@@ -5552,6 +5552,82 @@ (define-public repeat-masker
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")