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alexpreynolds committed Aug 18, 2017
2 parents 6da506a + 700b1d6 commit 9a9d686
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8 changes: 8 additions & 0 deletions Makefile
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Expand Up @@ -155,6 +155,10 @@ module_binaries:
-cp ${BINDIR}/bam2starch_sge-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2starch_sge
-cp ${BINDIR}/bam2starch_slurm-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2starch_slurm
-cp ${BINDIR}/bam2starch_gnuParallel-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/bam2starch_gnuParallel
-cp ${BINDIR}/starchcluster_sge-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starchcluster_sge
-cp ${BINDIR}/starchcluster_gnuParallel-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starchcluster_gnuParallel
-cp ${BINDIR}/starchcluster_slurm-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starchcluster_slurm
-cp ${BINDIR}/starch-diff-$(TYPICAL) ${BINDIR_MODULE_TYPICAL}/starch-diff
mkdir -p ${BINDIR_MODULE_MEGAROW}
-cp ${BINDIR}/sort-bed-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/sort-bed
-cp ${BINDIR}/update-sort-bed-slurm-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/update-sort-bed-slurm
Expand Down Expand Up @@ -194,6 +198,10 @@ module_binaries:
-cp ${BINDIR}/bam2starch_sge-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2starch_sge
-cp ${BINDIR}/bam2starch_slurm-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2starch_slurm
-cp ${BINDIR}/bam2starch_gnuParallel-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/bam2starch_gnuParallel
-cp ${BINDIR}/starchcluster_sge-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starchcluster_sge
-cp ${BINDIR}/starchcluster_gnuParallel-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starchcluster_gnuParallel
-cp ${BINDIR}/starchcluster_slurm-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starchcluster_slurm
-cp ${BINDIR}/starch-diff-$(MEGAROW) ${BINDIR_MODULE_MEGAROW}/starch-diff

#######################
# install details
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18 changes: 9 additions & 9 deletions README.md
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@@ -1,14 +1,14 @@
## BEDOPS v2.4.27: high-performance genomic feature operations ##
## BEDOPS v2.4.28: high-performance genomic feature operations ##

[![Build Status](https://travis-ci.org/bedops/bedops.svg?branch=master)](https://travis-ci.org/bedops/bedops) [![GitHub stars](https://img.shields.io/github/stars/bedops/bedops.svg)](https://github.com/bedops/bedops/stargazers) [![Project license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://github.com/bedops/bedops/blob/master/LICENSE) [![Documentation Status](https://readthedocs.org/projects/bedops/badge/?version=latest)](https://readthedocs.org/projects/bedops/?badge=latest)

<!-- <img src="http://bedops.readthedocs.io/en/latest/_static/logo_with_label_v2.png" align="right" style="max-width:33%" /> -->

### About ###

**BEDOPS v2.4.27** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.
**BEDOPS v2.4.28** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.27** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.
The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.28** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.


### Downloads ###
Expand All @@ -28,20 +28,20 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
<tr>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.27/bedops_linux_x86_64-v2.4.27.tar.bz2">x86-64 (64-bit)</a> binaries</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.28/bedops_linux_x86_64-v2.4.28.tar.bz2">x86-64 (64-bit)</a> binaries</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#linux">Installation instructions</a> for Linux hosts</li>
</ul>
</td>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.27/BEDOPS.2.4.27.pkg.zip">Intel (64-bit, 10.10-10.12)</a> installer package</li>
<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.28/BEDOPS.2.4.28.pkg.zip">Intel (64-bit, 10.10-10.12)</a> installer package</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#mac-os-x">Installation instructions</a> for Mac OS X hosts</li>
</ul>
</td>
<td valign="top">
<ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
<li><a href="https://github.com/bedops/bedops/archive/v2.4.27.tar.gz">Source code</a> (tar.gz)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.27.zip">Source code</a> (zip)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.28.tar.gz">Source code</a> (tar.gz)</li>
<li><a href="https://github.com/bedops/bedops/archive/v2.4.28.zip">Source code</a> (zip)</li>
<li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#installation-via-source-code">Compilation instructions</a></li>
</ul>
</td>
Expand All @@ -50,11 +50,11 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv

### Documentation ###

Complete documentation for **BEDOPS v2.4.27** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
Complete documentation for **BEDOPS v2.4.28** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>

### Citation ###

If you use **BEDOPS v2.4.27** in your research, please cite the following manuscript:
If you use **BEDOPS v2.4.28** in your research, please cite the following manuscript:

> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.
> [**BEDOPS: high-performance genomic feature operations**
Expand Down
2 changes: 2 additions & 0 deletions applications/bed/bedmap/src/Bedmap.cpp
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Expand Up @@ -650,6 +650,8 @@ namespace BedMap {
}
else if ( nm == visName<typename VTypes::Variance>() )
rtn = new typename VTypes::Variance(pt);
else if ( nm == visName<typename VTypes::WMean>() )
rtn = new typename VTypes::WMean(pt);

return rtn;
}
Expand Down
2 changes: 1 addition & 1 deletion applications/bed/conversion/src/convert2bed.h
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Expand Up @@ -53,7 +53,7 @@

#include "suite/BEDOPS.Constants.hpp"

#define C2B_VERSION "2.4.27"
#define C2B_VERSION "2.4.28"

typedef int boolean;
extern const boolean kTrue;
Expand Down
14 changes: 13 additions & 1 deletion applications/bed/sort-bed/src/Makefile
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Expand Up @@ -40,6 +40,7 @@ endif

dependency_names = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
debug_dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .do, $(dependency_names)))

FLAGS = $(SFLAGS) ${MEGAFLAGS} -s ${BLDFLAGS} ${LIBLOCATION} ${INCLUDES}
DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline -pedantic ${LIBLOCATION} ${INCLUDES}
Expand All @@ -62,6 +63,8 @@ build_debug: $(BINDIR)/debug.$(PROG)

dependencies: $(dependencies)

debug_dependencies: $(debug_dependencies)

update-sort-bed-slurm-${BINARY_TYPE}:
mkdir -p $(BINDIR) && cp update-sort-bed-slurm.py $(BINDIR)/update-sort-bed-slurm-${BINARY_TYPE}

Expand All @@ -77,7 +80,7 @@ $(BINDIR)/$(PROG) : $(dependencies)
$(BINDIR)/gprof.$(PROG) : $(dependencies)
mkdir -p $(BINDIR) && $(CXX) -o $@ ${TFLAG} $(GPROFFLAGS) $^ ${LIBRARIES}

$(BINDIR)/debug.$(PROG) : $(dependencies)
$(BINDIR)/debug.$(PROG) : $(debug_dependencies)
mkdir -p $(BINDIR) && $(CXX) -o $@ ${TFLAG} $(DFLAGS) $^ ${LIBRARIES}
rm -rf ${OBJDIR}

Expand All @@ -90,6 +93,15 @@ $(OBJDIR)/%.o : $(LIB3)/%.c
$(OBJDIR)/%.o : %.cpp
mkdir -p $(OBJDIR) && $(CXX) -c ${TFLAG} ${BLDFLAGS} $^ -o $@ ${INCLUDES}

$(OBJDIR)/%.do : $(LIB1)/%.cpp
mkdir -p $(OBJDIR) && $(CXX) -c ${TFLAG} $(DFLAGS) $^ -o $@ ${INCLUDES}

$(OBJDIR)/%.do : $(LIB3)/%.c
mkdir -p $(OBJDIR) && $(CXX) -c ${TFLAG} ${DFLAGS} $^ -o $@ ${INCLUDES}

$(OBJDIR)/%.do : %.cpp
mkdir -p $(OBJDIR) && $(CXX) -c ${TFLAG} ${DFLAGS} $^ -o $@ ${INCLUDES}

clean:
rm -rf ${OBJDIR}
rm -rf $(BINDIR)
4 changes: 2 additions & 2 deletions applications/bed/sort-bed/src/SortDetails.cpp
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Expand Up @@ -450,9 +450,9 @@ mergeSort(FILE* output, FILE **tmpFiles, unsigned int numFiles)
else if(0 == val)
{
if(starts[i] < starts[currMin])
currMin = static_cast<int>(i);
currMin = static_cast<int>(i), currRest = rests[i];
else if(starts[i] == starts[currMin] && ends[i] < ends[currMin])
currMin = static_cast<int>(i);
currMin = static_cast<int>(i), currRest = rests[i];
else if(starts[i] == starts[currMin] && ends[i] == ends[currMin])
{
if (currRest == NULL)
Expand Down
2 changes: 1 addition & 1 deletion applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
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Expand Up @@ -32,7 +32,7 @@
name = "update-sort-bed-migrate-candidates"
citation = " citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
authors = " authors: Alex Reynolds and Shane Neph"
version = " version: 2.4.27"
version = " version: 2.4.28"
usage = """ $ update-sort-bed-migrate-candidates [ --dry-run ] [ --debug ]
[ --write-list |
--resort-immediately |
Expand Down
2 changes: 1 addition & 1 deletion applications/bed/sort-bed/src/update-sort-bed-slurm.py
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Expand Up @@ -33,7 +33,7 @@
name = "update-sort-bed-slurm"
citation = " citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
authors = " authors: Alex Reynolds and Shane Neph"
version = " version: 2.4.27"
version = " version: 2.4.28"
usage = """ $ update-sort-bed-slurm [ --slurm-memory <MB> ]
[ --slurm-partition <SLURM partition> ]
[ --slurm-workdir <working directory> ]
Expand Down
4 changes: 2 additions & 2 deletions applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
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Expand Up @@ -33,7 +33,7 @@
name = "update-sort-bed-starch-slurm"
citation = " citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
authors = " authors: Alex Reynolds and Shane Neph"
version = " version: 2.4.27"
version = " version: 2.4.28"
usage = """ $ update-sort-bed-starch-slurm [ --slurm-memory <MB> ]
[ --slurm-partition <SLURM partition> ]
[ --slurm-workdir <working directory> ]
Expand Down Expand Up @@ -288,7 +288,7 @@ def main():
'--partition',
slurm_partition,
'--wrap',
'"srun ' + unstarch_path + ' ' + chromosome + ' ' + args.input_fn + ' | ' + sort_bed_path + ' - | ' + starch_path + ' - > ' + temp_dest + '"'
'"srun ' + unstarch_path + ' ' + chromosome + ' ' + args.input_original_fn + ' | ' + sort_bed_path + ' - | ' + starch_path + ' - > ' + temp_dest + '"'
]
if logger: logger.info('Submitting job via [%s]' % (' '.join(per_chromosome_sort_cmd_components)))
try:
Expand Down
4 changes: 2 additions & 2 deletions applications/bed/starch/src/Makefile
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Expand Up @@ -119,8 +119,8 @@ test: starch unstarch starchcat
make -C ${TEST} all

clean:
rm -f $(LOCALSTARCHLIB)
rm -rf $(LOCALSTARCHLIBDIR)
rm -f ${LOCALSTARCHLIBDEBUG}
rm -f ${LOCALSTARCHLIBGPROF}
rm -rf ${LOCALOBJDIR}
rm -rf ${BINDIR}
rm -rf ${BINDIR}
4 changes: 2 additions & 2 deletions applications/bed/starch/src/Makefile.darwin
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Expand Up @@ -31,7 +31,7 @@ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
BINDIR = ../bin
WARNINGS = -Weverything -Wno-c++98-compat-pedantic -Wno-padded
ARCH_VERSION = v2.2
BIN_VERSION = v2.4.27
BIN_VERSION = v2.4.28
TEST = ../test
TEST_OSX_BINDIR = ${TEST}/binaries/osx/${ARCH_VERSION}/bin

Expand Down Expand Up @@ -134,7 +134,7 @@ mkdirs:
mkdir -p ${BINDIR}

clean:
rm -f $(LOCALSTARCHLIB)
rm -rf $(LOCALSTARCHLIBDIR)
rm -f ${LOCALSTARCHLIBDEBUG}
rm -rf ${LOCALOBJDIR}
rm -rf ${LOCALSTARCHLIBDIR}
Expand Down
2 changes: 1 addition & 1 deletion applications/bed/starch/src/starch-diff.py
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Expand Up @@ -32,7 +32,7 @@
name = "starch-diff"
citation = " citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
authors = " authors: Alex Reynolds and Shane Neph"
version = " version: 2.4.27"
version = " version: 2.4.28"
usage = " $ starch-diff [ --chr <chr> ] starch-file-1 starch-file-2 [ starch-file-3 ... ]"
help = """
The 'starch-diff' utility compares the signatures of two or more specified
Expand Down
2 changes: 1 addition & 1 deletion applications/bed/starch/src/starchcluster_gnuParallel.tcsh
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Expand Up @@ -2,7 +2,7 @@

# author : sjn and apr
# date : Feb 2012
# version : v2.4.27
# version : v2.4.28

#
# BEDOPS
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2 changes: 1 addition & 1 deletion applications/bed/starch/src/starchcluster_sge.tcsh
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Expand Up @@ -2,7 +2,7 @@

# author : sjn and apr
# date : Feb 2012
# version : v2.4.27
# version : v2.4.28

#
# BEDOPS
Expand Down
2 changes: 1 addition & 1 deletion applications/bed/starch/src/starchcluster_slurm.tcsh
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Expand Up @@ -2,7 +2,7 @@

# author : sjn and apr
# date : 13 Sep 2016
# version : v2.4.27
# version : v2.4.28

#
# BEDOPS
Expand Down
2 changes: 1 addition & 1 deletion docs/conf.py
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Expand Up @@ -52,7 +52,7 @@
# The short X.Y version.
version = '2.4'
# The full version, including alpha/beta/rc tags.
release = '2.4.27'
release = '2.4.28'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
Expand Down
35 changes: 31 additions & 4 deletions docs/content/installation.rst
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Expand Up @@ -119,7 +119,7 @@ Compilation of BEDOPS on Linux requires GCC 4.8.2 (both ``gcc`` and ``g++`` and
$ cd bedops
$ make

.. tip:: BEDOPS now supports parallel builds. If you are compiling on a multicore or multiprocessor workstation, use ``make -j N`` where ``N`` is ``2``, ``4`` or however many cores or processors you have, in order to parallelize and speed up the build process.
.. tip:: BEDOPS supports parallel builds, which speeds up compilation considerably. If you are compiling on a multicore or multiprocessor workstation, edit the ``JPARALLEL`` variable in the top-level Makefile, or override it, specifying the number of cores or processors you wish to use to compile.

5. Once the build is complete, install compiled binaries and scripts to a local ``bin`` folder:

Expand All @@ -141,9 +141,9 @@ Compilation of BEDOPS on Linux requires GCC 4.8.2 (both ``gcc`` and ``g++`` and
Mac OS X
--------

In Mac OS X, you have two options to install BEDOPS via source code: Compile the code manually, or use the Homebrew package manager to manage installation of a prebuilt pacakge.
In Mac OS X, you have a few options to install BEDOPS via source code: Compile the code manually, or use the Bioconda or Homebrew package manager to manage installation.

Compilation of BEDOPS on Mac OS X via either procedure requires Clang/LLVM 3.5 or greater, which includes support for `C++11 <http://en.wikipedia.org/wiki/C%2B%2B11>`_ features required by core BEDOPS tools. Other tools may be required as described in the installation documentation that follows. GNU GCC is no longer required for compilation on OS X hosts.
Compilation of BEDOPS on Mac OS X requires Clang/LLVM 3.5 or greater, which includes support for `C++11 <http://en.wikipedia.org/wiki/C%2B%2B11>`_ features required by core BEDOPS tools. Other tools may be required as described in the installation documentation that follows. GNU GCC is no longer required for compilation on OS X hosts.

^^^^^^^^^^^^^^^^^^
Manual compilation
Expand Down Expand Up @@ -174,7 +174,7 @@ Manual compilation
$ cd bedops
$ make

.. tip:: BEDOPS now supports parallel builds. If you are compiling on a multicore or multiprocessor workstation, use ``make -j N`` where ``N`` is ``2``, ``4`` or however many cores or processors you have, in order to parallelize and speed up the build process.
.. tip:: BEDOPS supports parallel builds, which speeds up compilation considerably. If you are compiling on a multicore or multiprocessor workstation, edit the ``JPARALLEL`` variable in the top-level Makefile, or override it, specifying the number of cores or processors you wish to use to compile.

5. Once the build is complete, install compiled binaries and scripts to a local ``bin`` folder:

Expand All @@ -190,6 +190,33 @@ Manual compilation

Change this destination folder, as needed.

^^^^^^^^^^^^^^^^^^^^^^^^^
Installation via Bioconda
^^^^^^^^^^^^^^^^^^^^^^^^^

Bioconda is a bioinformatics resource that extends the Conda package manager with scientific software packages, including BEDOPS. We aim to keep the recipe concurrent with the present release; occasionally, it may be a minor version behind.

What follows are steps taken from the `Bioconda installation page <https://bioconda.github.io/>`_. Use this guide for the most current set of instructions, which we briefly cover here:

1. Follow the instructions on `Conda's website <http://conda.pydata.org/miniconda.html>`_ to install the Miniconda package, which installs the ``conda`` command-line tool.

2. If you have not already done so, add the Conda channels that Bioconda depends upon:

::

$ (conda config --add channels r)
$ conda config --add channels defaults
$ conda config --add channels conda-forge
$ conda config --add channels bioconda

3. Install the BEDOPS package:

::

$ conda install bedops

`Other recipes <https://bioconda.github.io/recipes.html#recipes>`_ are available for installation, as well.

^^^^^^^^^^^^^^^^^^^^^^^^^
Installation via Homebrew
^^^^^^^^^^^^^^^^^^^^^^^^^
Expand Down
2 changes: 1 addition & 1 deletion docs/content/reference/file-management/compression/starch-diff.rst
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Expand Up @@ -39,7 +39,7 @@ Use the ``--help`` option to list all options:

starch-diff
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version: 2.4.27
version: 2.4.28
authors: Alex Reynolds and Shane Neph

$ starch-diff [ --chr <chr> ] starch-file-1 starch-file-2 [ starch-file-3 ... ]
Expand Down
2 changes: 1 addition & 1 deletion docs/content/reference/file-management/compression/starch.rst
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Expand Up @@ -49,7 +49,7 @@ Use the ``--help`` option to list all options:

starch
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
binary version: 2.4.27 (creates archive version: 2.2.0)
binary version: 2.4.28 (creates archive version: 2.2.0)
authors: Alex Reynolds and Shane Neph

USAGE: starch [ --note="foo bar..." ]
Expand Down
2 changes: 1 addition & 1 deletion docs/content/reference/file-management/compression/starchcat.rst
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Expand Up @@ -57,7 +57,7 @@ Use the ``--help`` option to list all options:

starchcat
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version: 2.4.27
version: 2.4.28
authors: Alex Reynolds and Shane Neph

USAGE: starchcat [ --note="..." ]
Expand Down
2 changes: 1 addition & 1 deletion docs/content/reference/file-management/compression/starchstrip.rst
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Expand Up @@ -39,7 +39,7 @@ Use the ``--help`` option to list all options:

starchstrip
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
version: 2.4.27
version: 2.4.28
authors: Alex Reynolds and Shane Neph

USAGE: starchstrip [ --include | --exclude ] <chromosome-list> <starch-file>
Expand Down
2 changes: 1 addition & 1 deletion docs/content/reference/file-management/compression/unstarch.rst
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Expand Up @@ -43,7 +43,7 @@ Use the ``--help`` option to list all options:

unstarch
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
binary version: 2.4.27 (extracts archive version: 2.2.0 or older)
binary version: 2.4.28 (extracts archive version: 2.2.0 or older)
authors: Alex Reynolds and Shane Neph

USAGE: unstarch [ <chromosome> ] [ --elements |
Expand Down

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