I have code that did that, but it wasn't reliable enough to use like
that. For unknown reasons, there are programs that I couldn't call at
all.
The only reliable method that I found was to write a one-liner shell
script to be executed by sh, but this is an ugly, ugly hack.
The grabbing of stdin a
Once upon a time, Thomas Down wrote:
>
> A lot of these issues could probably be addressed by something
> like:
>
> public class ExecTools {
Okay, I've had a first stab at this -- you can see what I
ended up with in org.biojava.utils.ProcessTools. In my
tests so far, it seems to be working quite
On Mon, 2003-08-11 at 11:57, David Huen wrote:
> Would something hybrid like Jython be useful in this context? Perhaps they
> might have encountered and solved some of these problems.
I'd have a preference to an all-java solution if possible. Java code is
easier to maintain for the rest of us.
> "Thomas" == Thomas Down <[EMAIL PROTECTED]> writes:
[...]
Thomas> Yes, I quite agree. Although I think I'd prefer something
Thomas> more like:
Thomas>params.addParameter(NCBIBlast.PROGRAM_NAME, "blastn")
Thomas> Have you looked at the AnnotationType class? We could
a.org on
08/12/2003 10:39:04 PM
Sent by:[EMAIL PROTECTED]
To:"Keith James" <[EMAIL PROTECTED]>, "Thomas Down"
<[EMAIL PROTECTED]>
cc:[EMAIL PROTECTED]
Subject:RE: [Biojava-l] Running apps with Java
I would tend to agree with Keith. Mak
Hi there,
Apologies for the slight plug, but at the EBI we've been working on
something that might be of interest to people trying to do this. We have
a system called Soaplab that can be used to expose command line tools as
web services (trivial to then consume) and another project Taverna whic
IL PROTECTED]
Subject:Re: [Biojava-l] Running apps with Java
Once upon a time, Patrick McConnell wrote:
>
> Or, even better would be some sort of Parameters class to encapsulate all
> those parameters, providing optional parameters. Then, you could do
> something like this:
>
>NC
-Patrick
"Schreiber, Mark" <[EMAIL PROTECTED]>@biojava.org on
08/12/2003 10:39:04 PM
Sent by:[EMAIL PROTECTED]
To:"Keith James" <[EMAIL PROTECTED]>, "Thomas Down"
<[EMAIL PROTECTED]>
cc:[EMAIL PROTECTED]
Subject:RE: [Biojava-l]
> "Tom" == Tom Oinn <[EMAIL PROTECTED]> writes:
Tom> Isn't this what the ACD files in EMBOSS are doing? Perhaps not
Tom> reinventing the wheel would be good? Admittedly ACD is not the
Tom> most parsable file format to work with, but we have an XML
Tom> dialect of it which is (part of M
Once upon a time, Patrick McConnell wrote:
>
> Or, even better would be some sort of Parameters class to encapsulate all
> those parameters, providing optional parameters. Then, you could do
> something like this:
>
>NCBIBlastParameters params = new NCBIBlastParameters();
>params.addPara
James [mailto:[EMAIL PROTECTED]
Sent: Tue 12/08/2003 10:46 p.m.
To: Thomas Down
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Running apps with Java
>>>>> "Thomas" == Thomas Down &
On Monday 11 Aug 2003 3:03 pm, Francois Pepin wrote:
> I have code that did that, but it wasn't reliable enough to use like
> that. For unknown reasons, there are programs that I couldn't call at
> all.
>
> The only reliable method that I found was to write a one-liner shell
> script to be executed
I have implemented LocalProgram which runs programs based on an XML
description of the parameters. Program IO is handled in separate threads.
Also, local resources, such as paths to executables and databases, can be
loaded from XML. I have made the binaries, source, and documentation
availab
: Tue 12/08/2003 4:47 a.m.
To: Tom Oinn
Cc: biojava-l
Subject: Re: [Biojava-l] Running apps with Java
What do other people think about something like that?
We've basically got 2 problems here, running apps on the same ma
> Isn't this what the ACD files in EMBOSS are doing? Perhaps not
> reinventing the wheel would be good? Admittedly ACD is not the most
> parsable file format to work with, but we have an XML dialect of it
> which is (part of Martin's Soaplab).
>
> Martin - is the XML schema available somewhere?
On Tue, 12 Aug 2003, Schreiber, Mark wrote:
> Running on a remote machine (ie where the service is located by
> something like JNDI) might be best left to something like J2EE message
> driven beans or something similar. For good old biojava we should
> probably focus (at first) on local. After all
On Mon, Aug 11, 2003 at 11:59:46AM +1200, Schreiber, Mark wrote:
>
> What is the best way to invoke a native bioinformatics program in Java.
> People have reported that controlling processes directly has been patchy
> in Java, is this still the case or have JVMs evolved? If not then what
> is the
PROTECTED]
To: "Schreiber, Mark" <[EMAIL PROTECTED]>
cc:[EMAIL PROTECTED]
Subject:Re: [Biojava-l] Running apps with Java
On Mon, Aug 11, 2003 at 11:59:46AM +1200, Schreiber, Mark wrote:
>
> What is the best way to invoke a native bioinformatics program in Java.
> Peo
What do other people think about something like that?
We've basically got 2 problems here, running apps on the same machine
and running them on a remote machine.
If you can run apps on a remote machine, then you can obviously run them
on the local machine. But the machinery to do that is often pr
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