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author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2024-02-23 10:11:49 +0100 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2024-05-06 11:47:05 +0200 |
commit | 709e87caff3930abd223ffed631112f7d4233f8f (patch) | |
tree | eaf8f6e96d4161535ad667d63022d68a9afd8ec5 | |
parent | 57769fb0b34d65220b6234c78a7fa45b8593b2ab (diff) | |
download | guix-709e87caff3930abd223ffed631112f7d4233f8f.tar guix-709e87caff3930abd223ffed631112f7d4233f8f.tar.gz |
gnu: Add trust4.
gnu/packages/bioinformatics.scm (trust4): New variable.
Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf
-rw-r--r-- | gnu/packages/bioinformatics.scm | 76 |
1 files changed, 76 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a772229acb..6a0d30cba3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5930,6 +5930,82 @@ be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected.") (license license:osl2.1))) +(define-public trust4 + (package + (name "trust4") + (version "1.0.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/liulab-dfci/TRUST4") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "058wd5bklgcsb0r8l7n1ffakbj4c3ac5hjyvmaqhr3p233fl44z7")) + (modules '((guix build utils))) + (snippet '(begin + ;; Remove bundled samtools + (delete-file-recursively "samtools-0.1.19"))))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ;there are no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-samtools-headers + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile" + (("LINKPATH= -I./samtools-0.1.19 -L./samtools-0.1.19") + (string-append "LINKPATH= -I." + #$(this-package-native-input "samtools") + "/include/samtools" + " -L." + #$(this-package-native-input "samtools") + "/lib")) + (("./samtools-0.1.19/") + (string-append #$(this-package-native-input + "samtools") "/lib/"))) + (substitute* "alignments.hpp" + (("samtools-0.1.19") + (string-append #$(this-package-native-input + "samtools") "/include/samtools"))))) + (delete 'configure) ; No configure. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (scripts (string-append #$output + "/share/trust4/scripts"))) + (install-file "annotator" bin) + (install-file "bam-extractor" bin) + (install-file "fastq-extractor" bin) + (install-file "run-trust4" bin) + (install-file "trust4" bin) + ;; install scripts stored in the scrips dir + (for-each (lambda (file) + (chmod file #o555)) + (find-files "scripts" "\\.p(y|l)")) + (copy-recursively "scripts" scripts) + (delete-file-recursively "scripts") + ;; install the rest of the scripts that are in the main dir + (for-each (lambda (file) + (chmod file #o555) + (install-file file bin)) + (find-files "." "\\.(pl|py|sh)")))))))) + (native-inputs (list automake samtools-0.1)) + (inputs (list perl python-wrapper zlib)) + (home-page "https://github.com/liulab-dfci/TRUST4") + (synopsis "TCR and BCR assembly from RNA-seq data") + (description "This package is analyzing @acronym{TCR, T cell receptor} and +@acronym{BCR, B cell receptor} sequences using unselected RNA sequencing data, +profiled from fluid and solid tissues, including tumors. TRUST4 performs de +novo assembly on V, J, C genes including the hypervariable @acronym{CDR3, +complementarity-determining region 3} and reports consensus contigs of BCR/TCR +sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to +identify the corresponding gene and CDR3 details. TRUST4 supports both single-end +and paired-end bulk or single-cell sequencing data with any read length.") + (license license:gpl3))) + (define-public diamond (package (name "diamond") |