + "0zv0sc5amivxhb95vx2gfx6l9bh7n80fh7h47dalnwxxnfvnzai4")))) (build-system gnu-build-system) (arguments `(#:configure-flags |