On 07/09/2011 20:22, Edward Kirton wrote:
seems unnecessary since illumina switched over to fastqsanger now.
http://www.illumina.com/truseq/quality_101/quality_scores.ilmn
Eventually...unfortunately we still get a lot of fastqillumina :-(
Steve
Hi,
In my local instance of Galaxy ,I want to make change in "upload
files from file system" option which is used admin. in which file i
have to make changes ? i want to attach some more features in that.
Regards
shashi
___
Please keep
I haven't had a chance to do anything on this yet, but I'll see if I can work
something out in the near future.
-Dannon
On Sep 7, 2011, at 9:34 PM, Glen Beane wrote:
>
> On Sep 7, 2011, at 8:10 PM, Edward Kirton wrote:
>
>> i'm resurrecting this thread to see if there's any more support for t
Hi,
In my local instance of Galaxy ,I want to add one option in which i
can get files from remote system to galaxy in data library .
except url is there any option to get remote files from galaxy ?
Regards
___
Please keep all replies
On 09/08/2011 09:47 AM, Stephen Taylor wrote:
On 07/09/2011 20:22, Edward Kirton wrote:
seems unnecessary since illumina switched over to fastqsanger now.
http://www.illumina.com/truseq/quality_101/quality_scores.ilmn
Eventually...unfortunately we still get a lot of fastqillumina :-(
I m
Shashi,
Probably the best place to start is the upload_library_dataset method in
~/lib/galaxy/web/controllers/library_common.py.
good luck,
Greg Von Kuster
On Sep 8, 2011, at 6:42 AM, shashi shekhar wrote:
> Hi,
>
> In my local instance of Galaxy ,I want to make change in "upload
> files f
On 08/09/2011 14:17, Hans-Rudolf Hotz wrote:
On 09/08/2011 09:47 AM, Stephen Taylor wrote:
On 07/09/2011 20:22, Edward Kirton wrote:
seems unnecessary since illumina switched over to fastqsanger now.
http://www.illumina.com/truseq/quality_101/quality_scores.ilmn
Eventually...unfortunately
Dear Stephen (and others):
The sole reason for requiring fastq-sanger input to all of our wrappers was to
force the users to run their data through the groomer. It is slow, but it
checks data consistency in a way that is more robust than just checking 'four
lines per fastq block' and prevents a
Anton,
If a user is running a multi-core machine, a simple method to speed up FASTQ
-Groomer is to first split the original FASTQ file (e.g. into 10 smaller files
if you've got a 12-core machine), run FASTQ-Groomer on each file concurrently,
then join the 10 files back together. This allows fo
My co-worker solved it. You were both right about the Python version. This was
a very silly mistake.
export PATH=/opt/galaxy-python/python:$PATH
Should have been
export PATH=/opt/galaxy-python:$PATH
So I basically put the binary (and not the _path_ to the binary) in the $PATH
variable. This l
Hi, I am user of Galaxy Test.
I wonder is the Galaxy Test server down these 2 days? As the Tophat and
Cufflinks job running take me a lot of time to run compared to previous?
Thanks.
Best regards,
Crystal _
It's not an issue in the tmp dir but in the job_working_directory. I run most
of those other tools with no problems. I don't think we should make it a
requirement across the board and I think we can come up with alternative ways
to clean up the job_working_directory. I am hoping that you could a
Is there a python script associated with the macs.xml file?
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kanwei Li
Sent: Wednesday, August 24, 2011 5:41 PM
To: KOH Jia Yu Jayce
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] macs in
I don't believe so, it looks like they generate a long config script (as you
can see in the xml file) and executes that.
K
On Thu, Sep 8, 2011 at 1:51 PM, Chorny, Ilya wrote:
> Is there a python script associated with the macs.xml file?
>
> ** **
>
> *From:* galaxy-dev-boun...@lists.bx.psu
copied from another thread:
On Thu, Sep 8, 2011 at 7:30 AM, Anton Nekrutenko wrote:
> What we are thinking of lately is switching to unaligned BAM for
> everyting. One of the benefits here is the ability to add readgroups from
> day 1 simplifying multisample analyses down the road.
>
this seems
The use of (unaligned) BAM for readgroups seems like a good idea. At the very
least it prevents inconsistently hacking this information into the FASTQ
descriptor (a common problem with any simple format).
chris
On Sep 8, 2011, at 1:35 PM, Edward Kirton wrote:
> copied from another thread:
>
I would also like to voice my support for this feature. I wrote a wrapper
for bowtie that converts the SAM output to BAM after bowtie is finished just
to avoid the hassle of letting galaxy "know" that the SAM file existed
(didn't want to run Tophat).
After thinking about how I would go about deleti
I'm confused. Why would the symlink cause problems for Cuffcompare but not for
other tools that use symlinks (including Cufflinks and Cuffdiff)?
J.
On Sep 8, 2011, at 1:43 PM, Chorny, Ilya wrote:
> It’s not an issue in the tmp dir but in the job_working_directory. I run most
> of those other t
18 matches
Mail list logo
