Mercurial > repos > stevecassidy > wrassp

annotate r_wrapper.sh @ 0:6d6dc275b107 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
author stevecassidy
date Mon, 15 Aug 2016 23:48:20 -0400
parents
children dbcf9bc275e3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
1 #!/bin/sh
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
2
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
3 ### Run R providing the R script in $1 as standard input and passing
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
4 ### the remaining arguments on the command line
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
5
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
6 # Function that writes a message to stderr and exits
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
7 fail()
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
8 {
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
9 echo "$@" >&2
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
10 exit 1
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
11 }
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
12
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
13 # Ensure R executable is found
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
14 which R > /dev/null || fail "'R' is required by this tool but was not found on path"
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
15
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
16 # Extract first argument
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
17 infile=$1; shift
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
18
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
19 # Ensure the file exists
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
20 test -f $infile || fail "R input file '$infile' does not exist"
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
21
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
22 # Invoke R passing file named by first argument to stdin
6d6dc275b107 planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6
stevecassidy
parents:
diff changeset
23 R --vanilla --slave $* < $infile