(address . guix-patches@gnu.org)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20191205212114.4971-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (fast-screen): New variable.
---
gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
Toggle diff (63 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 74a44874ee..53e4c7296f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15341,3 +15341,56 @@ methylation metrics from them. MethylDackel requires an indexed fasta file
containing the reference genome as well.")
;; See https://github.com/dpryan79/MethylDackel/issues/85
(license license:expat)))
+
+(define-public fastq-screen
+ (package
+ (name "fastq-screen")
+ (version "0.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://www.bioinformatics.babraham.ac.uk/projects/"
+ "fastq_screen/fastq_screen_v" version ".tar.gz"))
+ (sha256
+ (base32
+ "0m7n9b1pr8rk1pd3va0mr69pd7gddcsvrvlk2s7907i02wkc1say"))))
+ (build-system trivial-build-system)
+ (arguments
+ ;; it is just an extraction processs
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let* ((tar (assoc-ref %build-inputs "tar"))
+ (gzip (assoc-ref %build-inputs "gzip"))
+ (out (assoc-ref %outputs "out"))
+ (doc (string-append out "/share/doc"))
+ (bin (string-append out "/bin")))
+ (setenv "PATH" (string-append tar "/bin:" gzip "/bin"))
+ (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
+ (chdir (string-append "fastq_screen_v" ,version))
+ (install-file "fastq_screen" bin)
+ (install-file "fastq_screen.conf.example" doc)
+ (install-file "fastq_screen_documentation.md" doc)
+ (install-file "RELEASE_NOTES.txt" doc)
+ #t))))
+ (inputs
+ `(("perl" ,perl)))
+ (native-inputs
+ `(("gzip" ,gzip)
+ ("tar" ,tar)))
+ (home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/")
+ (synopsis "FastQ Screen allows to search a large sequence dataset")
+ (description
+ "FastQ Screen is an application which allows you to search a large sequence
+dataset against a panel of different databases to build up a picture of where
+the sequences in your data originate. The program was built as a quality
+control check for sequencing pipelines but may also have uses in metagenomics
+studies where mixed samples are expected. The application generates both text
+and graphical output to inform you what proportion of your library was able to
+map, either uniquely or to more than one location, against each of your
+specified reference genomes. The user should therefore be able to identify a
+clean sequencing experiment in which the overwhelming majority of reads are
+probably derived from a single genomic origin.")
+ (license license:gpl3+)))
+
--
2.17.1