diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 53 | ||||
| -rw-r--r-- | gnu/packages/patches/plink-1.07-unclobber-i.patch | 69 |
2 files changed, 122 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31df2196dc..4eac8358a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1793,6 +1793,59 @@ Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.") (license license:public-domain))) +(define-public plink + (package + (name "plink") + (version "1.07") + (source + (origin + (method url-fetch) + (uri (string-append + "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-" + version "-src.zip")) + (sha256 + (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa")) + (patches (list (search-patch "plink-1.07-unclobber-i.patch"))))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:make-flags (list (string-append "LIB_LAPACK=" + (assoc-ref %build-inputs "lapack") + "/lib/liblapack.so") + "WITH_LAPACK=1" + "FORCE_DYNAMIC=1" + ;; disable phoning home + "WITH_WEBCHECK=") + #:phases + (modify-phases %standard-phases + ;; no "configure" script + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin/"))) + (mkdir-p bin) + (copy-file "plink" (string-append bin "plink")) + #t)))))) + (inputs + `(("zlib" ,zlib) + ("lapack" ,lapack))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") + (synopsis "Whole genome association analysis toolset") + (description + "PLINK is a whole genome association analysis toolset, designed to +perform a range of basic, large-scale analyses in a computationally efficient +manner. The focus of PLINK is purely on analysis of genotype/phenotype data, +so there is no support for steps prior to this (e.g. study design and +planning, generating genotype or CNV calls from raw data). Through +integration with gPLINK and Haploview, there is some support for the +subsequent visualization, annotation and storage of results.") + ;; Code is released under GPLv2, except for fisher.h, which is under + ;; LGPLv2.1+ + (license (list license:gpl2 license:lgpl2.1+)))) + (define-public sra-tools (package (name "sra-tools") diff --git a/gnu/packages/patches/plink-1.07-unclobber-i.patch b/gnu/packages/patches/plink-1.07-unclobber-i.patch new file mode 100644 index 0000000000..60cd97ba4a --- /dev/null +++ b/gnu/packages/patches/plink-1.07-unclobber-i.patch @@ -0,0 +1,69 @@ +GCC rightfully complains about redefined variables, as iterator declarations +appear inside loops with a loop variable of the same name. + +This patch has been sent upstream. + +--- a/sets.cpp 2015-06-25 11:22:08.252821681 +0200 ++++ b/sets.cpp 2015-06-25 11:22:23.239187985 +0200 +@@ -768,11 +768,11 @@ + ////////////////////////////////////////////// + // Reset original missing status + +- vector<Individual*>::iterator i = PP->sample.begin(); +- while ( i != PP->sample.end() ) ++ vector<Individual*>::iterator it = PP->sample.begin(); ++ while ( it != PP->sample.end() ) + { +- (*i)->missing = (*i)->flag; +- ++i; ++ (*it)->missing = (*it)->flag; ++ ++it; + } + + //////////////////////////////////////////////// + +--- a/elf.cpp 2009-10-10 18:00:21.000000000 +0200 ++++ b/elf.cpp 2015-06-25 11:34:06.136835756 +0200 +@@ -1175,10 +1175,10 @@ + << setw(8) << gcnt << " " + << setw(8) << (double)cnt / (double)gcnt << "\n"; + +- map<int,int>::iterator i = chr_cnt.begin(); +- while ( i != chr_cnt.end() ) ++ map<int,int>::iterator it = chr_cnt.begin(); ++ while ( it != chr_cnt.end() ) + { +- int c = i->first; ++ int c = it->first; + int x = chr_cnt.find( c )->second; + int y = chr_gcnt.find( c )->second; + +@@ -1189,7 +1189,7 @@ + << setw(8) << y << " " + << setw(8) << (double)x / (double)y << "\n"; + +- ++i; ++ ++it; + } + + } + +--- plink-1.07-src/idhelp.cpp 2009-10-10 18:00:22.000000000 +0200 ++++ plink-1.07-src/idhelp.cpp.patched 2015-06-25 11:37:39.387204086 +0200 +@@ -772,12 +772,12 @@ + for (int j = 0 ; j < jointField.size(); j++ ) + { + set<IDField*> & jf = jointField[j]; +- set<IDField*>::iterator j = jf.begin(); ++ set<IDField*>::iterator jit = jf.begin(); + PP->printLOG(" { "); +- while ( j != jf.end() ) ++ while ( jit != jf.end() ) + { +- PP->printLOG( (*j)->name + " " ); +- ++j; ++ PP->printLOG( (*jit)->name + " " ); ++ ++jit; + } + PP->printLOG(" }"); + } |