Re: [PATCH] Add plink.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

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Forgot to add the patch this recipe is referring to.  New patch
attached.


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From 85811f556f0db843f2c699465d317c10d4e85807 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 25 Jun 2015 12:04:05 +0200
Subject: [PATCH] gnu: Add plink.

* gnu/packages/bioinformatics.scm (plink): New variable.
* gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
---
 gnu/packages/bioinformatics.scm                   | 53 +++++++++++++++++
 gnu/packages/patches/plink-1.07-unclobber-i.patch | 69 +++++++++++++++++++++++
 2 files changed, 122 insertions(+)
 create mode 100644 gnu/packages/patches/plink-1.07-unclobber-i.patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7e94bf3..a4bb303 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2033,6 +2033,59 @@ 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 preseq
   (package
     (name "preseq")
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 0000000..60cd97b
--- /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(" }");
+ 	}
-- 
2.1.0