Subject: [PATCH] gnu: Add fast-screen.

From: Mădălin Ionel Patrașcu<[email-masked]>
Date: Thu, 5 Dec 2019 22:21:14 +0100

* gnu/packages/bioinformatics.scm (fast-screen): New variable.
---
 gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

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