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1
General Discussion / Re: "Affinity Profile"
« Last post by xiangjun on February 11, 2019, 03:07:41 pm »
Please see http://reducesuite.bussemakerlab.org/documentation/affinityprofile/ which you get by "AffinityProfile -h".

Best regards,

Xiang-Jun
2
General Discussion / Re: "Affinity Profile"
« Last post by ElliotRi on February 11, 2019, 08:45:15 am »
What examples of how to use the program are you exactly referring to, Xiang-Jun?
3
General Discussion / Re: Installation of REDUCE SUITE
« Last post by xiangjun on January 05, 2019, 10:58:32 am »
Thanks for your feedback. As shown in the output of step #4

Code: [Select]
To run the REDUCE Suite, you need to set up the followings:
          o the environment variable REDUCE_SUITE
          o add $REDUCE_SUITE/bin to your command line search path

        for your 'bash' shell, please add the following into ~/.bashrc:
          --------------------------------------------------------------
            export REDUCE_SUITE='C:/cygwin/home/USER/REDUCE-Suite-v2.2'
            export PATH='C:/cygwin/home/USER/REDUCE-Suite-v2.2/bin':$PATH
          --------------------------------------------------------------

        and then *logout* and *login again* to see the effects.
        (alternatively, you may run the commoand: source ~/.bashrc)

Best regards,

Xiang-Jun
4
General Discussion / Re: Installation of REDUCE SUITE
« Last post by shirin on January 05, 2019, 10:43:42 am »
Hi Xiang-Jun
Many thanks for your quick reply. these are my results. What is your suggestion for me?

1- code "which Perl": the result was "/cygdrive/d/Strawberry/perl/bin/perl"

2- code "perl ./bin/REDUCE_Suite_setup": the result was

$ perl ./bin/REDUCE_Suite_setup
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
To install the REDUCE Suite, do as follows:
  (0) Download the Suite from http://reducesuite.bussemakerlab.org/.
      Note that you *must* register and log in to see the download page.
      Assuming your downloaded tarball is on Mac OS X:
          REDUCE-Suite-v2.2-macosx-intel.tar.gz

  (1) tar zxvf REDUCE-Suite-v2.2-macosx-intel.tar.gz
        This will create a directory named REDUCE-Suite-v2.2/

  (2) cd REDUCE-Suite-v2.2/
        You are now in the REDUCE-Suite-v2.2/ directory

  (3) cd src
     >>> [optional] ONLY IF you compile REDUCE Suite from source <<<
        (3a) make
        (3b) cd ../   # back to REDUCE-Suite-v2.2/, as with step (2)

  (4) bin/REDUCE_Suite_setup
        To run the REDUCE Suite, you need to set up the followings:
          o the environment variable REDUCE_SUITE
          o add $REDUCE_SUITE/bin to your command line search path

        for your 'bash' shell, please add the following into ~/.bashrc:
          --------------------------------------------------------------
            export REDUCE_SUITE='C:/cygwin/home/USER/REDUCE-Suite-v2.2'
            export PATH='C:/cygwin/home/USER/REDUCE-Suite-v2.2/bin':$PATH
          --------------------------------------------------------------

        and then *logout* and *login again* to see the effects.
        (alternatively, you may run the commoand: source ~/.bashrc)

  (5) type MatrixREDUCE -h
           LogoGenerator -h
           HTMLSummary -h
      etc. for command-line help and worked examples

  (6) Note: to use HTMLSummary for the summary page, you need to install
            GhostScript. See $REDUCE_SUITE/config/pkg_settings.cfg for
            setting path to the command 'gs'. LogoGenerator generates
            the logo image in EPS format, and uses 'gs' to convert EPS
            into PDF, PNG, or JPG. Additionally, with ImageMagick, you
            can also get the logo image in GIF.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
5
General Discussion / Re: Installation of REDUCE SUITE
« Last post by xiangjun on January 05, 2019, 10:14:32 am »
Hi Shirin,

Sorry to hear your difficult experience in installing the REDUCE Suite. To help fix the issues you have, could you please try the followings and report back what you get?

Code: [Select]
which perl
Within the REDUCE-Suite-v2.2/ directory as in step #2, type:

Code: [Select]
perl ./bin/REDUCE_Suite_setup

Thanks,

Xiang-Jun
6
General Discussion / Re: Installation of REDUCE SUITE
« Last post by shirin on January 05, 2019, 09:17:16 am »
Dear Xiang-Jun
Hi
I have this problem too during the REDUCE suite installation, I have installed Perl "This is Perl 5, version 12, subversion 3 (v5.12.3)" but I face with this error again "-bash: bin/REDUCE_Suite_setup: /usr/bin/perl: bad interpreter: No such file or directory"
I do not know what is the reason and What should I do? could you please kindly help me.

sincerely,
Shirin
7
General Discussion / Re: Installation of REDUCE SUITE
« Last post by xiangjun on January 04, 2019, 02:51:05 pm »
Hi Mina,

Quote
/usr/bin/perl: bad interpreter: No such file or directory

The error message shows that you do not have Perl installed, at least it is not located at /usr/bin/perl.

If the error message or the instructions at "Set up the REDUCE Suite" does not make sense to you, please find a local expert for help.

Best regards,

Xiang-Jun
8
General Discussion / Installation of REDUCE SUITE
« Last post by mina on January 04, 2019, 11:09:29 am »
Dear Friends,
We have been trying to install REDUCE Suite in windows (Cygwin). We have gone toward step 4 in which, unfortunately, we receive the following error:
$ ./bin/REDUCE_Suite_setup
-bash: ./bin/REDUCE_Suite_setup: /usr/bin/perl: bad interpreter: No such file or directory

Could you please kindly give us advice on how to manage this problem?
Best Regards,
Mina
9
General Discussion / Re: "Affinity Profile"
« Last post by xiangjun on January 01, 2019, 11:46:54 am »
Hi Mina,

Thanks for using the REDUCE Suite and for posting your questions on the Forum.

Type AffinityProfile -h, and try the examples, on how to use the program. PSAM is a MatrixREDUCE-specific term and can be derived from running MatrixREDUCE. You may also run Convert2PSAM to convert commonly-used formats to PSAM. As with AffinityProfile -h, you can type -h or --help of these programs for helpful information with examples.

You may also want to try other (more sophisticated) software tools developed by the Bussemaker Lab.

Best regards,

Xiang-Jun
10
General Discussion / "Affinity Profile"
« Last post by mina on January 01, 2019, 04:58:35 am »
Hi,
I am a new user of REDUCE suite.
Is there anybody to help me in using "Affinity Profile". How could we find the PSAM file for our DNA queries to run the computational calculation of binding affinity.

Best Regards,
Mina
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊]. See also http://forum.x3dna.org and http://x3dna.org