toolExample.pl script bug report

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toolExample.pl script bug report

Casey Bergman
Dear Galaxy Team -

We stumbled across a potential bug in the toolExample.pl script on the Galaxy Add Tool Tutorial today:

http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial

In our hands, this script only works on fasta files that contain >1 sequence, and reports gc content only for the first n-1 sequences.

If you could confirm this and modify if possible, this might help other users.

All the best,

Casey Bergman, Ph.D.
Faculty of Life Sciences
University of Manchester
Michael Smith Building
Oxford Road, M13 9PT
Manchester, UK

Tel: +44-(0)161-275-1713
Lab: +44-(0)161-275-5980
Fax: +44-(0)161-275-5082
skype: caseymbergman

Email: [hidden email]
Web: http://bergmanlab.smith.man.ac.uk/






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Re: toolExample.pl script bug report

Anton Nekrutenko
Casey:

Indeed. Will fix shortly.

a.


Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



On Jul 12, 2011, at 11:51 AM, Casey Bergman wrote:

> Dear Galaxy Team -
>
> We stumbled across a potential bug in the toolExample.pl script on the Galaxy Add Tool Tutorial today:
>
> http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial
>
> In our hands, this script only works on fasta files that contain >1 sequence, and reports gc content only for the first n-1 sequences.
>
> If you could confirm this and modify if possible, this might help other users.
>
> All the best,
>
> Casey Bergman, Ph.D.
> Faculty of Life Sciences
> University of Manchester
> Michael Smith Building
> Oxford Road, M13 9PT
> Manchester, UK
>
> Tel: +44-(0)161-275-1713
> Lab: +44-(0)161-275-5980
> Fax: +44-(0)161-275-5082
> skype: caseymbergman
>
> Email: [hidden email]
> Web: http://bergmanlab.smith.man.ac.uk/
>
>
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/
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Re: toolExample.pl script bug report

Anton Nekrutenko
In reply to this post by Casey Bergman
Casey:

This 'elegant' script has been fixed. Thank for poiting this out!

a.


Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



On Jul 12, 2011, at 11:51 AM, Casey Bergman wrote:

> Dear Galaxy Team -
>
> We stumbled across a potential bug in the toolExample.pl script on the Galaxy Add Tool Tutorial today:
>
> http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial
>
> In our hands, this script only works on fasta files that contain >1 sequence, and reports gc content only for the first n-1 sequences.
>
> If you could confirm this and modify if possible, this might help other users.
>
> All the best,
>
> Casey Bergman, Ph.D.
> Faculty of Life Sciences
> University of Manchester
> Michael Smith Building
> Oxford Road, M13 9PT
> Manchester, UK
>
> Tel: +44-(0)161-275-1713
> Lab: +44-(0)161-275-5980
> Fax: +44-(0)161-275-5082
> skype: caseymbergman
>
> Email: [hidden email]
> Web: http://bergmanlab.smith.man.ac.uk/
>
>
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/