Shell script standardization and other minor changes

Changes

• Standardize shell scripts, including alignment, reference metadata creation, and tool wrapper scripts. Thanks to @mschilli87.
• Add ability to request multiple cores in alignment script.
• Remove dependent jars and instead get from Maven Central. Thanks to @lbergelson.
• In various programs, filter out reads with UMI == -, which is how STARsolo marks chimeric reads.
• Change the dependency between our R packages from Imports to Suggests.

Installation

Java

Download and unzip dropseq-3.0.1.zip . Wrapper scripts for all the command-line programs will be in the dropseq-3.0.1 directory that is created when unzipping.

R packages

Do this in the order below, because DropSeq.dropulation depends on DropSeq.utilities, and if you don't install that package first, the source version of DropSeq.utilities will be installed, which may be unstable.

install.packages("https://github.com/broadinstitute/Drop-seq/releases/download/v3.0.0/DropSeq.utilities_3.0.1.tar.gz") 
install.packages("https://github.com/broadinstitute/Drop-seq/releases/download/v3.0.0/DropSeq.dropulation_3.0.1.tar.gz")