Dear Developers,
I am running Bowtie2 through galaxy interface, previously it gives the the
mapping summary and convert the format to sam.. but now it directly convert
the fastq file to bam and doesnt give the mapping summary.
how to get the mapping summary from bowtie2 using galaxy interface..
Dear Developers,
I am running GATK for first time. In galaxy i use Unified Genotyper. I am
getting error as below mentioned.
# ERROR
--
# ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
et "NO_ET" line from the xml files.
>
>
>
> [image: Inactive hide details for sridhar srinivasan ---06/06/2013
> 06:30:48 AM---Dear Developers, I am running GATK for first time. In]sridhar
> srinivasan ---06/06/2013 06:30:48 AM---Dear Developers, I am running GATK
>
Dear Developers,
I am using GATK for first time. I am doing Targeted reseq Analysis. while i
am running Unified Genotyper in Galaxy interface. it gives error message as
mentioned below..
"ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-WBrGTf) does
not exist."
But i places the Fasta f
Dear Developers,
I am using GATK for first time. I am doing Targeted reseq Analysis. while i
am running Unified Genotyper in Galaxy interface. it gives error message as
mentioned below..
"ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-WBrGTf) does
not exist."
But i places the Fasta f
Dear Developers,
I could see the visualize icon in the History page below the output file..
Actually i am trying to plot the graph between the column 4 and 8 from the
output..
I tried using the visualize option, But takes long time to and i could'nt
get the plot..
Please suggest , how to get the
If that doesn't help, can you provide more details as to what's happening
> when you click the draw button?
>
> Thanks,
> Carl
>
>
>
> On Thu, Jul 11, 2013 at 5:22 AM, sridhar srinivasan <
> sridhar2bioi...@gmail.com> wrote:
>
>> Dear Developers,
&
Dear Developers,
Could you please tell me the possibilities of using the R package
cummeRband for visualization of RNA-seq data in galaxy??
Thanks
Sridhar
___
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in your mail client. To
Dear Developers,
I am using java jar files for softwares like fastqc, GATK. For running
these tools i install the softare and set path in bash_profile file.
My doubt is i placed the jar files in galaxy dist folder (
galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
)
is this enough to cal
und
> in the existing fastqc tool. That's the way of the future for all tool
> wrappers, so a good thing to start using. Plenty of docs on the wiki and
> examples in the test toolshed.
>
>
> On Fri, Jul 12, 2013 at 2:34 PM, sridhar srinivasan <
> sridhar2bioi...@gmail
Dear Developers,
I am GATK (beta ) Unified Genotyper module to get the indels and SNP.
I placed the jar file in (/galaxy-dist/tool-data/shared/jars/gatk) and i
link the reference genome in .loc file (gatk_sorted_picard_index.loc). I
could see the Name i mentioned in the .loc file is appearing in
data/galaxy/galaxy-dist/database/files/000/dataset_841.dat"
--metrics_file
"/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_842.dat"
* -R "" * --genotype_likelihoods_model "BOTH"
--standard_min_confidence_threshold_for_calling "30.0"
--standard_min_confidence_threshold_f
und is no way related to the initially
created database "postgreSQL" ??
Your suggestions are very much Apperiacted...
Thank you
Sridhar
On Fri, Jul 12, 2013 at 6:29 PM, Jeremy Goecks wrote:
> The toolshed has a wrapper for cummerbund:
>
> http://toolshed.g2.bx.psu.edu/view/jjoh
Dear users,
Could anybody suggest the valid DESeq toolshed for RNA sequencing???
Thanks
Sridhar
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Sure ..
Thanks for the reply..
On Tue, Aug 20, 2013 at 12:33 PM, Bjoern Gruening wrote:
> Hi Sridhar,
>
> we are developing a DESeq2 tool at the moment, if you want to join get
> in touch with me. Its developed here:
>
> https://github.com/bgruening/galaxytools/tree/master/deseq2
>
> I will
Hi All,
Thanks for the suggestions. I installed the Toolshed ( Differential_Count
(version 0.21) ). It asks for the input matrix - rows are contigs, columns
are counts for each sample.
Any idea on how to generate this matrix file??
Thanks
On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni <
m.m
ug 21, 2013 at 10:44 AM, Mahtab Mirmomeni <
m.mirmom...@student.unimelb.edu.au> wrote:
> You can use htseq_bams_to_count_matrix repository by fubar in the test
> toolshed.
>
>
> On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan <
> sridhar2bioi...@gmail.com> wrote
se_tool_dependency?repository_id=94e61e06dbd29e52&id=c32939704028ccc3>
> 0.7.5packagehtseq<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=96c0d701aac155a0>
> 0.5.4p3package
>
>
>
>
> On Wed, Aug 21, 2013 at 4:05 PM, S
irectory]/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/INSTALLATION.log
>
>
>
> On Wed, Aug 21, 2013 at 4:38 PM, Sridhar Srinivasan <
> sridhar2bioi...@gmail.com> wrote:
>
>> Hi Ross,
>>
>>
>> i Installed through admin interface .
&g
Dear All,
i am installing galaxy first time.
i face problem while installing the python eggs.
while running the Run.sh command it gives as
/home/sbsuser/.python-eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg-tmp/csamtools.so:6:
RuntimeWarning: __builtin__.file size changed, may
t; aebre...@uci.edu
>
>
> On Fri, May 3, 2013 at 12:24 AM, sridhar srinivasan <
> sridhar2bioi...@gmail.com> wrote:
>
>> Dear All,
>>
>> i am installing galaxy first time.
>>
>> i face problem while installing the python eggs.
>> while r
Hi ,
I am getting error during Installing galaxy locally.
Traceback (most recent call last):
File
"/illumina/apps/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
line 35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/illumina/apps/galaxy
gt; Also, see this old thread, where the same error has been reported before:
> http://lists.bx.psu.edu/**pipermail/galaxy-dev/2010-May/**002624.html<http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html>
>
>
>
> Regards, Hans-Rudolf
>
>
>
>
> On 05/0
ueue.monitor_thread
(most likely raised during interpreter shutdown):
Traceback (most recent call last):
Traceback (most recent call last):
On Thu, May 9, 2013 at 5:15 PM, Dannon Baker wrote:
> On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan <
> sridhar2bioi...@gmail.com>
Dear Developers,
After configuring the galaxy.. i could'nt see the history column in the web
page..
it shows the error as
"Content Encoding Error
The page you are trying to view cannot be shown because it uses an invalid
or unsupported form of compression."
Best
Sridhar
Hi after installing galaxy,
i could'nt see the history page in right end of galaxy web.
it shows
"""
Content Encoding Error
The page you are trying to view cannot be shown because it uses an invalid
or unsupported form of compression.
* Please contact the website owners to inform them of
of proxy server
> in front of it?
>
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
> On Mon, May 13, 2013 at 2:53 AM, sridhar srinivasan
> wrote:
> > Dear Developers,
> >
> > After configuring the galaxy.. i could'nt see the h
Hi Carl,
I am using firefox 3.6.18 and linux Red Hat/3.6-1.el5_6..
Thanks
Sridhar
On Mon, May 13, 2013 at 8:31 PM, Carl Eberhard wrote:
> Hello, Sridhar.
>
> Can you tell me the browser and operating system you're using?
>
> Thanks,
> Carl
>
>
>
> On Mo
Hi,
In backend i am getting this message
192.168.1.5 - - [15/May/2013:09:32:12 +0600] "GET / HTTP/1.1" 200 -
"http://192.168.1.5- -/" "Mozilla/5.0 (X11; U; Linux i686; en-US;
rv:1.9.2.18) Gecko/20110616 Red Hat/3.6-1.el5_6 Firefox/3.6.18"
Thanks
Sridhar
On 5/14
Dear Developers,
After installing galaxy, the history part of the webpage is not opening and
it shows
" Content Encoding Error
The page you are trying to view cannot be shown because it uses an invalid
or unsupported form of compression.
* Please contact the website owners to inform them
ttp://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002624.html>
>
>
>
> Regards, Hans-Rudolf
>
>
>
>
> On 05/08/2013 01:24 PM, sridhar srinivasan wrote:
>
>>
>> Hi ,
>>
>> I am getting error during Installing galaxy locally.
>>
>
FATAL: Ident authentication failed
for user "galaxy"
None None
Thanks
Sridhar
On Tue, May 21, 2013 at 3:08 PM, Hans-Rudolf Hotz wrote:
>
>
> On 05/21/2013 11:22 AM, sridhar srinivasan wrote:
>
>> Hi Rudolf,
>> Thanks for the reply..
>>
>> Could yo
e command line?
>
> psql -d galaxy_prod -p 5432 -h localhost -U galaxy
>
> and this should prompt for the password
> (again, I am not an PostgreSQL expert...)
>
>
> Regards, Hans-Rudolf
>
>
>
>
> On 05/21/2013 01:00 PM, sridhar srinivasan wrote:
>
>> He
Dear developers,
1. I recently installed galaxy locally. now i am trying to run bowtie2. In
reference genome section the genome is not listed.
2. Is there any way yo secure our data without using the Proxy(nginx).
I Appericiate your suggestions.
Thanks
Sridhar
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