diff options
| -rw-r--r-- | gnu-system.am | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 17 | ||||
| -rw-r--r-- | gnu/packages/patches/bedtools-32bit-compilation.patch | 171 |
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); - - |