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
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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
__
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
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 int
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 Galax
How do I add hg16 into the build-in index?
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My Galaxy Doesn't have enable_beta_job_managers option in universe_conf.ini
file.
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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 ./tophat_ou
: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 gett
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
Tophat2, Tophat, Bowtie2 returns the empty file. The output is in the
format:
*Galaxy5-[Bowtie2_on_data_4__mapped_reads]*
Whenever I open it by double clicking I get the empty file which 0 bytes
file size. I am using hg19 index. What might be the problem?
_
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
___
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no longer be accessible as a history item.
>
> Regards, Hans
>
>
>
>
> On 12/27/2012 11:19 AM, Sachit Adhikari wrote:
>
>> Hi Hans,
>>
>> Oh yes it is stored in database/files. What I wanted to know was if I
>> can change the output path of one or two t
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
workflo
ec 28, 2012, at 8:33 AM, Sachit Adhikari
> 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 outpu
Hello all,
*Happy New Year*
*
*
I have configured MySQL in Galaxy. I have edited universe_wsgi.ini file:
*database_connection = mysql://username:password@
/database_name?unix_socket=/var/run/mysqld/mysqld.sock *
*
*
I restarted the galaxy and all the galaxy_tables has been created but all
of thos
It turns out that I need to import the sqlite3 database in mysql. How can I
do this with Galaxy?
On Mon, Dec 31, 2012 at 4:15 AM, Sachit Adhikari <
sachit.techner...@gmail.com> wrote:
> Hello all,
>
> *Happy New Year*
> *
> *
> I have configured MySQL in Galaxy. I have
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 fund
Dear all,
This is the content of my workflow_step_connection table:
+++---+-++
| id | output_step_id | input_step_id|output_name|input_name |
+++---+-++
| 1 | 1 |
S, Emory University
>
>
> On Tue, Jan 1, 2013 at 6:21 AM, Sachit Adhikari
> wrote:
> > Dear all,
> >
> >
> > This is the content of my workflow_step_connection table:
> > +++---+
Oh Alright. Thanks James!
On Wed, Jan 2, 2013 at 9:34 PM, James Taylor wrote:
> To the "workflow_step" table.
>
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
> On Wed, Jan 2, 2013 at 10:48 AM, Sachit Adhikari
> wrote:
> > Ok
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 genome.r
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 sa
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 Sa
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 wrote:
> > Shall I replace:
> >
> > /orig/path/hg19hg19hg19
> /depot/data2/galaxy/bowtie2/hg19/h
Thanks, that's what I was missing.
On Wed, Feb 13, 2013 at 7:09 PM, Jeremy Goecks wrote:
> 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:
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
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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?
___
P
t;:
>
>
> # 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 o
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
>
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 --min-isoform-fract
-- Forwarded message --
From: Sachit Adhikari
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:
[2013-02-15 01:39:12] Reporting
13 at 8:02 PM, Jeremy Goecks wrote:
> This is not a known bug. For questions related to Tophat errors, you might
> try the Tophat mailing list:
>
> tophat.cuffli...@gmail.com
>
> Good luck,
> J.
>
> On Feb 15, 2013, at 6:02 AM, Sachit Adhikari wrote:
>
> Galaxy
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 --stop-dae
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 wrote:
> Hello,
> I installed galaxy server on ubuntu recently, I can upload small fastq
> files (~600 Mb), but when I am uploading
Hi,
These are the R libraries. Have anyone written a wrapper for these
libraries "lumi", "DESeq" "edgeR"?
Thanks,
Sachit
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h to try
> them out. Best installed on a test instance you plan on destroying because
> the R 3.0 dependency is about to swap over to Bjorns better one - should be
> done later this week when I get some time.
>
> Be warned it takes a long time to auto-install - 10-15 minutes or so on my
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 repo
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
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
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