3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: eholzhauser on May 12, 2016, 02:50:03 pm

Title: Redirect Auxiliary File Output
Post by: eholzhauser 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
Title: Re: Redirect Auxiliary File Output
Post by: xiangjun 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
Title: Re: Redirect Auxiliary File Output
Post by: eholzhauser 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
Title: Re: Redirect Auxiliary File Output
Post by: xiangjun 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
Title: Re: Redirect Auxiliary File Output
Post by: eholzhauser on May 13, 2016, 10:32:27 am: I'm using CentOS Linux release 7.2.1511.

Thanks again,
Erwin
Title: Re: Redirect Auxiliary File Output
Post by: xiangjun on May 13, 2016, 10:37:29 am: OK. Please download (already updated) DSSR again, and report back how it goes.

Xiang-Jun
Title: Re: Redirect Auxiliary File Output
Post by: eholzhauser 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
Title: Re: Redirect Auxiliary File Output
Post by: xiangjun 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
Title: Re: Redirect Auxiliary File Output
Post by: eholzhauser 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
Title: Re: Redirect Auxiliary File Output
Post by: xiangjun 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