Hello. I would like to integrate this great tool Trim Galore in the local
Galaxy. Has anyone did this before? If so, please provide me with the
wrapper and .xml file? How can I integrate it?
Best wishes,
Sachit
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Hello. I would like to integrate this great tool Trim Galore in the local
Galaxy. How can I do that? Thanks in advance.
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Galaxy analysis and other features on the public server
at
Hi there Alicia! To find the tool in the Galaxy tool search, first you have
to put your tool files in tools with .xml files then you have to edit
tool_conf.xml file. Here's the step by step tutorial:
http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial
Regards,
Sachit
On Fri, Oct 5, 2012
Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy. Are
those tools must be installed in order to work in Galaxy. For example: I am
using Debian machine(Don't have tophat and bowtie installed). Will tophat
and bowtie work in my local galaxy? Thanks
I don't think you understood my question very well. Tophat and Bowtie are
available by default in Galaxy. Tophat and Bowtie however is not installed
in my operating system. Will it still work in Galaxy?
On Mon, Oct 8, 2012 at 3:22 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de
Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local
machine, I need to close the terminal and restart the terminal again.
However, in server I integrated several tools, now I need to restart the
server to test it. I used ./run.sh --reload doesn't restart the server and
I
it.
Hope this helps,
Enis
On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari
sachit.techner...@gmail.com wrote:
Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local
machine, I need to close the terminal and restart the terminal again.
However, in server I integrated
I am getting this error in Bowtie2 and Tophat2:
Data table named 'bowtie2_indexes' is required by tool but not configured
Data table named 'tophat2_indexes' is required by tool but not configured.
How can I solve it? Thanks
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mailing list: galaxy-...@bx.psu.edu
Best,
J.
On Oct 19, 2012, at 2:58 AM, Sachit Adhikari wrote:
I am getting this error in Bowtie2 and Tophat2:
Data table named 'bowtie2_indexes' is required by tool but not configured
Data table named 'tophat2_indexes' is required by tool but not configured
I am getting this error at the top while opening Bismark Mapper:
Data table named 'bismark_bs_indeces' is required by tool but not
configured.
I got Bismark from official toolshed.
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Hi all,
I am seeing this error while clicking on Bismark in Galaxy. I got the
Bismark for galaxy tool shed. I tried to get another bismark wrapper
developed by Bjoern. I didnt know how to download that. What's the error?
Thanks
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Where are the user's information stored in Galaxy? I can't find the
information in universe_wsgi.
Regards,
Sachit
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at
We have found that, in Galaxy, when we add dataset to a library under
Manage data libraries, Galaxy sometimes detects the type of the file and
sometimes does not. What I have noticed is that it detects the type of the
file when we select Copy file into Galaxy under Copy data into Galaxy?
option
Hi list,
We have found that, in Galaxy, when we add dataset to a library under
Manage data libraries, Galaxy sometimes detects the type of the file and
sometimes does not. What I have noticed is that it detects the type of the
file when we select Copy file into Galaxy under Copy data into Galaxy?
TopHat2 needs built-in index/ reference genome in order for it to run. I
need to add hg 16 index into the build-in index / reference gnome list. I
already have the file. How can I add it?
Regards,
Sachit
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How do I add hg16 into the build-in index?
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using reply all in your
This is the error I am getting while running Tophat. What's causing this? I
have the default hg19 index files.
Error in tophat:
[Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3)
---
[Tue Dec 18 10:08:33 2012] Preparing output location
:57:07] Checking for Samtools
Samtools version: 0.1.18.0
[2012-12-19 06:57:07] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (test_ref.*.bt
On Wed, Dec 19, 2012 at 10:38 AM, Sachit Adhikari
sachit.techner...@gmail.com wrote:
This is the error I am getting while
I downloaded the entire directory of UCSC for the reference gnome of
Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference
gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
with the files:
genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2
Also, do I have make all the reference files executable?
On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari
sachit.techner...@gmail.com wrote:
I downloaded the entire directory of UCSC for the reference gnome of
Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference
gnome
Hi,
These are the R libraries. Have anyone written a wrapper for these
libraries lumi, DESeq edgeR?
Thanks,
Sachit
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at
Thank you Björn and Ross. I will install the tools from the admin
interface.
On Mon, Jul 8, 2013 at 12:35 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Sachit,
we are working currently on a DESeq2 wrapper. Not yet finised sorry.
There is also a edgeR Test
Hi group,
The galaxy stores the output of the job on files/043/dataset_*ID*.dat.
I have two questions here.:
1) Can I find the ID of my output from the Galaxy history? I tried Edit
Attributes, Annotations, tags but couldn't find it.
2) Can I rename my output while initiating the task? If I can
Hi group,
The galaxy stores the output of the job on files/043/dataset_*ID*.dat.
I have two questions here.:
1) Can I find the ID of my output from the Galaxy history? I tried Edit
Attributes, Annotations, tags but couldn't find it.
2) Can I rename my output while initiating the task? If I can
, 2013 at 5:21 AM, Sachit Adhikari
sachit.techner...@gmail.com wrote:
Hi group,
The galaxy stores the output of the job on files/043/dataset_ID.dat.
I have two questions here.:
1) Can I find the ID of my output from the Galaxy history? I tried Edit
Attributes, Annotations, tags
...@googlemail.comwrote:
On Wed, Jul 24, 2013 at 10:35 AM, Sachit Adhikari
sachit.techner...@gmail.com wrote:
Hi,
By i do you mean Edit attributes button? There are four sub-headings on
that: Attributes, Convert format, Datatype and permissions but I can't
see
data file's full path on any of them
Thanks Peter for clearing this out.
On Wed, Jul 24, 2013 at 4:33 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Wed, Jul 24, 2013 at 11:15 AM, Sachit Adhikari
sachit.techner...@gmail.com wrote:
Yes, but unfortunately that didn't work too. I have already tried the
solution you provided
Hi,
This is my third post regarding this matter but however I didn't get any
reply. I am trying to find a tool for r Illumina Methylation. Is there any
available on the tool shed or test tool shed?
Thanks,
Sachit
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Hi Bjoern,
Thank you for your reply. To be precise I am looking for a wrapper of *
lumi. *http://www.bioconductor.org/packages/2.12/bioc/html/lumi.html
Do we have that in main tool shed or test tool shed or in github?
Thanks,
Sachit
On Mon, Jul 29, 2013 at 2:53 PM, Bjoern Gruening
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