Roel Janssen <r...@gnu.org> writes: > From 07f041559f7f023c56c23f81ac7e90441c44f91b Mon Sep 17 00:00:00 2001 > From: Roel Janssen <r...@gnu.org> > Date: Tue, 22 Mar 2016 16:06:45 +0100 > Subject: [PATCH 8/8] gnu: Add vcflib.
> * gnu/packages/bioinformatics.scm (tabixpp-vcflib): New variable. > * gnu/packages/bioinformatics.scm (vcflib): New variable. These should be two separate patches. > +;; This version works with FreeBayes while the released version doesn't. The > +;; release creates a variable with the name "vcf" somewhere, which is also > the > +;; name of a namespace in vcflib. Is there an upstream bugreport about this? If so it would be good to link to it. > +(define-public tabixpp-vcflib > + (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7")) > + (package (inherit tabixpp) > + (name "tabixpp-vcflib") > + (version (string-append "0-1." (string-take commit 7))) > + (source (origin > + (method url-fetch) > + (uri (string-append "https://github.com/ekg/tabixpp/archive/"; > + commit ".tar.gz")) > + (file-name (string-append name "-" version > "-checkout.tar.gz")) No need to append “-checkout”. > + (sha256 > + (base32 > "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77"))))))) > + > (define-public smithwaterman > (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) > (package > @@ -5017,4 +5033,82 @@ automatically handles index file generation and use.") > tree using C++ templates, allowing the insertion of arbitrary types into the > tree.") > (license license:expat)))) > + > +(define-public vcflib > + (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92")) > + (package > + (name "vcflib") > + (version (string-append "0-1." (string-take commit 7))) > + (source (origin > + (method url-fetch) > + (uri (string-append "https://github.com/vcflib/vcflib/archive/"; > + commit ".tar.gz")) The indentation is off here. “(method” is way too far to the left. Also “commit” is misaligned. > + (file-name (string-append name "-" version ".tar.gz")) > + (sha256 > + (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8")))) > + (build-system gnu-build-system) > + (inputs > + `(("intervaltree" ,intervaltree) > + ("htslib" ,htslib) > + ("zlib" ,zlib))) > + (native-inputs > + `(("python" ,python-2) > + ("perl" ,perl) > + ("r" ,r) > + ("node" ,node) > + ("tabixpp-src" ,(package-source tabixpp-vcflib)) > + ("smithwaterman-src" ,(package-source smithwaterman)) > + ("multichoose-src" ,(package-source multichoose)) > + ("fsom-src" ,(package-source fsom)) > + ("filevercmp-src" ,(package-source filevercmp)) > + ("fastahack-src" ,(package-source fastahack)))) Not a fan of this, but I cannot think of a better way to do this. > + (arguments > + `(#:tests? #f ; There are no tests to run. > + #:phases > + (modify-phases %standard-phases > + (delete 'configure) > + (add-after 'unpack 'unpack-submodule-sources > + (lambda* (#:key inputs #:allow-other-keys) > + (let ((unpack (lambda (source target) > + (with-directory-excursion target > + (zero? (system* "tar" "xvf" > + (assoc-ref inputs source) > + "--strip-components=1")))))) > + (and > + (unpack "fastahack-src" "fastahack") > + (unpack "filevercmp-src" "filevercmp") > + (unpack "fsom-src" "fsom") > + (unpack "multichoose-src" "multichoose") > + (unpack "smithwaterman-src" "smithwaterman") > + (unpack "tabixpp-src" "tabixpp"))))) > + (add-after 'unpack-submodule-sources 'fix-makefile > + (lambda* (#:key inputs #:allow-other-keys) > + (substitute* '("Makefile") > + (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) What is this for? Where does this version number come from? Should it match this package’s version? > + (replace 'build > + (lambda* (#:key inputs make-flags #:allow-other-keys) > + (with-directory-excursion "tabixpp" > + (zero? (system* "make"))) > + (zero? (system* "make" "CC=gcc" > + (string-append > + "CFLAGS=\"" "-Itabixpp " > + "-I" (assoc-ref inputs "htslib") "/include " > + "-I" (assoc-ref inputs "intervaltree") "/include " > + "\"") "all")))) Instead of replacing the build phase try to use make-flags. > + (replace 'install > + (lambda* (#:key outputs #:allow-other-keys) > + (let* ((out (assoc-ref outputs "out")) > + (bin (string-append out "/bin")) > + (lib (string-append out "/lib"))) > + (for-each (lambda (file) > + (install-file file bin)) > + (find-files "bin" ".*")) > + (install-file "libvcflib.a" lib))))))) Remember to return “#t”. > + (home-page "https://github.com/vcflib/vcflib/";) > + (synopsis "Library for parsing and manipulating VCF files") > + (description "Vcflib provides methods to manipulate and interpret > +sequence variation as it can be described by VCF. It is both an API for > parsing > +and operating on records of genomic variation as it can be described by the > VCF > +format, and a collection of command-line utilities for executing complex > +manipulations on VCF files.") Please use double-spacing between sentences. I wonder what it means that “Vcflib ... is ... an API”. I think this should say “It offers an API for parsing” or “It is a library for parsing”. > + (license license:expat)))) There are no license headers in most (all?) of the files. There’s a bug report for that: https://github.com/vcflib/vcflib/issues/16 I think this is not a problem, though, as the README file says that the “MIT” license applies to the project. ~~ Ricardo
