Thanks jf, that worked:
(ns msms
(:gen-class)
(:use [clojure.contrib.shell-out :only (sh)]))
(defn get-msms-pts-OSX
[{pdb-file :pdb-file density :density radius :radius :as all :or
{density "1.0" radius "1.5"}}]
(if (contains? all :pdb-file)
(sh "bash" :in (str "/Users/daviddreisigmeyer/msms_MacOSX_2.6.1/
pdb_to_xyzr " pdb-file
" >
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr && "
"msms.MacOSX.2.6.1"
" -if
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr"
" -of
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold -
no_header -density "
density " -probe_radius " radius " && "
"rm -f
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr"
"
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.face"))
(println "No pdb-file provided in get-msms-pts-OSX.")))
Without the && in the system call:
(defn get-msms-pts-OSX
[{pdb-file :pdb-file density :density radius :radius :as all :or
{density "1.0" radius "1.5"}}]
(if (contains? all :pdb-file)
((sh "bash" :in (str "/Users/daviddreisigmeyer/msms_MacOSX_2.6.1/
pdb_to_xyzr " pdb-file
" >
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr"))
(sh "bash" :in (str "msms.MacOSX.2.6.1"
" -if
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr"
" -of
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold -
no_header -density "
density " -probe_radius " radius))
(sh "bash" :in (str "rm -f /Users/daviddreisigmeyer/lisps/clojure/
dpa/src/hold.xyzr"
"
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.face")))
(println "No pdb-file provided in get-msms-pts-OSX.")))
I'd get the error:
java.lang.String cannot be cast to clojure.lang.IFn
Here it would only call the first command. If I added a println
statement
(defn get-msms-pts-OSX
((println "Hi")
(sh "bash" :in (str "/Users/daviddreisigmeyer/msms_MacOSX_2.6.1/
pdb_to_xyzr " pdb-file
" >
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr"))
(sh "bash" :in (str "msms.MacOSX.2.6.1"
" -if
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.xyzr"
" -of
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold -
no_header -density "
density " -probe_radius " radius))
(sh "bash" :in (str "rm -f /Users/daviddreisigmeyer/lisps/clojure/
dpa/src/hold.xyzr"
"
/Users/daviddreisigmeyer/lisps/clojure/dpa/src/hold.face")))
(println "No pdb-file provided in get-msms-pts-OSX.")))
it would run all three commands, and then print this error:
No message.
[Thrown class java.lang.NullPointerException]
Can you see why this would be?
Thanks again for your help,
-Dave
On Aug 8, 12:00 am, j-g-faustus <[email protected]> wrote:
> On Aug 7, 4:46 pm, Dave <[email protected]> wrote:
>
> > (execute (str "/../pdb_to_xyzr " pdb-file " > /..")))
>
> > Here it seemed to run (the above error isn't shown) but nothing
> > happened and the REPL become unresponsive again.
>
> I think the issue is that Runtime.exec doesn't start a shell, just a
> subprocess, so things that are normally handled by the shell (like
> redirection and pipes) doesn't work.
> On
> (execute "env | grep PATH")
> I get "env: |: no such file or directory" - pipes and redirections are
> passed as arguments to the first command rather than being handled by
> the shell.
>
> > When I try:
> > (sh :in (str "/...pdb_to_xyzr" pdb-file " > /...hold.xyzr")))
> > I get the following:
> > No matching method found: exec for class java.lang.Runtime
>
> :in is the "standard in" for a command, but you haven't specified
> which command.
>
> If you use "sh" as the command you get a shell and can use normal
> shell syntax for the :in parameter.
>
> So this works:
> user=> (sh "sh" :in "env | grep PATH")
> "PATH=/usr/bin:/bin:/usr/sbin:/sbin\n"
> user=> (sh "sh" :in "env > tmp.txt")
> ""
>
> > Does anyone know why this doesn't seem to work:
>
> > (defn test-execute [ls-arg1 ls-arg2]
> > (execute (str "ls -" ls-arg1))
> > (execute (str "ls -" ls-arg2)))
>
> As far as I can tell it does - it executes both commands, but returns
> only the result of the last one.
> If you want both, wrap them in a list or vector:
> (defn test-execute [ls-arg1 ls-arg2]
> (list
> (execute (str "ls -" ls-arg1))
> (execute (str "ls -" ls-arg2))))
>
> Regards
> jf
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