Re: [EMBOSS] specify primer3 directory?
This works as well. I didn't look at eprimer32 because for some reason I
thought the "32" was a 32 bit version or something..
Turns out eprimer32 is built to work with 2.x versions of primer3.
As Petar suggested, for a non default install of primer3 you need to modify
some files before everything will work.
To provide more detail in case others are interested, in thal_main.c you
need to modify lines 306-307:
} else if ((stat("/opt/primer3_config", &st) == 0) &&
S_ISDIR(st.st_mode)) {
tmp_ret = get_thermodynamic_values("/opt/primer3_config/", &o);
and in primer3_boulder_main.c you need to modify lines 517-521:
} else if ((stat("/opt/primer3_config", &st) == 0) &&
S_ISDIR(st.st_mode)) {
thermodynamic_params_path =
(char*) malloc(strlen("/opt/primer3_config/") * sizeof(char) + 1);
if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */
strcpy(thermodynamic_params_path, "/opt/primer3_config/");
These changes apply to unix - I saw different places in those files that
would need to be changed if you were doing this in windows.
Has anyone got emboss and eprimer32 working and installed in galaxy? Or a
similar primer design tool in galaxy?
Thanks for the help everyone.
Message: 6
Date: Fri, 14 Sep 2012 11:06:47 +0300
From: Petar Petrov
Subject: Re: [EMBOSS] specify primer3 directory?
To: emboss@lists.open-bio.org
Message-ID: <20120914110647.sacof6lkgscoo...@webmail.oulu.fi>
Content-Type: text/plain; charset=windows-1251; DelSp="Yes";
format="flowed"
Hi Paul,
which version of primer3 do you use? What operating system? How did
you install primer3 and EMBOSS?
If it is primer3 version 2.* I think you should use eprimer32 wrapper
instead and it expects primer3_core to be called primer32_core. To
make primer3 aware of another location of the primer3_config
directory: it seems that two files need to be modified before
compiling: thal_main.c and primer3_boulder_main.c (in the subfolder
src).
Hope this helps.
regards,
Petar
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Re: [EMBOSS] specify primer3 directory?
Hi Paul, which version of primer3 do you use? What operating system? How did you install primer3 and EMBOSS? If it is primer3 version 2.* I think you should use eprimer32 wrapper instead and it expects primer3_core to be called primer32_core. To make primer3 aware of another location of the primer3_config directory: it seems that two files need to be modified before compiling: thal_main.c and primer3_boulder_main.c (in the subfolder src). Hope this helps. regards, Petar Quoting Paul Tanger : Hi, I have a local install of emboss and I'm trying to get eprimer3 to work, but I'm getting this error: "Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified" primer3 is installed, but not in the default location (which I think is /opt/primer3_config ?) . How do I specify where primer3 is installed? Or is the cause of this error something else? googled for an answer for a while, but couldn't find one. Thanks! ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] specify primer3 directory?
That worked - Thanks so much! On Thu, Sep 13, 2012 at 4:37 PM, Drummond, Iain A. wrote: > I ran into (I think) similar problems running primer3 with Emboss eprimer3. > > It turned out that the most recent version of primer3 (2.x.x) will not run > with the current Emboss eprimer3; you have to downgrade primer3 to 1.1.4 to > get it to work. > > The Emboss folks know this I think. > > -Iain > > > --- > Iain Drummond, Ph.D. > Associate Professor > Nephrology Division, Massachusetts General Hospital, > Department of Genetics, Harvard Medical School and > Program in Developmental and Regenerative Biology, Harvard Medical School > > Address for mailing: > > Nephrology Division, MGH > 149 13th Street, Rm 149-8000 > Charlestown MA 02129 > > 617 726 5647 (office) > 617 724 9693 (lab) > 617 726 5669 (fax) > > idrum...@receptor.mgh.harvard.edu > idrumm...@partners.org > > HTTP://danio.mgh.harvard.edu <°)-< > > > > On 9/13/12 4:24 PM, "Paul Tanger" wrote: > >> Hi, >> I have a local install of emboss and I'm trying to get eprimer3 to >> work, but I'm getting this error: >> >> "Error: thermodynamic approach chosen, but path to thermodynamic >> parameters not specified" >> >> primer3 is installed, but not in the default location (which I think >> is /opt/primer3_config ?) . >> How do I specify where primer3 is installed? Or is the cause of this >> error something else? >> >> googled for an answer for a while, but couldn't find one. >> >> Thanks! >> ___ >> EMBOSS mailing list >> EMBOSS@lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] specify primer3 directory?
Paul,
You might want to have a look at section 5 of the primer3 documentation
("CHANGES FROM VERSION 2.2.3"). They changed the default for
PRIMER_THERMODYNAMIC_ALIGNMENT from 0 to 1. If this is left at 1, then you
also need to supply a value for PRIMER_THERMODYNAMIC_PARAMETERS_PATH.
You can revert to the old defaults using this command-line argument.
--default_version=1
Scott
Scott Markel, Ph.D.
Principal Bioinformatics Architect email: smar...@accelrys.com
Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
10188 Telesis Court, Suite 100 voice: +1 858 799 5603
San Diego, CA 92121 fax: +1 858 799 5222
USA web: http://www.accelrys.com
http://www.linkedin.com/in/smarkel
Secretary, Board of Directors:
International Society for Computational Biology
Chair: ISCB Publications and Communications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics
-Original Message-
From: emboss-boun...@lists.open-bio.org
[mailto:emboss-boun...@lists.open-bio.org] On Behalf Of Paul Tanger
Sent: Thursday, 13 September 13 2012 1:25 PM
To: emboss@lists.open-bio.org
Subject: [EMBOSS] specify primer3 directory?
Hi,
I have a local install of emboss and I'm trying to get eprimer3 to
work, but I'm getting this error:
"Error: thermodynamic approach chosen, but path to thermodynamic
parameters not specified"
primer3 is installed, but not in the default location (which I think
is /opt/primer3_config ?) .
How do I specify where primer3 is installed? Or is the cause of this
error something else?
googled for an answer for a while, but couldn't find one.
Thanks!
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Re: [EMBOSS] specify primer3 directory?
Paul,
Yup, sorry about that. I should have stopped my answer after the paragraph
about the primer3 change.
Scott
-Original Message-
From: ptan...@rams.colostate.edu [mailto:ptan...@rams.colostate.edu] On Behalf
Of Paul Tanger
Sent: Thursday, 13 September 13 2012 2:59 PM
To: Scott Markel
Cc: emboss@lists.open-bio.org
Subject: Re: [EMBOSS] specify primer3 directory?
Thanks, maybe this is the problem but the solution you suggest doesn't
seem to work because that is a primer3 qualifier not an eprimer3
qualifier.
I get this error:
[paultanger@bspmgenomics bin]$ ./eprimer3
~/QTL-project/30scaffolds_affyMAI_CG.fsa ~/QTL-project/test2
--default_version=1
Died: Unknown qualifier --default_version=1
On Thu, Sep 13, 2012 at 3:49 PM, Scott Markel wrote:
> Paul,
>
> You might want to have a look at section 5 of the primer3 documentation
> ("CHANGES FROM VERSION 2.2.3"). They changed the default for
> PRIMER_THERMODYNAMIC_ALIGNMENT from 0 to 1. If this is left at 1, then you
> also need to supply a value for PRIMER_THERMODYNAMIC_PARAMETERS_PATH.
>
> You can revert to the old defaults using this command-line argument.
>
> --default_version=1
>
> Scott
>
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect email: smar...@accelrys.com
> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
> San Diego, CA 92121 fax:+1 858 799 5222
> USA web:http://www.accelrys.com
>
> http://www.linkedin.com/in/smarkel
> Secretary, Board of Directors:
> International Society for Computational Biology
> Chair: ISCB Publications and Communications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
>
>
> -Original Message-
> From: emboss-boun...@lists.open-bio.org
> [mailto:emboss-boun...@lists.open-bio.org] On Behalf Of Paul Tanger
> Sent: Thursday, 13 September 13 2012 1:25 PM
> To: emboss@lists.open-bio.org
> Subject: [EMBOSS] specify primer3 directory?
>
> Hi,
> I have a local install of emboss and I'm trying to get eprimer3 to
> work, but I'm getting this error:
>
> "Error: thermodynamic approach chosen, but path to thermodynamic
> parameters not specified"
>
> primer3 is installed, but not in the default location (which I think
> is /opt/primer3_config ?) .
> How do I specify where primer3 is installed? Or is the cause of this
> error something else?
>
> googled for an answer for a while, but couldn't find one.
>
> Thanks!
> ___
> EMBOSS mailing list
> EMBOSS@lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
>
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Re: [EMBOSS] specify primer3 directory?
Thanks, maybe this is the problem but the solution you suggest doesn't
seem to work because that is a primer3 qualifier not an eprimer3
qualifier.
I get this error:
[paultanger@bspmgenomics bin]$ ./eprimer3
~/QTL-project/30scaffolds_affyMAI_CG.fsa ~/QTL-project/test2
--default_version=1
Died: Unknown qualifier --default_version=1
On Thu, Sep 13, 2012 at 3:49 PM, Scott Markel wrote:
> Paul,
>
> You might want to have a look at section 5 of the primer3 documentation
> ("CHANGES FROM VERSION 2.2.3"). They changed the default for
> PRIMER_THERMODYNAMIC_ALIGNMENT from 0 to 1. If this is left at 1, then you
> also need to supply a value for PRIMER_THERMODYNAMIC_PARAMETERS_PATH.
>
> You can revert to the old defaults using this command-line argument.
>
> --default_version=1
>
> Scott
>
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect email: smar...@accelrys.com
> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
> San Diego, CA 92121 fax:+1 858 799 5222
> USA web:http://www.accelrys.com
>
> http://www.linkedin.com/in/smarkel
> Secretary, Board of Directors:
> International Society for Computational Biology
> Chair: ISCB Publications and Communications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
>
>
> -Original Message-
> From: emboss-boun...@lists.open-bio.org
> [mailto:emboss-boun...@lists.open-bio.org] On Behalf Of Paul Tanger
> Sent: Thursday, 13 September 13 2012 1:25 PM
> To: emboss@lists.open-bio.org
> Subject: [EMBOSS] specify primer3 directory?
>
> Hi,
> I have a local install of emboss and I'm trying to get eprimer3 to
> work, but I'm getting this error:
>
> "Error: thermodynamic approach chosen, but path to thermodynamic
> parameters not specified"
>
> primer3 is installed, but not in the default location (which I think
> is /opt/primer3_config ?) .
> How do I specify where primer3 is installed? Or is the cause of this
> error something else?
>
> googled for an answer for a while, but couldn't find one.
>
> Thanks!
> ___
> EMBOSS mailing list
> EMBOSS@lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
>
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