On 26/07/15 05:26, Ricardo Wurmus wrote:
Hi Ben,
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-dir
+ (lambda _ (chdir "core") #t))
+ ;; on advice from the MAFFT authors, do not distribute mafft-profile,
+ ;; mafft-distance mafft-homologs.rb
What does this mean? Are they non-free software? If so, they should be
removed in a snippet.
Sorry for the confusion. MAFFT itself is all free software, but on the
website it allows you to download a version "with-extensions" which
includes non-free software.
I contacted the MAFFT authors and they suggested that there was no need
to distribute these three programs in a mafft package. I've updated the
comment to clarify.
I'm actually a bit confused as to the difference between a snippet vs. a
patch stage as above - when is each appropriate? Snippets are only for
removing non-free software?
+ (add-after 'enter-dir 'patch-makefile
+ (lambda _
+ (substitute* "Makefile"
+ (("^SCRIPTS = mafft mafft-homologs.rb")
+ "SCRIPTS = mafft")
+ (((string-append "^PROGS = dvtditr dndfast7 dndblast"
+ " sextet5 mafft-distance"))
+ "PROGS = dvtditr dndfast7 dndblast sextet5")
+ (((string-append "splittbfast disttbfast tbfast "
+ "mafft-profile f2cl mccaskillwrap"))
+ "splittbfast disttbfast tbfast f2cl mccaskillwrap")
This line looks particularly unclear. It took me a little too long to
find the difference in the replacement. Is there a nicer regular
expression that you could use to indicate the removal of
“mafft-profile”?
I've added comments and alignment.
ben
>From ce50d7382c8f7f092faa56ff5316134417a9eca1 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Sun, 26 Jul 2015 13:01:01 +1000
Subject: [PATCH] gnu: Add mafft.
* gnu/packages/bioinformatics.scm (mafft): New variable
---
gnu/packages/bioinformatics.scm | 59 +++++++++++++++++++++++++++++++++++++----
1 file changed, 54 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 38f01a8..11ef454 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -54,6 +54,54 @@
#:use-module (gnu packages xml)
#:use-module (gnu packages zip))
+(define-public aragorn
+ (package
+ (name "aragorn")
+ (version "1.2.36")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn";
+ version ".tgz"))
+ (sha256
+ (base32
+ "1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda _
+ (zero? (system* "gcc"
+ "-O3"
+ "-ffast-math"
+ "-finline-functions"
+ "-o"
+ "aragorn"
+ (string-append "aragorn" ,version ".c")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (man (string-append out "/share/man/man1")))
+ (mkdir-p bin)
+ (copy-file "aragorn"
+ (string-append bin "/aragorn"))
+ (mkdir-p man)
+ (copy-file "aragorn.1"
+ (string-append man "/aragorn.1")))
+ #t)))))
+ (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN";)
+ (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
+ (description
+ "Aragorn identifies transfer RNA, mitochondrial RNA and
+transfer-messenger RNA from nucleotide sequences, based on homology to known
+tRNA consensus sequences and RNA structure. It also outputs the secondary
+structure of the predicted RNA.")
+ (license license:gpl2)))
+
(define-public bamtools
(package
(name "bamtools")
@@ -148,7 +196,7 @@ computational cluster.")
(define-public bedtools
(package
(name "bedtools")
- (version "2.22.0")
+ (version "2.24.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/archive/v";
@@ -156,7 +204,7 @@ computational cluster.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
+ "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))))
(build-system gnu-build-system)
(native-inputs `(("python" ,python-2)))
(inputs `(("samtools" ,samtools)
@@ -1409,7 +1457,7 @@ sequencing tag position and orientation.")
"0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; no automated tests, though there are tests in the readme
+ `(#:tests? #f ; no automated tests, though there are tests in the read me
#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
(string-append "BINDIR=" (string-append
(assoc-ref %outputs "out")
@@ -1424,10 +1472,11 @@ sequencing tag position and orientation.")
;; distribute mafft-profile, mafft-distance, or
;; mafft-homologs.rb as they are too "specialised".
(substitute* "Makefile"
+ ;; remove mafft-homologs.rb from SCRIPTS
(("^SCRIPTS = mafft mafft-homologs.rb")
"SCRIPTS = mafft")
- ;; remove mafft-distance from PROGS
- (((string-append "^PROGS = dvtditr dndfast7 dndblast"
+ ;; remove mafft-distance from PROGS
+ (((string-append "^PROGS = dvtditr dndfast7 dndblast"
" sextet5 mafft-distance"))
"PROGS = dvtditr dndfast7 dndblast sextet5")
;; remove mafft-profile from PROGS
--
2.4.3
