[Bioperl-l] RepeatMasker Re: Bioperl-l Digest, Vol 75, Issue 10

[John M.C. Ma]

Hi,

Sorry that I thought it was the same as 2138, as I never used -noint.
I used -species and -noisy-- but it does not matter any more. I tried
to run it without parameters and it crashed in the same way as 2138.

John Ma


On Tue, Jul 7, 2009 at 11:00 AM, <bioperl-l-request at lists.open-bio.org> wrote:
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> Today's Topics:
>
>   1. Re:  RepeatMasker still did not act upon Bug 2138: Any
>      workarounds? (Robert Buels)
>   2.  RepeatMasker (Robert Hubley)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 06 Jul 2009 17:13:06 -0700
> From: Robert Buels <rmb32 at cornell.edu>
> Subject: Re: [Bioperl-l] RepeatMasker still did not act upon Bug 2138:
>        Any workarounds?
> To: manchunjohn-ma at uiowa.edu, BioPerl List
>        <bioperl-l at lists.open-bio.org>
> Message-ID: <4A529312.9040905 at cornell.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> John M.C. Ma wrote:
>> And as of today, they are now at 3.2.8, and the problem is not fixed.
>> And I don't want my project to be stalled-- any tips for a workaround?
>
> FORK!
>
> Just kidding.  Mostly.
>
> Actually, svn vendor branches or something similar can be a good option
> for unpleasant things like this, see
> http://svnbook.red-bean.com/en/1.5/svn.advanced.vendorbr.html
>
> Rob
>
>
> --
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 07 Jul 2009 06:58:01 -0700
> From: Robert Hubley <rhubley at systemsbiology.org>
> Subject: [Bioperl-l] RepeatMasker
> To: bioperl-l at bioperl.org
> Message-ID: <4A535469.4060603 at systemsbiology.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> This list email as forwarded to us by a colleague.  I fixed this bug
> awhile back and I just double checked 3.2.8 and don't see any problems
> with the options -noint or -lcambig.  Could someone help us determine
> how this is breaking bio-perl?
>
> Thanks,
>
> -Robert
>
> |We have told the guys at RepeatMasker that RM-3.1.6 have a problem
> |causing Bio::Tools::RepeatMasker to crash in November 2006 (Bug 2138).
> |And as of today, they are now at 3.2.8, and the problem is not fixed.
> |And I don't want my project to be stalled-- any tips for a workaround?
> ||
> ||Hi,
> ||
> ||Perhaps you already know about this, but in RepeatMasker 3.1.6 -noint
> ||cannot be used because of error 'Unknown option: noint-species'.
> ||This is caused by line 1131 having no space after the "-noint".
> ||Likewise, -lcambig on 1128 would probably suffer a similar problem.
> ||
> ||Will this be fixed in the next version, and how often do you release new
> ||versions?
>
>
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> End of Bioperl-l Digest, Vol 75, Issue 10
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>