Merge pull request #8 from drneavin/v1.0.4

V1.0.4

Singularity.Demuxafy

@@ -3,7 +3,7 @@ From: continuumio/miniconda3
 
 %labels
 	Author = Drew Neavin
-	Image_version = 1.0.2
+	Image_version = 2.0.0
 
 %environment
     export PATH=/opt:/usr/games:/opt/conda/envs/py37/bin:/opt/conda/bin:/opt/Demultiplexing_Doublet_Detecting_Docs/scripts:opt/Demultiplexing_Doublet_Detecting_Docs/mods:/opt/bedtools2/bin:/opt/vartrix-v1.1.3-x86_64-linux/:opt/vcflib/bin:/opt/vcflib/scripts:/opt/souporcell:/opt/souporcell/troublet/target/release:/opt/minimap2-2.7:/root/.cargo/bin:/opt/freebayes/scripts:/opt/popscle/bin/:/opt/conda/envs/py37/lib/python3.7/site-packages/scSplit/:$PATH
@@ -20,9 +20,7 @@ From: continuumio/miniconda3
     yes | apt upgrade
     yes | apt-get install build-essential
     apt-get install -y --no-install-recommends apt-utils
-#    apt-get install -y gcc-7 g++-7 gfortran-7 libgfortran-7-dev
-#    update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 60 --slave /usr/bin/g++ g++ /usr/bin/g++-7
-#    update-alternatives --config gcc
+
     gcc --version
     yes | apt-get install wget
     yes | apt-get install curl
@@ -34,43 +32,47 @@ From: continuumio/miniconda3
     yes | apt-get upgrade
     apt install -y ca-certificates gnupg2
     apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7'
-#    add-apt-repository 'deb http://cloud.r-project.org/bin/linux/debian buster-cran40/'
     add-apt-repository 'deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/'
     apt-get update
     apt install -y r-base
     apt install -y r-base-dev
+    apt install -y  r-cran-devtools
+#    apt -y install r-cran-seurat
     apt-get update
     apt-get install -y libv8-dev
     apt-get update
     apt install -y ncdu
+    apt install -y libgeos-dev
 
 
 	add-apt-repository 'deb http://security.debian.org/debian-security jessie/updates main'
 	apt-get update -y && apt-get install -y --no-install-recommends libssl1.0.0
 
-        yes | apt-get install libncurses5-dev
-        yes | apt-get install zlib1g-dev
-        yes | apt-get install libbz2-dev
-        yes | apt-get install liblzma-dev
-        yes | apt-get install zlib1g
-        yes | apt-get install zlib1g-dev
-        apt-get install -y pkg-config
-        apt-get install -y libcurl4-openssl-dev
-        apt-get install -y graphviz
-        apt-get install -y graphviz-dev
-        apt-get install -y libxml2
-        apt-get install -y libxml2-dev
-        apt-get install -y bzip2
-        apt-get install -y libssl-dev
-        apt-get install -y devscripts
-		apt-get install -y tabix
-		apt-get install -y libcairo2-dev ## for complex heatmap
-		apt-get install -y libgmp-dev
-		apt-get install -y libgtk2.0-dev
-		apt-get install -y xvfb
-		apt-get install -y xauth
-		apt-get install -y xfonts-base
-		apt-get install -y libxt-dev
+    yes | apt-get install libncurses5-dev
+    yes | apt-get install zlib1g-dev
+    yes | apt-get install libbz2-dev
+    yes | apt-get install liblzma-dev
+    yes | apt-get install zlib1g
+    yes | apt-get install zlib1g-dev
+    apt-get install -y pkg-config
+    apt-get install -y libcurl4-openssl-dev
+    apt-get install -y graphviz
+    apt-get install -y graphviz-dev
+    apt-get install -y libxml2
+    apt-get install -y libxml2-dev
+    apt-get install -y bzip2
+    apt-get install -y libssl-dev
+    apt-get install -y devscripts
+    apt-get install -y tabix
+    apt-get install -y libcairo2-dev ## for complex heatmap
+    apt-get install -y libgmp-dev
+    apt-get install -y libgtk2.0-dev
+    apt-get install -y xvfb
+    apt-get install -y xauth
+    apt-get install -y xfonts-base
+    apt-get install -y libxt-dev
+    apt-get install -y libhdf5-dev
+
 
     cd /opt
 		wget https://github.com/Kitware/CMake/releases/download/v3.14.4/cmake-3.14.4.tar.gz
@@ -91,8 +93,8 @@ From: continuumio/miniconda3
 
 	### Install bedtools2 for souporcell ###
     cd /opt
-    wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz
-        tar -zxvf bedtools-2.28.0.tar.gz
+    wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools-2.30.0.tar.gz
+        tar -zxvf bedtools-2.30.0.tar.gz
         cd bedtools2
         make
 
@@ -144,6 +146,7 @@ From: continuumio/miniconda3
 
 
 	### Install python dependencies  ###
+    /opt/conda/envs/py37/bin/pip install pytorch-lightning==1.3.1 torch==1.11.0 torchmetrics==0.7.2 torchvision==0.12.0
     yes | conda install pytorch torchvision cudatoolkit=11.0.221 -c pytorch ## solo
 	/opt/conda/envs/py37/bin/pip install scvi-tools ## required for solo
     /opt/conda/envs/py37/bin/pip install setuptools==57.5.0 ##scSplit, souporcell
@@ -162,6 +165,7 @@ From: continuumio/miniconda3
     /opt/conda/envs/py37/bin/pip install h5py
     /opt/conda/envs/py37/bin/pip install xgboost
 	/opt/conda/envs/py37/bin/pip install argparse
+
 
 	### Install R libraries ###
 	## Base helper packages ##
@@ -173,25 +177,28 @@ From: continuumio/miniconda3
     R --slave -e 'install.packages("remotes", repos = "http://cran.us.r-project.org")'
     R --slave -e 'install.packages("xgboost", repos = "http://cran.us.r-project.org")'
     R --slave -e 'install.packages("argparse", repos = "http://cran.us.r-project.org")'
-    R --slave -e 'install.packages("https://cran.r-project.org/src/contrib/BH_1.75.0-0.tar.gz", repos=NULL,type="source")'
+    R --slave -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.3-4.tar.gz", repos=NULL, type="source")'
 
 	# ## Other helper pacages ##
+    R --slave -e 'install.packages("hdf5r", repos = "http://cran.us.r-project.org")'
     R --slave -e 'devtools::install_github(repo="knausb/vcfR")'
     R --slave -e 'install.packages("Cairo",repo="http://cran.us.r-project.org")' ### Required for Complex Heatmap
     R --slave -e 'BiocManager::install("ComplexHeatmap")'
     R --slave -e 'install.packages("lsa", repos = "http://cran.us.r-project.org")'
     R --slave -e 'install.packages("ComplexUpset", repos = "http://cran.us.r-project.org")'
 
 	## Single Cell packages ##
-#    R --slave -e 'install.packages("BH", repos = "http://cran.us.r-project.org")'
-    R --slave -e 'install.packages("Seurat", repos = "http://cran.us.r-project.org")'
+    R --slave -e 'install.packages("BH", repos = "http://cran.us.r-project.org")'
+    R --slave -e 'remotes::install_version("SeuratObject", version = "4.0.4")'
+    R --slave -e 'remotes::install_version("Seurat", version = "4.1.0")'
+#    R --slave -e 'install.packages("Seurat", repos = "http://cran.us.r-project.org")'
 
 	# Doublet Detecting packages ##
 	R --slave -e 'install.packages("xgboost" ,repo="http://cran.us.r-project.org")' ### Depdnency for scDblFinder and scds
 	R --slave -e 'BiocManager::install("mbkmeans")' ### Depdnency for scDblFinder and scds
     R --slave -e 'devtools::install_github("kostkalab/scds", ref="master")' ### One of the dependencies = SCE so dont need to install separately
     R --slave -e 'BiocManager::install("scDblFinder")'
-    R --slave -e 'devtools::install_github("EDePasquale/DoubletDecon")'
+    R --slave -e 'devtools::install_github("drneavin/DoubletDecon")' ### Forked and changed on August 2, 2022 because of errors with original directory and poor response from author of repo so unlikely to fix
     R --slave -e 'remotes::install_github("chris-mcginnis-ucsf/DoubletFinder")'
 
 
@@ -294,7 +301,7 @@ From: continuumio/miniconda3
 
 	### Get the github repo with scripts for workflow ###
 	cd /opt
-		git clone  --branch v1.0.2 https://github.com/drneavin/Demultiplexing_Doublet_Detecting_Docs.git
+		git clone --branch v1.0.4 https://github.com/drneavin/Demultiplexing_Doublet_Detecting_Docs.git
                 cd Demultiplexing_Doublet_Detecting_Docs
                 rm -rf references ## Only hosting on  github for people to download if they want, no need to take up extra space in the image
                 rm -rf docs ## doc files, dont need in image		
@@ -315,7 +322,7 @@ From: continuumio/miniconda3
 	cd /opt
 	rm cmake-3.14.4.tar.gz
 	rm v2.7.tar.gz
-	rm bedtools-2.28.0.tar.gz
+    rm bedtools-2.30.0.tar.gz
 	rm vartrix-v1.1.3-x86_64-linux.tar.gz
 	rm htslib-1.13.tar.bz2
 	rm samtools-1.13.tar.bz2

docs/source/CombineResults.rst

@@ -1,9 +1,12 @@
 .. _Combine-docs:
 
-Combining Results
-=================
+Comparing and Combining Results
+==================================
 
-After you have run each of the Demultiplexing and Doublet Detecting softwares you would like, it is helpful to convert them to similar nomenclature and combine the results into a single dataframe.
+.. _preprint: https://www.biorxiv.org/content/10.1101/2022.03.07.483367v1
+
+
+After you have run each of the Demultiplexing and/or Doublet Detecting softwares you would like, it is helpful to convert them to similar nomenclature and combine the results into a single dataframe.
 In addition, we have found it helpful to generate summaries of each of the combinations of softwares identified.
 To help streamline this process, we have provided a script that will easily integrate all the softwares you have run into a single dataframe and can do the following:
 
@@ -404,4 +407,4 @@ Here's a deeper look at the contents of each of these results:
 
 Citation
 --------
-If you used the Demuxafy platform for analysis, please reference our paper (REFERENCE).
+If you used the Demuxafy platform for analysis, please reference our preprint_.