From f895a7a4d41a37871b044e48984d460bc896db68 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 May 2018 18:35:43 +0200 Subject: gnu: trim-galore: Update to 0.4.5. * gnu/packages/bioinformatics.scm (trim-galore): Update to 0.4.5. [source]: Fetch from git. [arguments]: Remove custom unpack phase. --- gnu/packages/bioinformatics.scm | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 98149f2674..bba7056db2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11141,25 +11141,22 @@ with narrow binding events such as transcription factor ChIP-seq.") (define-public trim-galore (package (name "trim-galore") - (version "0.4.2") + (version "0.4.5") (source (origin - (method url-fetch) - (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" - "projects/trim_galore/trim_galore_v" - version ".zip")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/FelixKrueger/TrimGalore.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn")))) + "0x5892l48c816pf00wmnz5vq0zq6170d3xc8zrxncd4jcz7h1p71")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests #:phases (modify-phases %standard-phases - ;; The archive contains plain files. - (replace 'unpack - (lambda* (#:key source #:allow-other-keys) - (zero? (system* "unzip" source)))) (delete 'configure) (delete 'build) (add-after 'unpack 'hardcode-tool-references -- cgit v1.2.3 From 126c9e3ff798d06a8398337bb8c3bb09b3da3d35 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 May 2018 18:36:23 +0200 Subject: gnu: bismark: Update to 0.19.1. * gnu/packages/bioinformatics.scm (bismark): Update to 0.19.1. [source]: Fetch from git; remove non-free software in snippet. [arguments]: Update install phase. --- gnu/packages/bioinformatics.scm | 61 +++++++++++++++++++++++++---------------- 1 file changed, 38 insertions(+), 23 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bba7056db2..1996cfa3b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11568,47 +11568,62 @@ Browser.") (define-public bismark (package (name "bismark") - (version "0.16.3") + (version "0.19.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/FelixKrueger/Bismark/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/FelixKrueger/Bismark.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq")))) + "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84")) + (snippet + '(begin + ;; highcharts.js is non-free software. The code is available under + ;; CC-BY-NC or proprietary licenses only. + (delete-file "bismark_sitrep/highcharts.js") + #t)))) (build-system perl-build-system) (arguments - `(#:tests? #f ; there are no tests + `(#:tests? #f ; there are no tests #:phases (modify-phases %standard-phases (delete 'configure) (delete 'build) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin")) - (docdir (string-append (assoc-ref outputs "out") - "/share/doc/bismark")) - (docs '("Bismark_User_Guide.pdf" - "RELEASE_NOTES.txt")) - (scripts '("bismark" - "bismark_genome_preparation" - "bismark_methylation_extractor" - "bismark2bedGraph" - "bismark2report" - "coverage2cytosine" - "deduplicate_bismark" - "bismark_sitrep.tpl" - "bam2nuc" - "bismark2summary"))) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/bismark")) + (docdir (string-append out "/share/doc/bismark")) + (docs '("Docs/Bismark_User_Guide.html")) + (scripts '("bismark" + "bismark_genome_preparation" + "bismark_methylation_extractor" + "bismark2bedGraph" + "bismark2report" + "coverage2cytosine" + "deduplicate_bismark" + "filter_non_conversion" + "bam2nuc" + "bismark2summary"))) + (mkdir-p share) (mkdir-p docdir) (mkdir-p bin) (for-each (lambda (file) (install-file file bin)) scripts) (for-each (lambda (file) (install-file file docdir)) docs) + (copy-recursively "Docs/Images" (string-append docdir "/Images")) + + (substitute* "bismark2report" + (("\\$RealBin/bismark_sitrep") + (string-append share "/bismark_sitrep"))) + (copy-recursively "bismark_sitrep" + (string-append share "/bismark_sitrep")) + ;; Fix references to gunzip (substitute* (map (lambda (file) (string-append bin "/" file)) -- cgit v1.2.3 From 2c5289b2635c911b467455935d63cff78f53c60f Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 12 May 2018 11:01:21 +1000 Subject: gnu: diamond: Update to 0.9.22. * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.22. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1996cfa3b3..7a121557db 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2079,7 +2079,7 @@ accurately delineate genomic rearrangements throughout the genome.") (define-public diamond (package (name "diamond") - (version "0.9.21") + (version "0.9.22") (source (origin (method url-fetch) (uri (string-append @@ -2088,7 +2088,7 @@ accurately delineate genomic rearrangements throughout the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1cf98vcsiwcv3c4apg50w1240v1mpw0zln1sdw3g692dqa4y041z")))) + "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target -- cgit v1.2.3