Reproduction of snakemake issue #916

README.md

This demonstrates the issue discussed in https://bitbucket.org/snakemake/snakemake/issues/916/integrated-r-scripts-and-directory

To reproduce that and test any fixes, simply clone this github respository and chmod -R a-w it. Then go to a different directory and snakemake -s path/to/the/snakefile/here. With an unpatched copy of snakemake you'll get a permissions error. Note that the Snakefile has examples using R and Rmd files, so you'll need to ensure that R is in your PATH.

from_python.py

#!/usr/bin/env python
import sys
import local_script
of = open(snakemake.output[0], "w")
of.write("got here\n")
of.write("__file__ is {}\n".format(__file__))
of.write("local_script.contents {}\n".format(local_script.contents))
of.write("local_script.__file__ {}\n".format(local_script.__file__))
of.write("sys.path: {}\n".format(", ".join(sys.path)))
of.close()

from_R.R

of = snakemake@output[[1]]
sink(of)
sessionInfo()
sink()

from_Rmd.Rmd

Blah blah blah

```{r}
print(snakemake)
summary(cars)
```

```{r}
sessionInfo()
```

local_script.py

contents = "blah blah blah"

Snakefile

rule all:
    input: "from_python", "from_R", "from_Rmd.html"


rule blah:
    input:
    output: "from_python"
    script: "from_python.py"


rule foobar:
    input:
    output: "from_R"
    script: "from_R.R"


rule quux:
    output: "from_Rmd.html"
    script: "from_Rmd.Rmd"