https://github.com/galaxyproject/galaxy
Raw File
Tip revision: 7c671f8421b0b96ba8df06a4678e00cfe614f16f authored by Dannon Baker on 12 February 2015, 13:28:37 UTC
Fix path manipulation during fetch_eggs. This getting an external version of pkg_resources (and not ours in lib/) is what is causing the weird egg fetching errors. Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard version identifiers.
Tip revision: 7c671f8
r_wrapper.sh
#!/bin/sh

### Run R providing the R script in $1 as standard input and passing 
### the remaining arguments on the command line

# Function that writes a message to stderr and exits
fail()
{
    echo "$@" >&2
    exit 1
}

# Ensure R executable is found
which R > /dev/null || fail "'R' is required by this tool but was not found on path" 

# Extract first argument
infile=$1; shift

# Ensure the file exists
test -f $infile || fail "R input file '$infile' does not exist"

# Invoke R passing file named by first argument to stdin
R --vanilla --slave $* < $infile
back to top