gnu: bedtools: Update to 2.25.0.

* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'.  Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.

3 files changed, 3 insertions, 186 deletions

diff --git a/gnu-system.am b/gnu-system.am
index 7c4112a7e6..7105e13219 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -416,7 +416,6 @@ dist_patch_DATA =						\
   gnu/packages/patches/avidemux-install-to-lib.patch		\
   gnu/packages/patches/avrdude-fix-libusb.patch			\
   gnu/packages/patches/bash-completion-directories.patch	\
-  gnu/packages/patches/bedtools-32bit-compilation.patch         \
   gnu/packages/patches/bowtie-fix-makefile.patch		\
   gnu/packages/patches/bigloo-gc-shebangs.patch			\
   gnu/packages/patches/binutils-ld-new-dtags.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index df0e23da89..55b7cb1c86 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;;
@@ -207,7 +207,7 @@ computational cluster.")
 (define-public bedtools
   (package
     (name "bedtools")
-    (version "2.24.0")
+    (version "2.25.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
@@ -215,8 +215,7 @@ computational cluster.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
-              (patches (list (search-patch "bedtools-32bit-compilation.patch")))))
+                "1ywcy3yfwzhl905b51l0ffjia55h75vv3mw5xkvib04pp6pj548m"))))
     (build-system gnu-build-system)
     (native-inputs `(("python" ,python-2)))
     (inputs `(("samtools" ,samtools)
@@ -225,16 +224,6 @@ computational cluster.")
      '(#:test-target "test"
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-makefile-SHELL-definition
-           (lambda _
-             ;; patch-makefile-SHELL cannot be used here as it does not
-             ;; yet patch definitions with `:='.  Since changes to
-             ;; patch-makefile-SHELL result in a full rebuild, features
-             ;; of patch-makefile-SHELL are reimplemented here.
-             (substitute* "Makefile"
-               (("^SHELL := .*$")
-                (string-append "SHELL := " (which "bash") " -e \n")))
-             #t))
          (delete 'configure)
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
diff --git a/gnu/packages/patches/bedtools-32bit-compilation.patch b/gnu/packages/patches/bedtools-32bit-compilation.patch
deleted file mode 100644
index bc567f3f6b..0000000000
--- a/gnu/packages/patches/bedtools-32bit-compilation.patch
+++ /dev/null
@@ -1,171 +0,0 @@
-Fixed in upstream, see
-https://github.com/arq5x/bedtools2/issues/271
-
-From b47dbefcb57f8e6c4fe397f64346338620740b71 Mon Sep 17 00:00:00 2001
-From: arq5x <arq5x@virginia.edu>
-Date: Wed, 15 Jul 2015 15:15:23 -0600
-Subject: [PATCH] settle on uint32_t signature for QuickString. Resolves #267
- and #271?
-
----
- src/coverageFile/coverageFile.cpp | 24 ++++++++++++------------
- src/utils/general/QuickString.cpp | 27 ++++++++++++++-------------
- src/utils/general/QuickString.h   |  6 +++---
- 3 files changed, 29 insertions(+), 28 deletions(-)
-
-diff --git a/src/coverageFile/coverageFile.cpp b/src/coverageFile/coverageFile.cpp
-index 859cfdc..0fb544b 100644
---- a/src/coverageFile/coverageFile.cpp
-+++ b/src/coverageFile/coverageFile.cpp
-@@ -83,11 +83,11 @@ void CoverageFile::giveFinalReport(RecordOutputMgr *outputMgr) {
- 		float depthPct = (float)basesAtDepth / (float)_totalQueryLen;
- 
- 		_finalOutput = "all\t";
--		_finalOutput.append(depth);
-+		_finalOutput.append(static_cast<uint32_t>(depth));
- 		_finalOutput.append("\t");
--		_finalOutput.append(basesAtDepth);
-+		_finalOutput.append(static_cast<uint32_t>(basesAtDepth));
- 		_finalOutput.append("\t");
--		_finalOutput.append(_totalQueryLen);
-+		_finalOutput.append(static_cast<uint32_t>(_totalQueryLen));
- 		_finalOutput.append("\t");
- 		format(depthPct);
- 
-@@ -138,7 +138,7 @@ size_t CoverageFile::countBasesAtDepth(size_t depth) {
- 
- void CoverageFile::doCounts(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
- {
--	_finalOutput = hits.size();
-+	_finalOutput = static_cast<uint32_t>(hits.size());
- 	outputMgr->printRecord(hits.getKey(), _finalOutput);
- }
- 
-@@ -147,9 +147,9 @@ void CoverageFile::doPerBase(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
- 	//loop through all bases in query, printing full record and metrics for each
- 	const Record * queryRec = hits.getKey();
- 	for (size_t i= 0; i < _queryLen; i++) {
--		_finalOutput = i +1;
-+		_finalOutput = static_cast<uint32_t>(i+1);
- 		_finalOutput.append("\t");
--		_finalOutput.append(_depthArray[i]);
-+		_finalOutput.append(static_cast<uint32_t>(_depthArray[i]));
- 
- 		outputMgr->printRecord(queryRec, _finalOutput);
- 	}
-@@ -181,11 +181,11 @@ void CoverageFile::doHist(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
- 		size_t numBasesAtDepth = iter->second;
- 		float coveredBases = (float)numBasesAtDepth / (float)_queryLen;
- 
--		_finalOutput = depth;
-+		_finalOutput = static_cast<uint32_t>(depth);
- 		_finalOutput.append("\t");
--		_finalOutput.append(numBasesAtDepth);
-+		_finalOutput.append(static_cast<uint32_t>(numBasesAtDepth));
- 		_finalOutput.append("\t");
--		_finalOutput.append(_queryLen);
-+		_finalOutput.append(static_cast<uint32_t>(_queryLen));
- 		_finalOutput.append("\t");
- 		format(coveredBases);
- 
-@@ -199,11 +199,11 @@ void CoverageFile::doDefault(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
- 	size_t nonZeroBases = _queryLen - countBasesAtDepth(0);
- 	float coveredBases = (float)nonZeroBases / (float)_queryLen;
- 
--	_finalOutput = hits.size();
-+	_finalOutput = static_cast<uint32_t>(hits.size());
- 	_finalOutput.append("\t");
--	_finalOutput.append(nonZeroBases);
-+	_finalOutput.append(static_cast<uint32_t>(nonZeroBases));
- 	_finalOutput.append("\t");
--	_finalOutput.append(_queryLen);
-+	_finalOutput.append(static_cast<uint32_t>(_queryLen));
- 	_finalOutput.append("\t");
- 	format(coveredBases);
- 
-diff --git a/src/utils/general/QuickString.cpp b/src/utils/general/QuickString.cpp
-index 0757009..a83263e 100644
---- a/src/utils/general/QuickString.cpp
-+++ b/src/utils/general/QuickString.cpp
-@@ -105,11 +105,11 @@ QuickString &QuickString::operator = (uint32_t val) {
- 	return *this;
- }
- 
--QuickString &QuickString::operator = (size_t val) {
--	clear();
--	append(val);
--	return *this;
--}
-+// QuickString &QuickString::operator = (size_t val) {
-+// 	clear();
-+// 	append(val);
-+// 	return *this;
-+// }
- 
- QuickString &QuickString::operator = (float val) {
- 	clear();
-@@ -158,10 +158,11 @@ QuickString &QuickString::operator += (uint32_t num) {
- 	return *this;
- }
- 
--QuickString &QuickString::operator += (size_t num) {
--	append(num);
--	return *this;
--}
-+// QuickString &QuickString::operator += (size_t num) {
-+// 	append(num);
-+// 	return *this;
-+// }
-+
- QuickString &QuickString::operator += (float num) {
- 	append(num);
- 	return *this;
-@@ -273,12 +274,12 @@ void QuickString::append(int num) {
- }
- 
- void QuickString::append(uint32_t num) {
--	int2str((int)num, *this, true);
-+ 	int2str((int)num, *this, true);
- }
- 
--void QuickString::append(size_t num) {
--	int2str((int)num, *this, true);
--}
-+// void QuickString::append(size_t num) {
-+// 	int2str((int)num, *this, true);
-+// }
- 
- void QuickString::append(float num) {
- 	append(ToString(num));
-diff --git a/src/utils/general/QuickString.h b/src/utils/general/QuickString.h
-index b43fdfc..6e6fa94 100644
---- a/src/utils/general/QuickString.h
-+++ b/src/utils/general/QuickString.h
-@@ -38,7 +38,7 @@ class QuickString {
- 	QuickString &operator = (char);
- 	QuickString &operator = (int);
- 	QuickString &operator = (uint32_t);
--	QuickString &operator = (size_t);
-+	//QuickString &operator = (size_t);
- 	QuickString &operator = (float);
- 	QuickString &operator = (double);
- 	QuickString &operator += (const QuickString &);
-@@ -47,7 +47,7 @@ class QuickString {
- 	QuickString &operator += (char);
- 	QuickString &operator += (int);
- 	QuickString &operator += (uint32_t);
--	QuickString &operator += (size_t);
-+	//QuickString &operator += (size_t);
- 	QuickString &operator += (float);
- 	QuickString &operator += (double);
- 
-@@ -74,7 +74,7 @@ class QuickString {
- 	//for better performance.
- 	void append(int num);
- 	void append(uint32_t num);
--	void append(size_t num);
-+	//void append(size_t num);
- 	void append(float num);
- 	void append(double num);
- 
-