miniconda update

.gitignore

@@ -0,0 +1,2 @@
+zUMIs-env/
+zUMIs-miniconda.tar.bz2

README.md

@@ -1,5 +1,20 @@
 # Welcome to zUMIs :wrench: :red_car::dash: :wrench:
 
+## Quickstart
+Nobody likes reading long README files so here is how you get going:
+Fetch zUMIs by cloning the repository:
+```
+git clone https://github.com/sdparekh/zUMIs.git`
+```
+Start anaylysing your data:
+```
+zUMIs/zUMIs-master.sh -c -y my_config.yaml
+```
+zUMIs now comes with its own [miniconda](https://docs.conda.io/en/latest/miniconda.html) environment, so you do not need to deal with dependencies or installations (use the -c flag to use conda).
+If you wish to use your own dependencies, head to the [zUMIs wiki](https://github.com/sdparekh/zUMIs/wiki/Installation#dependencies) to see what is required. 
+
+
+## Intro
 zUMIs is a fast and flexible pipeline to process RNA-seq data with (or without) UMIs.
 
 The input to this pipeline is simply fastq files. In the most common cases, you will have a read containing the cDNA sequence and other read(s) containing UMI and Cell Barcode information. Furthermore, you will need a STAR index for your genome and GTF annotation file.
@@ -11,9 +26,11 @@ You can read more about zUMIs in our [paper](https://doi.org/10.1093/gigascience
 ## Loom output
 The loom format is increasing in popularity and compatible with downstream analysis using python out of the box.
 We provide a script to convert zUMIs output into loom file automatically based on the [loomR package from the Satija lab](https://satijalab.org/loomR/loomR_tutorial.html). Please make sure you have loomR installed.
-To convert zUMIs output to loom, simply run `Rscript rds2loom.R myRun.yaml`.
+zUMIs will try to automatically do this, otherwise convert zUMIs output to loom by simply running `Rscript rds2loom.R myRun.yaml`.
 
 ## Changelog
+19 Feb 2020: [zUMIs2.7.0 released](https://github.com/sdparekh/zUMIs/releases/tag/2.7.0): Simplify installation greatly by a cond-pack of miniconda with all dependencies. The conda environment is used with `zUMIs-master.sh -c`, with the old behavior staying as the default. 
+
 13 Feb 2020: zUMIs2.6.3: Faster demultiplexing using python/pysam. Made forking of UMI collapse worker threads more robust.
 
 06 Feb 2020: zUMIs2.6.2: Changes to the hamming distance UMI collapse to avoid overcollapsing of highly expressed genes.

UMIstuffFUN.R

@@ -382,7 +382,7 @@ demultiplex_bam <- function(opt, bamfile, nBCs){
     dir.create( paste0(opt$out_dir,"/zUMIs_output/demultiplexed/") )
   }
 
-  installed_py <- system("pip3 freeze", intern = TRUE)
+  installed_py <- system("pip freeze", intern = TRUE)
 
   if(any(grepl("pysam==",installed_py))){
     print("Using python implementation to demultiplex.")

misc/rds2loom.R

@@ -16,11 +16,11 @@ rds_to_loom <- function(zUMIsRDS){
   for(type in names(rds)){
     for(quant in names(rds[[type]])){
       outfile <- paste0(opt$out_dir,"/zUMIs_output/expression/",opt$project,".",type,".",quant,".all.loom")
-      loomR::create(filename = outfile, data = as.matrix(rds[[type]][[quant]][["all"]]), transpose = TRUE,overwrite = TRUE)
+      loomR::create(filename = outfile, data = as.matrix(rds[[type]][[quant]][["all"]]), do.transpose = TRUE,overwrite = TRUE)
 
       for(d in names(rds[[type]][[quant]][["downsampling"]])){
         outfile <- paste0(opt$out_dir,"/zUMIs_output/expression/",opt$project,".",type,".",quant,".",d,".loom")
-        loomR::create(filename = outfile, data = as.matrix(rds[[type]][[quant]][["downsampling"]][[d]]), transpose = TRUE,overwrite = TRUE)
+        loomR::create(filename = outfile, data = as.matrix(rds[[type]][[quant]][["downsampling"]][[d]]), do.transpose = TRUE,overwrite = TRUE)
 
       }
     }
@@ -46,4 +46,4 @@ checkLoomR() #check for loomR package
 rds_loc <- paste0(opt$out_dir,"/zUMIs_output/expression/",opt$project,".dgecounts.rds")
 rds_to_loom(rds_loc)
 
-q()
+q()

zUMIs-master.sh

@@ -3,7 +3,7 @@
 # Pipeline to run UMI-seq analysis from fastq to read count tables.
 # Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann
 # Contact: [email protected] or [email protected]
-vers=2.6.3b
+vers=2.7.0
 currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh | grep '^vers=' | cut -f2 -d "="`
 if [ "$currentv" != "$vers" ]; then echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------"; fi
 
@@ -38,6 +38,10 @@ function usage () {
 ## Program path ##
 	-d  <zUMIs-dir>   	 : Directory containing zUMIs scripts.  Default: path to this script.
 
+## Miniconda environment
+
+  -c : Use zUMIs dependencies in the preinstalled conda enviroment.
+
 zUMIs version $vers
 
 EOF
@@ -46,10 +50,12 @@ EOF
 # Define the default variables #
 zumisdir=$(dirname `readlink -f $0`)
 
-while getopts ":y:d:h" options; do #Putting <:> between keys implies that they can not be called without an argument.
+
+while getopts ":y:d:ch" options; do #Putting <:> between keys implies that they can not be called without an argument.
   case $options in
   y ) yaml=$OPTARG;;
   d ) zumisdir=$OPTARG;;
+  c ) conda=true;;
   h ) usage
           exit 1;;
   \? ) echo -e "\n This key is not available! Please check the usage again: -$OPTARG"
@@ -109,6 +115,43 @@ if grep -q 'Rscript_exec:' $yaml
     echo "Rscript_exec: $Rexc" >> $yaml
 fi
 
+#check for conda usage!
+if [[ $conda = true ]]; then
+  echo "Using miniconda environment for zUMIs!"
+  samtoolsexc=samtools
+  if grep -q 'samtools_exec:' $yaml; then
+      sed -i '/samtools_exec:/d' $yaml
+  fi
+  echo "samtools_exec: $samtoolsexc" >> $yaml
+  pigzexc=pigz
+  if grep -q 'pigz_exec:' $yaml; then
+      sed -i '/pigz_exec:/d' $yaml
+  fi
+  echo "pigz_exec: $pigzexc" >> $yaml
+  starexc=STAR
+  if grep -q 'STAR_exec:' $yaml; then
+      sed -i '/STAR_exec:/d' $yaml
+  fi
+  echo "STAR_exec: $starexc" >> $yaml
+  Rexc=Rscript
+  if grep -q 'Rscript_exec:' $yaml; then
+      sed -i '/Rscript_exec:/d' $yaml
+  fi
+  echo "Rscript_exec: $Rexc" >> $yaml
+
+  zumisenv=$zumisdir/zUMIs-env
+  miniconda=$zumisdir/zUMIs-miniconda.tar.bz2
+  #check if zUMIs environment has been unpacked from tar
+  if [[ ! -d $zumisenv ]] || [[ $zumisdir/zUMIs-miniconda.partaa -nt $zumisenv ]] ; then
+    [ -d $zumisenv ] || mkdir -p $zumisenv
+    cat $zumisdir/zUMIs-miniconda.parta* > $miniconda
+    tar -xj --overwrite -f $miniconda -C $zumisenv
+  fi
+  #activate zUMIs environment!
+  source $zumisenv/bin/activate
+  conda-unpack
+fi
+
 if grep -q 'zUMIs_directory:' $yaml
   then
     sed -i "s|zUMIs_directory:.*|zUMIs_directory: $zumisdir|" $yaml
@@ -261,3 +304,9 @@ then
   fi
   date
 fi
+
+
+#close conda enviroment if necessary
+if [ $conda = true ]; then
+  source $zumisenv/bin/deactivate
+fi