of memory, especially in
case of NGS analysis.
- Raj
-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: Wednesday, April 04, 2012 5:09 PM
To: Praveen Raj Somarajan
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Auto delete dataset after workflow run
]
Sent: Saturday, September 15, 2012 5:46 PM
To: Praveen Raj Somarajan
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Why doesn't bowtie in galaxy accepting
colorspacereads directly?
Raj:
It does support colorspace files, but you have to convert them to fastq first.
That sounds bad
Thanks Brad. I can probably look into the xml tool definition and change.
Meantime, I'll go with the current solution of converting files.
Raj
From: Langhorst, Brad [mailto:langho...@neb.com]
Sent: Monday, September 17, 2012 5:15 PM
To: Praveen Raj Somarajan
Cc: galaxy-dev@lists.bx.psu.edu
Hi All,
I'm wondering why the Bowtie version in (even latest) Galaxy does NOT support
.csfasta/.qual input files directly, though it is mentioned under Map with
Bowtie for SOLiD. This is the case of BWA for SOLiD as well. One would
expect direct support on colorspace files. Do you have any
Hello,
Just want to clarify two questions:
1) Is there a way to get the absolute path of a dataset directly from the
interface? This is sometimes useful to create a local directory of all required
files (by using symlink) if we know the full path.
2) How do we create a data library from
Hello All,
Is there a way to set auto delete some datafiles at the end of workflow run?
I'm asking this because it is sometimes useful to delete some outputs (say
intermediate files, .logs, etc), for example auto delete .sam file after
executing sam-to-bam tool, which would free-up lot of
, 2012 5:09 PM
To: Praveen Raj Somarajan
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Auto delete dataset after workflow run?
On Wed, Apr 4, 2012 at 12:30 PM, Praveen Raj Somarajan
pravee...@ocimumbio.com wrote:
Hello All,
Is there a way to set auto delete some datafiles at the end
Hello Vipin,
Good to see this. just a quick question, does your interface has the
functionality to define groups (say normal or control) for replicates/samples,
as the way we define in edgeR/DESeq R script.
Carlos, I think BAM input would be okay as it can be connected with tophat in
the
Hello Dannon,
Thanks for resolving the issue of snpEff HTML display. It's working well with
the new changeset. But the gene file link in the bottom
(dataset_*.dat.genes.txt) is still in broken state, says could not find file.
Any update on this?
-Raj
-Original Message-
From:
Hello Dev team,
I normally use hg incoming to check for any updates and hg pull -u to
install new updates if available. I noticed that there are files created with
.sample extension after the update (for all config files) - eg
universe_wsgi.ini.sample is modified with new updates, but
/modifications
in such files which might me useful for me.
Raj.
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 22, 2012 4:18 PM
To: Praveen Raj Somarajan
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Clarification on galaxy update process
Hi Raj,
The files
Hi Dev Team,
Do you have any plan to integrate PolyPhen2 to Galaxy? I feel, it would be good
if you can, as this extends the functionality of NGS analysis and (definetly)
it would be value addition to Galaxy as well.
Let me know your comments.
Best,
Raj
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