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Author Topic: Redirect Auxiliary File Output  (Read 9397 times)

Offline eholzhauser

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Redirect Auxiliary File Output
« on: May 12, 2016, 02:50:03 pm »
Hello Dr. Lu,

I was wondering if there is a command to redirect the output of the auxiliary files used by DSSR?

I'm developing a web server for RNA 3D structure alignment and am using DSSR for base-pairing annotation. Currently, DSSR always creates the auxiliary files in the directory from which DSSR is called. In my case, DSSR is called by a JAR file in a directory where I don't want to allow write permissions.

Thank you,
Erwin

Offline xiangjun

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Re: Redirect Auxiliary File Output
« Reply #1 on: May 12, 2016, 03:07:06 pm »
Hi Erwin,

Thanks for using DSSR. Does the --prefix option fit the bill? For example, the following command will direct all the dssr-* auxiliary files to the system /tmp folder:

Code: [Select]
x3dna-dssr -i=./1ehz.pdb --prefix=/tmp/dssr
HTH,

Xiang-Jun


Offline eholzhauser

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Re: Redirect Auxiliary File Output
« Reply #2 on: May 12, 2016, 04:00:54 pm »
Dr. Lu,

That fit the bill, thank you!

I have a follow-up question, but it may be too ambiguous. Do you know what could cause DSSR to send "open_file failed: Permission denied" to the error stream? I'm assuming DSSR needs read permission to the directory where the input PDB / mmCIF structure is, and read/write permission to the directories where output / auxiliary output are created. When I run the JAR that calls DSSR on my server from the CLI, everything works fine--the auxiliary files and output go where I expect them to. However, when I execute the JAR from the web interface that I'm building, I get that message from DSSR. The web interface runs with permissions set up for Apache, so somewhere, I haven't given Apache the appropriate permissions that I have as a user of the server. So, I am wondering where all I should take care to give DSSR appropriate read/write permissions.

Thanks again, and sorry for the wall of text,
Erwin

Offline xiangjun

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Re: Redirect Auxiliary File Output
« Reply #3 on: May 12, 2016, 06:47:35 pm »
I've come up with a solution for you to test. What computer OS are you using?

Xiang-Jun

Offline eholzhauser

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Re: Redirect Auxiliary File Output
« Reply #4 on: May 13, 2016, 10:32:27 am »
I'm using CentOS Linux release 7.2.1511.

Thanks again,
Erwin

Offline xiangjun

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Re: Redirect Auxiliary File Output
« Reply #5 on: May 13, 2016, 10:37:29 am »
OK. Please download (already updated) DSSR again, and report back how it goes.

Xiang-Jun

Offline eholzhauser

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Re: Redirect Auxiliary File Output
« Reply #6 on: May 13, 2016, 11:37:16 am »
I downloaded the Linux 64-bit compiled version on the Downloads page. I still get the same error: "open_file failed: Permission denied".

Thanks for the continued help,
Erwin

Offline xiangjun

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Re: Redirect Auxiliary File Output
« Reply #7 on: May 13, 2016, 12:17:26 pm »
Try again, with the revised DSSR, and report back if it works. Remember you need to set the --prefix option to a folder where DSSR can write files to.

Xiang-Jun

Offline eholzhauser

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Re: Redirect Auxiliary File Output
« Reply #8 on: May 13, 2016, 03:20:47 pm »
I apologize for the late reply, but my issue was resolved with the last revised DSSR!

Thanks,
Erwin

Offline xiangjun

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Re: Redirect Auxiliary File Output
« Reply #9 on: May 13, 2016, 03:25:01 pm »
Glad to hear that!

It is through interactions with responsive users like you that DSSR has been continuously refined. As always, any DSSR-related questions are welcome on the public Forum.

Best regards,

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.