Java and R tools for analyzing Drop-seq data

Drop-seq questions may be directed to dropseq@gmail.com.
You may also use this address to be added to the Drop-seq Google group.

See Releases to download binaries.

See Drop-seq alignment cookbook for detailed usage of these tools.

See Census-seq computational protocols for detailed usage of Census-Seq tools.

See Donor Assignment cookbook for detailed usage of donor assignment and doublet detection tools.

Download source:

git clone https://github.com/broadinstitute/Drop-seq.git 
cd Drop-seq

There are two options for building and installing Java code.

• Build the executable jarfile, a single wrapper script from which all command-line programs can be invoked, installed in the cloned git sandbox.
• Build a zipfile containing the executable jarfile and wrapper scripts for all command-line programs. The zipfile can be installed in an arbitrary location.

./gradlew installDist

The wrapper script will be dropseq/build/install/dropseq/bin/dropseq. dropseq.bat for Windows.

./gradlew distZip

unzip -d <install-location> ./dropseq/build/distributions/dropseq-<version>.zip

Note that the name of the zipfile will be based on the tagged version and state of your git sandbox.

The files will be deployed into a subdirectory of <install-location> above, with name based on the name of the zipfile.

You are encouraged to use the pre-built binaries in Releases, but if you want to build from (possibly unstable) sources, you can build from github source as follows:

For each library in src/R/packages, you can install using devtools::install_github, e.g.

devtools::install_github("broadinstitute/Drop-seq", subdir="/src/R/packages/DropSeq.utilities")  

Alternately, you can download sources and use R CMD BUILD and R CMD INSTALL as usual.