Has anyone created a tool for running RepeatMasker http://www.repeatmasker.org/ within Galaxy? It's something we'd like to do so we can create workflows where the fasta is masked before being searched with blast.
Thanx,
Russell Smithies New Zealand
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Hi Russell,
i have a working wrapper. I will upload it to the toolshed soon, but if you like to test it before, that would be nice.
kind regards, Bjoern
Am Montag, den 28.11.2011, 11:57 +1300 schrieb Smithies, Russell:
Has anyone created a tool for running RepeatMasker http://www.repeatmasker.org/ within Galaxy?
It’s something we’d like to do so we can create workflows where the fasta is masked before being searched with blast.
Thanx,
Russell Smithies
New Zealand
Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.
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Hi Björn, I'd be keen to test it before release if that's OK. I'm surprised there's not one already? I would have thought it was a key tool in most bioinformaticians toolbox.
Thanx,
Russell Smithies Infrastructure Team T 03 489 9085 M 0274 734 600 E russell.smithies@agresearch.co.nz
Invermay Agricultural Centre Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand T +64 3 489 3809 F +64 3 489 3739 www.agresearch.co.nz
-----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Monday, 28 November 2011 12:12 p.m. To: Smithies, Russell Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tool for RepeatMasker?
Hi Russell,
i have a working wrapper. I will upload it to the toolshed soon, but if you like to test it before, that would be nice.
kind regards, Bjoern
Am Montag, den 28.11.2011, 11:57 +1300 schrieb Smithies, Russell:
Has anyone created a tool for running RepeatMasker http://www.repeatmasker.org/ within Galaxy?
It’s something we’d like to do so we can create workflows where the fasta is masked before being searched with blast.
Thanx,
Russell Smithies
New Zealand
Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.
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The blast+ wrappers have DUST capability ON by default....
-----Oorspronkelijk bericht----- Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Smithies, Russell Verzonden: maandag 28 november 2011 1:27 Aan: 'Björn Grüning' CC: 'galaxy-dev@lists.bx.psu.edu' Onderwerp: Re: [galaxy-dev] tool for RepeatMasker?
Hi Björn, I'd be keen to test it before release if that's OK. I'm surprised there's not one already? I would have thought it was a key tool in most bioinformaticians toolbox.
Thanx,
Russell Smithies Infrastructure Team T 03 489 9085 M 0274 734 600 E russell.smithies@agresearch.co.nz
Invermay Agricultural Centre Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand T +64 3 489 3809 F +64 3 489 3739 www.agresearch.co.nz
-----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Monday, 28 November 2011 12:12 p.m. To: Smithies, Russell Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tool for RepeatMasker?
Hi Russell,
i have a working wrapper. I will upload it to the toolshed soon, but if you like to test it before, that would be nice.
kind regards, Bjoern
Am Montag, den 28.11.2011, 11:57 +1300 schrieb Smithies, Russell:
Has anyone created a tool for running RepeatMasker http://www.repeatmasker.org/ within Galaxy?
It’s something we’d like to do so we can create workflows where the fasta is masked before being searched with blast.
Thanx,
Russell Smithies
New Zealand
Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.
_
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:
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galaxy-dev@lists.galaxyproject.org
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Björn Grüning -
Bossers, Alex -
Smithies, Russell