On Mon, 9 Aug 2010 09:37:14 -0700 (PDT)
Dave wrote:
> 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
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/daviddreisigmey
On Aug 7, 4:46 pm, Dave 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 thi
Thanks everyone. I have already tried the full path:
(defn get-msms-pts-OSX
;; Finds the msms points for a density (optional DEFAULT = 1.0) and
radius (optional DEFAULT = 1.5)
[pdb-file density radius]
(execute (str "/Users/daviddreisigmeyer/msms_MacOSX_2.6.1/
pdb_to_xyzr " pdb-file
On Aug 7, 7:27 am, Meikel Brandmeyer wrote:
> (defn to-env
> [env-vars-map]
> (->> env-vars-map
> (map #(str (name (key %)) "=" (val %)))
> into-array))
>
> And an invocation:
>
> user=> (to-env {:PATH "/bin:/usr/bin" :HOME "/Users/mb" :foo "bar"})
> #
> user=> (seq *1)
> ("PATH=/bin:/
> :)
(inc ":)")
On Sat, Aug 7, 2010 at 7:27 AM, Meikel Brandmeyer wrote:
> Hi,
>
> Am 07.08.2010 um 05:06 schrieb j-g-faustus:
>
>> I don't think there's a direct way to create a String array in Clojure
>
> (defn to-env
> [env-vars-map]
> (->> env-vars-map
> (map #(str (name (key %)) "=" (
Hi,
Am 07.08.2010 um 05:06 schrieb j-g-faustus:
> I don't think there's a direct way to create a String array in Clojure
(defn to-env
[env-vars-map]
(->> env-vars-map
(map #(str (name (key %)) "=" (val %)))
into-array))
And an invocation:
user=> (to-env {:PATH "/bin:/usr/bin" :HOME
On Aug 7, 5:06 am, j-g-faustus wrote:
> I don't think there's a direct way to create a String array
> in Clojure
Correction - there is: (into-array String ["a" "b"])
jf
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On Aug 6, 11:50 pm, Dave wrote:
> I get the error:
>
> Cannot run program "pdb_to_xyzr": error=2, No such file or directory
> [Thrown class java.io.IOException]
You may have a path problem.
Try running "env" in the same fashion - I get a very basic path (just
"/bin" and "/usr/bin") and none of
Also, this only shows the 2nd call (with ls-arg2):
(defn test-execute [ls-arg1 ls-arg2]
(execute (str "ls -" ls-arg1))
(execute (str "ls -" ls-arg2)))
so maybe the difficulty above is some problem with how the multiple
system calls are performed. If I only use this:
(d
I having some trouble with system calls using clojure (actually a
whole lot more than that but this is the current day's difficulty).
Below, test-execute works, but get-msms-pts-OSX seems to hang, as in
nothing happens and the REPL is unresponsive afterwards. If I run the
output of the
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