diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 50 |
1 files changed, 25 insertions, 25 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3e93d94651..019c46adbd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -252,7 +252,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (define-public bamtools (package (name "bamtools") - (version "2.4.1") + (version "2.5.1") (source (origin (method url-fetch) (uri (string-append @@ -261,7 +261,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk")))) + "1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no "check" target @@ -285,7 +285,7 @@ BAM files.") (define-public bcftools (package (name "bcftools") - (version "1.5") + (version "1.8") (source (origin (method url-fetch) (uri (string-append @@ -293,12 +293,11 @@ BAM files.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz")) - (patches (search-patches "bcftools-regidx-unsigned-char.patch")) + "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa")) (modules '((guix build utils))) (snippet ;; Delete bundled htslib. - '(delete-file-recursively "htslib-1.5")))) + '(delete-file-recursively "htslib-1.8")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -338,7 +337,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (define-public bedops (package (name "bedops") - (version "2.4.14") + (version "2.4.33") (source (origin (method url-fetch) (uri (string-append "https://github.com/bedops/bedops/archive/v" @@ -346,7 +345,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v")))) + "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m")))) (build-system gnu-build-system) (arguments '(#:tests? #f @@ -2080,7 +2079,7 @@ accurately delineate genomic rearrangements throughout the genome.") (define-public diamond (package (name "diamond") - (version "0.9.19") + (version "0.9.21") (source (origin (method url-fetch) (uri (string-append @@ -2089,7 +2088,7 @@ accurately delineate genomic rearrangements throughout the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0c4y8l90vdxmglb0w37y0413v11qzcwg8sdmy9k0c0gr3bsq7dzs")))) + "1cf98vcsiwcv3c4apg50w1240v1mpw0zln1sdw3g692dqa4y041z")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -2340,7 +2339,8 @@ dynamic programming or a variety of heuristics.") (string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) (substitute* "src/CMakeLists.txt" (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") - (string-append (assoc-ref inputs "bamtools") "/lib/bamtools"))) + (string-append (assoc-ref inputs "bamtools") "/lib")) + (("libprotobuf.a") "libprotobuf.so")) #t))))) (inputs `(("boost" ,boost) @@ -3453,7 +3453,7 @@ The main functions of FastQC are: (define-public htslib (package (name "htslib") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) (uri (string-append @@ -3461,7 +3461,7 @@ The main functions of FastQC are: version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy")))) + "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0")))) (build-system gnu-build-system) (inputs `(("openssl" ,openssl) @@ -4575,7 +4575,7 @@ partial genes, and identifies translation initiation sites.") (define-public roary (package (name "roary") - (version "3.11.0") + (version "3.12.0") (source (origin (method url-fetch) @@ -4584,7 +4584,7 @@ partial genes, and identifies translation initiation sites.") version ".tar.gz")) (sha256 (base32 - "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i")))) + "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff")))) (build-system perl-build-system) (arguments `(#:phases @@ -4921,7 +4921,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) @@ -4930,7 +4930,7 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77")))) + "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9")))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -5769,7 +5769,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (define-public star (package (name "star") - (version "2.5.3a") + (version "2.6.0a") (source (origin (method url-fetch) (uri (string-append "https://github.com/alexdobin/STAR/archive/" @@ -5777,7 +5777,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a")) + "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56")) (modules '((guix build utils))) (snippet '(begin @@ -5964,13 +5964,13 @@ Cuffdiff or Ballgown programs.") (define-public taxtastic (package (name "taxtastic") - (version "0.6.4") + (version "0.8.5") (source (origin (method url-fetch) (uri (pypi-uri "taxtastic" version)) (sha256 (base32 - "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929")))) + "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk")))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -6605,7 +6605,7 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.7.1") + (version "2.8.0") (source (origin (method url-fetch) @@ -6615,7 +6615,7 @@ SELECT or UPDATE queries to an end-point.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f")) + "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin @@ -9063,14 +9063,14 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8")))) + "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy")))) (build-system python-build-system) (propagated-inputs `(("python-jinja2" ,python-jinja2) |