: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:
Hi All,
Thanks for the suggestions. I installed
, Aug 21, 2013 at 4:05 PM, Sridhar Srinivasan
sridhar2bioi...@gmail.com wrote:
Hi All,
I installed the toolshed htseq_bams_to_count_matrix repository , i gave
the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count
reads over from your current history: in this section
/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 .
for pysam and freetype it showed new... and rest installed..
Thanks
On Wed, Aug 21
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 bjoern.gruen...@gmail.com
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:
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
??
Your suggestions are very much Apperiacted...
Thank you
Sridhar
On Fri, Jul 12, 2013 at 6:29 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote:
The toolshed has a wrapper for cummerbund:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund
On Jul 12, 2013, at 12:03 AM, sridhar srinivasan
--standard_min_confidence_threshold_for_calling 30.0
--standard_min_confidence_threshold_for_emitting 30.0'
Thanks
Sridhar
On Tue, Jun 11, 2013 at 1:01 PM, sridhar srinivasan
sridhar2bioi...@gmail.com wrote:
Hello Linda,
Thanks for your suggestions.
i removed the line from xml file but now i am getting different
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
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
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,
I could see the visualize icon in the History page below the output
file.. Actually i am trying to plot
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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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
. 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.com wrote:
Dear Developers,
I am using java jar files for softwares
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
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
for first time. In galaxy i use Unified Genotyper. I am
From: sridhar
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):
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,
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
:24 PM, sridhar srinivasan wrote:
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
None None
Thanks
Sridhar
On Tue, May 21, 2013 at 3:08 PM, Hans-Rudolf Hotz h...@fmi.ch wrote:
On 05/21/2013 11:22 AM, sridhar srinivasan wrote:
Hi Rudolf,
Thanks for the reply..
Could you please tell how to check and set the PostgreSQL ..
I provide the correct username and password
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:
Hello Rudolf,
I tried with the IP address it gave the error as
Is the server running on host 192.168.1.1
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 5/14/13, sridhar srinivasan sridhar2bioi
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
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
using any kind 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
sridhar2bioi...@gmail.com wrote:
Dear Developers,
After configuring the galaxy.. i could'nt see the history column
, sridhar srinivasan
sridhar2bioi...@gmail.com wrote:
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
...@gmail.com wrote:
On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan
sridhar2bioi...@gmail.com wrote:
and it is working.. but i could'nt connect to the webpage
http://127.0.0.1:8080/ from another system in same network..
By default, galaxy will only be serving on 127.0.0.1 (localhost
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
the same error has been reported before:
http://lists.bx.psu.edu/**pipermail/galaxy-dev/2010-May/**002624.htmlhttp://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
, sridhar srinivasan
sridhar2bioi...@gmail.com wrote:
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
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,
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