From dbd1953d7ca8d3264fdef4c7909561d99a001ce1 Mon Sep 17 00:00:00 2001 From: Hirak Sarkar Date: Thu, 7 Feb 2019 14:36:05 -0500 Subject: [PATCH 1/7] fixed the OSX compilation --- include/strict_fstream.hpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/strict_fstream.hpp b/include/strict_fstream.hpp index 21173c7..7713e84 100644 --- a/include/strict_fstream.hpp +++ b/include/strict_fstream.hpp @@ -27,7 +27,7 @@ static std::string strerror() { buff = "Unknown error"; } -#elif (_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE +#elif (_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600 || defined(__APPLE__)) && ! _GNU_SOURCE // XSI-compliant strerror_r() if (strerror_r(errno, &buff[0], buff.size()) != 0) { From 42f2f997c868c28c62432ad3cbf6b75af34d6751 Mon Sep 17 00:00:00 2001 From: Hirak Sarkar Date: Thu, 7 Feb 2019 19:54:06 -0500 Subject: [PATCH 2/7] fixed the OSX compilation --- CMakeLists.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index d2ef185..b4ff281 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -9,13 +9,13 @@ set(CMAKE_CXX_STANDARD 11) set(CMAKE_CXX_STANDARD_REQUIRED ON) set(KSW_FLAGS "-march=native -DHAVE_KALLOC") -set(RBF_CPP_FLAGS "-g -mbmi2 -msse4 -pthread -std=c++11 -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -openmp -Wno-unknown-pragmas -Wno-unused-function") -set(WARN_ALL_THINGS "-fdiagnostics-color=always -Wall -Wcast-align -Wcast-qual -Wconversion -Wctor-dtor-privacy -Wdisabled-optimization -Wdouble-promotion -Wextra -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wno-sign-conversion -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wredundant-decls -Wshadow -Wstrict-aliasing=1 -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Wno-unknown-pragmas -Wuseless-cast") +set(RBF_CPP_FLAGS "-mbmi2 -msse4 -pthread -std=c++11 -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -openmp -Wno-unknown-pragmas -Wno-unused-function -O3") +#set(WARN_ALL_THINGS "-fdiagnostics-color=always -Wall -Wcast-align -Wcast-qual -Wconversion -Wctor-dtor-privacy -Wdisabled-optimization -Wdouble-promotion -Wextra -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wno-sign-conversion -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wredundant-decls -Wshadow -Wstrict-aliasing=1 -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Wno-unknown-pragmas -Wuseless-cast") #set(WARN_ALL_THINGS "-fdiagnostics-color=always -Wall -Wcast-align -Wcast-qual -Wconversion -Wctor-dtor-privacy -Wdisabled-optimization -Wdouble-promotion -Wduplicated-branches -Wduplicated-cond -Wextra -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wno-sign-conversion -Wnoexcept -Wnull-dereference -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wredundant-decls -Wrestrict -Wshadow -Wstrict-aliasing=1 -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Wno-unknown-pragmas -Wuseless-cast") -set(OPT_FLAGS "-O3 -g -ffast-math -fPIC -funroll-loops -mmmx -msse -msse2 -msse3 -msse4 -msse4.2 -march=native -fno-strict-aliasing") +#set(OPT_FLAGS "-O3 -g -ffast-math -fPIC -funroll-loops -mmmx -msse -msse2 -msse3 -msse4 -msse4.2 -march=native -fno-strict-aliasing") #set(OPT_FLAGS "-fprofile-generate -O3 -DNDEBUG -funroll-loops -mmmx -msse -msse2 -msse3 -msse4 -msse4.2 -march=native -fno-strict-aliasing") #set(OPT_FLAGS "-fprofile-use -fprofile-correction -O3 -DNDEBUG -funroll-loops -mmmx -msse -msse2 -msse3 -msse4 -msse4.2 -march=native -fno-strict-aliasing") set(DEBUG_FLAGS "-pg -g -gstabs -no-pie") From fc7bb32cb42be02c4108e7912ac72688b7e3e60c Mon Sep 17 00:00:00 2001 From: Hirak Sarkar Date: Thu, 7 Feb 2019 20:05:08 -0500 Subject: [PATCH 3/7] fixed the OSX compilation --- CMakeLists.txt | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index b4ff281..0f6a744 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -8,8 +8,7 @@ list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake") set(CMAKE_CXX_STANDARD 11) set(CMAKE_CXX_STANDARD_REQUIRED ON) -set(KSW_FLAGS "-march=native -DHAVE_KALLOC") -set(RBF_CPP_FLAGS "-mbmi2 -msse4 -pthread -std=c++11 -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -openmp -Wno-unknown-pragmas -Wno-unused-function -O3") +set(RBF_CPP_FLAGS "-pthread -std=c++11 -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -openmp -Wno-unknown-pragmas -Wno-unused-function -O3") #set(WARN_ALL_THINGS "-fdiagnostics-color=always -Wall -Wcast-align -Wcast-qual -Wconversion -Wctor-dtor-privacy -Wdisabled-optimization -Wdouble-promotion -Wextra -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wno-sign-conversion -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wredundant-decls -Wshadow -Wstrict-aliasing=1 -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Wno-unknown-pragmas -Wuseless-cast") #set(WARN_ALL_THINGS "-fdiagnostics-color=always -Wall -Wcast-align -Wcast-qual -Wconversion -Wctor-dtor-privacy -Wdisabled-optimization -Wdouble-promotion -Wduplicated-branches -Wduplicated-cond -Wextra -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wno-sign-conversion -Wnoexcept -Wnull-dereference -Wold-style-cast -Woverloaded-virtual -Wpedantic -Wredundant-decls -Wrestrict -Wshadow -Wstrict-aliasing=1 -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Wno-unknown-pragmas -Wuseless-cast") From 74a382353cde6950d66544e241755a67b4c6a3b7 Mon Sep 17 00:00:00 2001 From: The Gitter Badger Date: Fri, 8 Feb 2019 02:31:49 +0000 Subject: [PATCH 4/7] Add Gitter badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3d859ff..f8752c4 100644 --- a/README.md +++ b/README.md @@ -93,7 +93,7 @@ The above process are required to be executed sequencially, for ease of use we uploaded the de-Bruijn graph and reference transcripts are uploaded in zenodo. -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2556439.svg)](https://doi.org/10.5281/zenodo.2556439) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2556439.svg)](https://doi.org/10.5281/zenodo.2556439) [![Join the chat at https://gitter.im/minnow-sim/community](https://badges.gitter.im/minnow-sim/community.svg)](https://gitter.im/minnow-sim/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) From b0b83b8a3e2db6fd47c6cdf6c0f41035a98bef59 Mon Sep 17 00:00:00 2001 From: Hirak Sarkar Date: Thu, 7 Feb 2019 21:42:28 -0500 Subject: [PATCH 5/7] Update README.md --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 3d859ff..4bf06d1 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,9 @@ [![Build Status](https://travis-ci.org/COMBINE-lab/minnow.svg?branch=master)](https://travis-ci.org/COMBINE-lab/minnow) +[![Join the chat at https://gitter.im/minnow-sim](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/minnow-sim?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) + # Minnow ( read level simulator for dscRNA-seq data) + Most analysis pipelines validate their results using known marker genes (which are not widely available for all types of analysis) and by using simulated data from gene-count-level simulators. Typically, the impact of using different read-alignment or UMI deduplication methods has not been widely explored. Assessments based on simulation tend to start at the level of assuming a simulated count matrix, ignoring the effect that different approaches for resolving UMI counts from the raw read data may produce. Here, we present minnow, a comprehensive sequence-level droplet-based single-cell RNA-seq (dscRNA-seq) experiment simulation framework. Minnow accounts for important sequence-level characteristics of experimental scRNA-seq datasets and models effects such as PCR amplification, CB (cellular barcodes) and UMI (Unique Molecule Identifiers) selection, and sequence fragmentation and sequencing. Minnow is a read level simulator for droplet based single cell RNA-seq data. Minnow simulates the reads by sampling sequences from the underlying de-Bruijn graph (using `--dbg`) of the reference transcriptome or alternatively just samples sequences from the reference transcriptome. As the `--dbg` option also enables other features of the software, it is useful to describe those. From aad8fae792e9c7377783da0e4d9c7c9c83cf00c4 Mon Sep 17 00:00:00 2001 From: Hirak Sarkar Date: Fri, 8 Feb 2019 14:10:35 -0500 Subject: [PATCH 6/7] Update README.md --- README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4bf06d1..6dbb77b 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ [![Build Status](https://travis-ci.org/COMBINE-lab/minnow.svg?branch=master)](https://travis-ci.org/COMBINE-lab/minnow) +[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/) [![Join the chat at https://gitter.im/minnow-sim](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/minnow-sim?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) # Minnow ( read level simulator for dscRNA-seq data) @@ -19,7 +20,11 @@ Minnow is a read level simulator for droplet based single cell RNA-seq data. Min [tutorial](https://combine-lab.github.io/alevin-tutorial/2019/running-minnow/) -## Installation + +## Installation +### Via conda +`conda install minnow -c bioconda` + Minnow is written in C++14 and tested in a ubuntu server, please let us know if you have difficulty compiling it in your own machine. ```console From e19ea1b65ef119ab81f0cd1ca62ab58fdd64542e Mon Sep 17 00:00:00 2001 From: Hirak Sarkar Date: Fri, 8 Feb 2019 16:13:40 -0500 Subject: [PATCH 7/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6dbb77b..4a4c3f4 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ Minnow is a read level simulator for droplet based single cell RNA-seq data. Min ## Installation ### Via conda `conda install minnow -c bioconda` - +### Manual installation (latest) Minnow is written in C++14 and tested in a ubuntu server, please let us know if you have difficulty compiling it in your own machine. ```console