/proposal/review/google/gsoc2013/saketkc/51001.
I would love to know your suggestions/comments.
I am relatively new to Galaxy, and some of my questions in the process
might be elementary, so kindly bear with it :)
Thanks
Saket Choudhary
As part of a warmup, I added a tool for perming eQTL analysis using PANAMA(
http://ml.sheffield.ac.uk/qtl/panama/).
By default PANAMA writes to stderr and creates a PANAM_results.csv file in
the same directory as the input files.
I wrote a python wrapper
preference - they all work.
Use whatever you find most convenient but remember you may need to
maintain it :)
On Mon, Jun 3, 2013 at 9:05 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary sake...@gmail.com
wrote:
As part of a warmup, I added a tool
, this is just a
suggestion. But as you correctly pointed out, there is a need to organise
the data to ensure the correct dataset is fed to PANAMA or for that matter
the other tools I am working on.
Saket
On Tue, Jun 4, 2013 at 8:39 PM, Saket Choudhary sake...@gmail.com wrote:
Thanks Ross and Peter
Hi Sebastian,
I work behind a proxy too(In my case I have to supply a username and
password too )
I have the following thins setup in my ~/.bashrc:
export http_proxy= http://username:password@proxy-url:proxy-port/
then source it:
$ source ~/.bashrc
or maybe relogin .
and the .hgrc settings
You might want to ssh out and check if that is allowed. If you can ssh out,
you should be able to clone from bitbucket ssh too [ Though you might not
be able to push, depending on whether or not you own the repository]
On 18 June 2013 19:59, Saket Choudhary sake...@gmail.com wrote:
Hi
If you have any suggestions for the VCF4.1 issue or otherwise. please do
let me know.
Thanks
Saket Choudhary
Undergraduate
Dept. of Chemical Engineering
IIT Bombay
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Not much accomplished this week. I plan to write one more blogspot
detailing the datamodel I learnt about galaxy.
http://galaxy-gsoc2013.blogspot.com/2013/07/week-2-accomplishments-and-week-3-plans.html
On 24 June 2013 14:11, Saket Choudhary sake...@gmail.com wrote:
Hi Everyone,
Just wrote
HI Vijayalakshmi,
You can take tools/plotting/plotter.py as an example :
See line 81 :
png_out = out_file + '.png' # force it to png
So in your case :
You can force it to pdf :
output_file = sys.argv[2] +.pdf
I think this should work.
Saket
On 2 July 2013 23:37, vijayalakshmi
Here is a short post explaining the data model. Not ver elaborately
written, so incase you you find a mistake or something poorly
explained , please drop a comment.
http://galaxy-gsoc2013.blogspot.in/2013/07/understanding-datamodel-of-galaxy.html
On 1 July 2013 16:06, Saket Choudhary sake
Week 3 and Week 4 Plans:
http://galaxy-gsoc2013.blogspot.in/2013/07/week-3-accomplishments-and-week-4-plans.html
On 6 July 2013 16:46, Saket Choudhary sake...@gmail.com wrote:
Here is a short post explaining the data model. Not ver elaborately
written, so incase you you find a mistake
Apologies if my previous suggestion confused you :
http://dev.list.galaxyproject.org/error-while-writing-to-pdf-in-python-tp4660463p4660464.html
You may first generate the pdf :
input_file = sys.argv[1]
output_file = sys.argv[2]
#txt_in = options.exp_data # + '.txt' ## NOT REQUIRED
On 11 July 2013 04:31, Saket Choudhary sake...@gmail.com wrote:
Apologies if my previous suggestion confused you :
http://dev.list.galaxyproject.org/error-while-writing-to-pdf-in-python-tp4660463p4660464.html
You may first generate the pdf :
input_file = sys.argv[1]
output_file
Hi All,
Week 4 blog post :
http://galaxy-gsoc2013.blogspot.com/2013/07/week-4-accomplishments-and-week-5-plans.html
Do drop in your comments , if any.
Thanks
Saket
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Was stuck up with my approach of wrapping the Workflows in a toolbox
and hence this blog post is a bit delayed.
http://galaxy-gsoc2013.blogspot.in/2013/07/week-5-update.html
Saket
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Week 6 updates are here :
http://galaxy-gsoc2013.blogspot.in/2013/07/week-6-update.html
Thanks
Saket
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Hi Everyone,
Here is an update for the last 2 weeks:
http://galaxy-gsoc2013.blogspot.com/2013/08/week-7-and-week-8-update.html
Saket
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Update here : http://galaxy-gsoc2013.blogspot.in/2013/09/blog-post.html
--
Saket
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I wrote a very short update here:
http://galaxy-gsoc2013.blogspot.in/2013/09/penultimate-update.html
Saket
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Project!
Saket Choudhary
Senior Undergraduate
Department of Chemical Engineering
IIT Bombay
India
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Hi Bjoern,
On 21 October 2013 13:38, Bjoern Gruening bjoern.gruen...@gmail.com wrote:
Hi,
one of our users has created a large workflow with 300 steps. Yes he
really loves Galaxy :)
Unfortunately, its not possible to use the graphical user interface
anymore with so many steps. You can't
Hi Bjoern,
On 21 October 2013 14:11, Bjoern Gruening bjoern.gruen...@gmail.com wrote:
Hi Saket,
On 21 October 2013 13:38, Bjoern Gruening bjoern.gruen...@gmail.com wrote:
Hi,
one of our users has created a large workflow with 300 steps. Yes he
really loves Galaxy :)
Unfortunately,
Hey Luca,
I am behind a proxy too, that requires authentication. In my case all
the tests that fail are due to the '/test/base/twilltestcase.py',
caused by 'twill.commands.go' returning a 403 instead of a 200. I
believe that is the case with you too. The documentation[1] says that
twill respects
Hi Luca,
On 3 February 2014 18:07, Luca Toldo lucato...@gmail.com wrote:
dear Galaxians,
my server is behind a proxy with user authentication.
Wget and hg work fine however unfortunately when I try to install from the
tool shed I get error since the system is using urllib2 that is known not
Hi Ketan,
You can specify selected=true[1]
[1]
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coption.3E_tag_set
On 19 February 2014 20:14, Ketan Maheshwari ketancmaheshw...@gmail.com wrote:
Hello,
In my tool UI, I have a select tool as follows:
param name=site
I happened to copy Peter's .travis.yml for running tests for some of
my packages. However the process has not been smooth at all.
See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value
'['condel_input.tabular']' in form
On 17 April 2014 15:34, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary sake...@gmail.com wrote:
I happened to copy Peter's .travis.yml for running tests for some of
my packages.
Background information:
http://blastedbio.blogspot.co.uk/2013/09
version of paste in my PYTHONPATH.
But it happens even if I run these under a virtualenv.
Saket
On 17 April 2014 18:03, Saket Choudhary sake...@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary sake...@gmail.com wrote
385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
On Thu, Apr 17, 2014 at 10:43 PM, Saket Choudhary sake...@gmail.com wrote:
Just to add, that is the case with all the tests:
$ sh run_functional_tests.sh
Ran 436 tests in 19.153s
FAILED (errors=434)
All tests fail locally
/23206181#L1721
On testtoolshed: http://testtoolshed.g2.bx.psu.edu/view/saketkc/condel
Installation fails, because pycurl fails to install which I shall
report in other thread.
Saket
On 17 April 2014 18:45, Saket Choudhary sake...@gmail.com wrote:
Culprit: System Proxy.
I am behind a proxy
John pointed out that the error its the upload of the test file itself
which is failing. I can locate the input files
in test-data/
https://travis-ci.org/saketkc/galaxy_tools/jobs/23238748#L1723
Any clues as to where exactly am I going wrong?
On 17 April 2014 19:40, Saket Choudhary sake
Can I throw in a bounty for this one? ;-)
On 18 April 2014 03:09, Saket Choudhary sake...@gmail.com wrote:
John pointed out that the error its the upload of the test file itself
which is failing. I can locate the input files
in test-data/
https://travis-ci.org/saketkc/galaxy_tools/jobs
On 18 April 2014 14:59, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Apr 17, 2014 at 10:39 PM, Saket Choudhary sake...@gmail.com wrote:
John pointed out that the error its the upload of the test file itself
which is failing. I can locate the input files
in test-data/
https://travis
On 18 April 2014 18:06, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, Apr 18, 2014 at 11:47 AM, Saket Choudhary sake...@gmail.com wrote:
On 18 April 2014 14:59, Peter Cock p.j.a.c...@googlemail.com wrote:
Very strange. Adding ls test-data to the TravisCI list worked,
and showed the input
* fork your repository.
On 18 April 2014 18:42, Saket Choudhary sake...@gmail.com wrote:
On 18 April 2014 18:06, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, Apr 18, 2014 at 11:47 AM, Saket Choudhary sake...@gmail.com wrote:
On 18 April 2014 14:59, Peter Cock p.j.a.c...@googlemail.com
Choudhary sake...@gmail.com wrote:
* fork your repository.
On 18 April 2014 18:42, Saket Choudhary sake...@gmail.com wrote:
On 18 April 2014 18:06, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, Apr 18, 2014 at 11:47 AM, Saket Choudhary sake...@gmail.com
wrote:
On 18 April 2014 14:59, Peter
I am trying to visualise VCF exported from:
ftp://ngs.sanger.ac.uk/production/cosmic/CosmicCodingMuts_v68.vcf.gz
However I get the following error: (Both on Galaxy Main and Local installation)
Input error: Chromosome 1 found in your input file but not in your genome file.
needLargeMem: trying to
Any comments on this?
http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1
On 17 April 2014 19:54, Saket Choudhary sake...@gmail.com wrote:
My attempt to 'package' pycurl on testtoolshed fails with the following error:
src/pycurl.c: In function ‘do_multi_info_read’: src
23:31, Björn Grüning bjoern.gruen...@gmail.com wrote:
Hi Saket,
is there any script installed with that package? --install-scripts may be
needed. Also I'm wondering if there is no dependency on curl-lib?
Cheers,
Bjoern
Am 29.04.2014 19:16, schrieb Saket Choudhary:
Any comments
Hi all,
I was a Google Summer of Code Student for Galaxy Project for the year
2013. One of my main tasks was to implement 'nested workflows' for
Galaxy. See [1]
This took me more time than I had expected and after sending a
declined PR(See [2]) I re-attempted something similar with PR# 370.
I was wondering if there is a possibility of a 'Tool'Shed for
Visualisation registry plugins(custom plugins, developed by
users/developers)?
The motivation for this comes from a small 'tool' I wrote for
visualiing fastq phred scores using box plots[Still under development]
here:
I recently updated tests for one of my wrappers and came across this
strange behaviour:
The twill based testing reports a failure:
https://travis-ci.org/saketkc/galaxy_tools/jobs/29956682#L1463
whereas, the API based testing shows success:
https://travis-ci.org/saketkc/galaxy_tools/jobs/29956683
,
not sure when that is happening though...
Peter
On Tue, Jul 15, 2014 at 9:31 AM, Saket Choudhary sake...@gmail.com
wrote:
I recently updated tests for one of my wrappers and came across this
strange
behaviour:
The twill based testing reports a failure:
https://travis-ci.org/saketkc
On 17 July 2014 22:29, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Jul 17, 2014 at 5:55 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Not a problem Peter, it's a somewhat subtle bug to have, and there isn't
a lot of documentation on the wiki about writing new datatypes (though I
plan
which
should then be set to $CURL.
Is there a way to check the logs, something I attempted by doing this:
action type=shell_commandecho $INSTALL_DIR/action
action type=shell_commandecho $CURL/action
Or any alternate way to debug?
On 29 April 2014 14:25, Saket Choudhary sake...@gmail.com
Dave,
I have similar issues with my repositories:
https://testtoolshed.g2.bx.psu.edu/view/saketkc/pycurl_test
This was uploaded on 14th August.
https://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1
shows no test results for the month of August. The last test was run on
Is there a way to retrieve fileX.json in history using the DataProviders?
Using https://wiki.galaxyproject.org/DataProviders I tried base and
line, but I am looking for retrieving the contents of fileX.json as
a json object itself.
Saket
(in python: json.loads( your_string
), in javascript: JSON.parse( yourString ))
Let me know if that doesn't work,
Carl
On Mon, Sep 1, 2014 at 2:25 AM, Saket Choudhary sake...@gmail.com wrote:
Is there a way to retrieve fileX.json in history using the DataProviders?
Using https
I am trying to reset metadata on all my repositories at once using the
Reset metadata on my repositories button on
https://testtoolshed.g2.bx.psu.edu/ It fails with:
Internal Server Error
Galaxy was unable to successfully complete your request
URL:
I have had the same issue. A little debugging here:
https://travis-ci.org/saketkc/galaxy_tools/builds/41209515#L84
I first thought that there was a conflict with system installed
paramiko, but it is not:
https://travis-ci.org/saketkc/galaxy_tools/builds/41210153#L60
A clean install of
/37353814) - so I
suggest creating a virtualenv and testing Galaxy inside of that.
Hope this helps.
-John
On Mon, Nov 17, 2014 at 12:52 PM, Saket Choudhary sake...@gmail.com wrote:
I have had the same issue. A little debugging here:
https://travis-ci.org/saketkc/galaxy_tools/builds/41209515
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