Hello group,
I am trying to write lumi wrapper for Galaxy. Is anyone is writing or
already have written lumi wrapper for Galaxy. I couldn't find in both
galaxy main tool shed and test tool shed.
Regards
Sachit
___
Please keep all replies
LinkedIn
galaxy-...@bx.psu.ed,
I'd like to add you to my professional network on LinkedIn.
- sachit
sachit adhikari
Software Engineer at ZurelSoft Nepal
Nepal
Confirm that you know sachit adhikari:
https://www.linkedin.com/e/1kvf56-hjf9os56-3g/isd/15160415460/FH4R02On/?hs
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
, Sachit Adhikari
sachit.techner...@gmail.com wrote:
Hi,
These are the R libraries. Have anyone written a wrapper for these
libraries lumi, DESeq edgeR?
Thanks,
Sachit
___
Please keep all replies on the list by using reply all
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
Galaxy recommends to upload the file more than 2 GB via FTP. Browser can't
handle the large file upload.
Thank you!
On Sat, Apr 20, 2013 at 3:07 AM, Nishant THAKUR tha...@ciml.univ-mrs.frwrote:
Hello,
I installed galaxy server on ubuntu recently, I can upload small fastq
files (~600 Mb),
Hi,
First make sure that the you are editing the correct universe_wsgi.ini
file. Secondly, you must restart your server after you make changes to your
settings file i.e universe_wsgi.ini. If you are running your server
in daemon mode use following command to stop your server:
*sh run.sh
Galaxy is working fine in command line whereas in Galaxy at last i got this
error:
[2013-02-15 01:39:12] Reporting output tracks
[FAILED]
Error running /usr/local/bin/tophat_reports --min-anchor 8
--splice-mismatches 0 --min-report-intron 50 --max-report-intron
50
-- Forwarded message --
From: Sachit Adhikari sachit.techner...@gmail.com
Date: Fri, Feb 15, 2013 at 11:02 AM
Subject: Error while writing data in tophat2
To: galaxy-dev@lists.bx.psu.edu
Galaxy is working fine in command line whereas in Galaxy at last i got this
error:
[2013-02
:
# Dataset files are stored in this directory.
file_path = database/files
if this is, what you want?
Regards, Hans-Rudolf
On 02/14/2013 05:40 AM, Sachit Adhikari wrote:
I want to redirect all the output of Galaxy to another
directory(actually a external hard drive with full write access
with your data
and/or your Tophat settings.
Good luck,
J.
On Feb 13, 2013, at 8:22 AM, Sachit Adhikari wrote:
Ok sorry. I did that, but the output of splice junctions is empty. The
other outputs looks fine. What might be the problem?
Thanks,
Sachit
On Wed, Feb 13, 2013 at 1:20 PM, Jeremy
I got this error which executing tophat2 in Galaxy:
Error in tophat:
[2013-02-13 02:02:43] Beginning TopHat run (v2.0.7)
---
[2013-02-13 02:02:43] Checking for Bowtie
Bowtie version:2.0.6.0
[2013-02-13 02:02:43] Checking for
Ok sorry. I did that, but the output of splice junctions is empty. The
other outputs looks fine. What might be the problem?
Thanks,
Sachit
On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote:
Shall I replace:
/orig/path/hg19hg19hg19
Thanks, that's what I was missing.
On Wed, Feb 13, 2013 at 7:09 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote:
Error in tophat:
[2013-02-13 02:02:43] Beginning TopHat run (v2.0.7)
---
[2013-02-13 02:02:43] Checking for Bowtie
I want to redirect all the output of Galaxy to another directory(actually a
external hard drive with full write access). How can I do that? Thanks
___
Please keep all replies on the list by using reply all
in your mail client. To manage your
Tophat2 output on accepted hits, deletions and insertions is fine
whereas splice
junctions output is only:
track name=junctions description=TopHat junctions
I am running tophat2 with hg19 reference genome? What might be the problem?
___
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
Greetings all,
These are various tables related to workflow in Galaxy that I found in the
database. There are very similar tables like: workflow and stored_workflow,
workflow_step_tag_association, stored_workflow_tag_association etc. I want
to know what does specific table holds. What are the
, 2012, at 8:33 AM, Sachit Adhikari sachit.techner...@gmail.com
wrote:
Hi Dannon,
Thank you for your answer. What I meant by the last question is that:
When I create a workflow (tophat-bowtie-bowtie2). The input is first
processed by tophat and the output of tophat is processed by bowtie
I have searched the mailing list and found that the output, histories and
workflows are stored in ~/database/files. To do a little experiment I
deleted all the inside that directory. I then open my Galaxy and browse the
workflow. But the workflow is still there. I was wondering where is the
Hello Everyone,
*Merry Christmas and Happy New Year*
*
*
I was wondering where are the output of the tools stored in the machine
where the galaxy is hosted? And, can I change the path of the output of the
tools?
Thanks,
Sachit
___
Please
: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
It seems like tophat2 does not support --transcriptome-mismatches option
but Galaxy is still configured to call tophat2 with this option when run
with Full parameter setting option within Galaxy. Is there new wrapper
with this fix? If not, how to remove this option from Galaxy so that
tophat2 is
How do I add hg16 into the build-in index?
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
My Galaxy Doesn't have enable_beta_job_managers option in universe_conf.ini
file.
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the
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?
Hello Everyone,
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
Hello Everyone,
I am about to write a syncing tool for Galaxy like Dropbox using Python
with the progress bar. How do I integrate it with galaxy? It would be easy
for client to upload files using the syncing tool. Are there any syncing
tools available for Galaxy?
Thanks
29 matches
Mail list logo
