Re: [galaxy-dev] Converting .gff3 to 12-column .bed

[Jennifer Jackson]

Hi Lindsay,

Nice to hear that Vipin's server worked out for you.

A reduction in the number of lines is completely expected. You should 
have the same number of lines in the BED12 file as you have unique "ID"s 
in the GFF3 file, if you want to double check. This is the same as the 
number of unique transcripts in any of the files, if summed up correctly.


Why is this? A GFF3 file has one line per feature. Part of an exon, etc. 
with further (this can vary) annotation that tells you if it is 5' UTR, 
or CDS, etc. When converting GFF3 -> BED12, all the features for a 
particular transcript are rolled up into a single line of output. 
Transcripts will have a unique "ID" by GFF3 specification - and all 
features that belong to that transcript will have it in the GFF3 file's 
attributes field (it is usually the first attribute listed).


When you converted just GFF3 -> BED6, each feature was individually 
converted into a distinct line of BED formatted output, there was no 
summing up to group the information for the transcript as a whole.


The Galaxy wiki has more - GFF3 can represent other kinds of data, and 
that is covered in the link-outs to the original spec, but this is the 
gist of the meaning for your specific data.


Glad I could help before, and that Vipin had the tool online & available 
to simplify things!


Best,

Jen
Galaxy team

On 11/12/13 4:12 PM, Lindsay Rutter wrote:

Hello Jennifer:

Thank you for your very helpful and detailed explanation!

I ended up using the site that Vipin provided in his message 
(https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed).


Indeed, it produced a file with 12 columns that appears to be in a 
reasonable bed format (including the 10th column being an integer, 
with the 11th and 12th column consisting of that integer number of 
items separated by commas).


However, I noticed that the number of lines in the file went 
from 183,748 (in the .gff3 file) to 11,506 (in the 12-column .bed file).


In your opinion, does this seem like a reasonable reduction in number 
of lines? I was not expecting that (in fact, I was expecting the 
number of lines would stay the same, as they did going from .gff3 to 
6-column .bed file), but I am quite inexperienced using these files.


Thanking you...
Lindsay




On Mon, Nov 11, 2013 at 11:15 AM, Jennifer Jackson > wrote:


Hello,

There are no tools directly on the public Galaxy site to transform
a GFF3 dataset into a BED12 dataset. However, the Tool Shed has a
repository called ' fml_gff3togtf' that includes a tool for this
purpose, for use in a local install. The description is a bit
bothersome in that it a slightly incorrect datatype statement, so
be sure to test out the results. (the word "wiggle" has no place
in this statement: "
gff3_to_bed_converter.py: This tool converts gene transcript annotation from 
GFF3 format to UCSC wiggle 12 column BED format.")
http://getgalaxy.org
http://usegalaxy.org/toolshed

I see your post at Biostar, and it might be helpful to let you
know what a BED12 file represents (plus I'll post this there, may
help others):
http://www.biostars.org/p/85869/

A BED12 file describes the complete, often spliced, alignment of a
sequence to a reference genome. This does not include minor base
variation, it is a macro alignment. You can think of each of the
blocks as being "exons", although there is no magic here - if the
sequence or genome had quality problems, or significant variation
(large insertion or deletion), that could cause the alignment to
fragment as well.
Here is the data description:
http://wiki.galaxyproject.org/Learn/Datatypes#Bed

To see examples, at UCSC (genome.ucsc.edu
), EST or mRNA track will have this as the
primary table format. All gene track can also be in BED12 format,
or in a related one, genePred:
http://genome.ucsc.edu/FAQ/FAQformat.html#format9

UCSC also has line-command utilities to convert between the
formats, pre-compiled versions are here:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads

Either way, you can convert the data, then load up into the public
Galaxy (usegalaxy.org ) and proceed with
your analysis. BEDTools works well with BED12 files. There is
definitely information loss attempting to transform BED6 -> BED12,
as the global alignment is lost. And adjusting attributes such as
score or name are often a preference, so you can alter these
however you want, as long as the attribute formatting rules for
the columns are followed.

Hopefully this helps,

Jen
Galaxy team


On 11/9/13 3:29 PM, lrutter @iastate.edu  wrote:

Hello Galaxy:

I am trying overall to convert a .gff3 file to 12-column .bed file.

I first tried GFF-to-BED converter, but it gave a 6-column .bed file

Re: [galaxy-dev] dynamic_options selected value as input for second dynamic_options function call

[Hans van Leeuwen]

Hi,

I found a working workaround using the deprecated  tags:


  

  
  

  


This works; both select lists (on separate GUI pages) are dynamically
generated when the called function connects to a database to retrieve the
options.  However, as it is recommended not to use  tags any longer,
can anyone suggest how to write above example using  and 
tags instead? I have searched a lot but can't find out how to do it.

Thank you,

Hans
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[galaxy-dev] Write all intermediate workflow data to /tmp/ only

[Ben Gift]

I'm working with a lot of data on a cluster (condor). If I save all the
workflow intermediate data, as Galaxy does by default (and rightfully so),
it fills the drives.

How can tell Galaxy to use /tmp/ to store all intermediate data in a
workflow, and keep the result?

I imagine I'll have to work on how Galaxy handles jobs, but I'm hoping
there is something built in for this.

Thanks
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Re: [galaxy-dev] Error editing users associated with a quota

[Peter Cock]

On Tue, Nov 12, 2013 at 3:12 PM, John Chilton  wrote:
> On Tue, Nov 12, 2013 at 3:32 AM, Peter Cock  wrote:
>> On Mon, Nov 11, 2013 at 6:55 PM, John Chilton  wrote:
>>> Hey Peter,
>>>
>>>   Does your universe_wsgi.ini have "enable_quotas = True" set?
>>>
>>> -John
>>
>> No,
>>
>> $ grep enable_quotas universe_wsgi.ini
>> (nothing)
>>
>> I had suspected the quotas might not be working...
>>
>> If the default is not to enable quotas, then the "Manage quotas"
>> entry of the "Admin" page ought perhaps to be disabled?
>
> I was going to make you Trello card for this entirely logical request
> and then I decided in the time it would take the Trello interface to
> load I could do a pull request instead.
>
> https://bitbucket.org/galaxy/galaxy-central/pull-request/258/only-show-manage-quotas-if-quotas-are/diff
>

Thanks - at some point I will need to set enable_quotas = True,
and retest to see if the original bug persists.

Peter
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Re: [galaxy-dev] Error editing users associated with a quota

[John Chilton]

On Tue, Nov 12, 2013 at 3:32 AM, Peter Cock  wrote:
> On Mon, Nov 11, 2013 at 6:55 PM, John Chilton  wrote:
>> Hey Peter,
>>
>>   Does your universe_wsgi.ini have "enable_quotas = True" set?
>>
>> -John
>
> No,
>
> $ grep enable_quotas universe_wsgi.ini
> (nothing)
>
> I had suspected the quotas might not be working...
>
> If the default is not to enable quotas, then the "Manage quotas"
> entry of the "Admin" page ought perhaps to be disabled?

I was going to make you Trello card for this entirely logical request
and then I decided in the time it would take the Trello interface to
load I could do a pull request instead.

https://bitbucket.org/galaxy/galaxy-central/pull-request/258/only-show-manage-quotas-if-quotas-are/diff

>
> Peter
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Re: [galaxy-dev] BAM/BAI index file test problem on (Test) Tool Shed

[Peter Cock]

On Tue, Nov 12, 2013 at 2:37 PM, John Chilton  wrote:
> This sounds a lot like this;
> http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p4662444.html.
>
> When using the local job runner (as the test framework likely does), I
> believe samtools needs to be on Galaxy's path. I don't think it is
> enough to just have it available as a "tool dependency" (installed via
> tool shed or not).
>
> As workarounds Dave could either install the samtools OS package or
> place the tool shed install of this on Galaxy's path before starting?
> .Alternatively, I guess the underlying problem could be solved -
> though it is not entirely clear the best path forward on that, only
> that is a real problem.
>
> -John

Yes, that sounds like the same problem - and I agree a short term
hack would be to put samtools on the test system.

On Tue, Nov 12, 2013 at 2:35 PM, Greg Von Kuster  wrote:
> Hello Peter,
>
> Thanks for reporting this - I've added the following Trello card for this 
> issue.
>
> https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1
>
> Greg Von Kuster

That Trello link seems to be broken for me :(

Peter
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Re: [galaxy-dev] BAM/BAI index file test problem on (Test) Tool Shed

[John Chilton]

This sounds a lot like this;
http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p4662444.html.

When using the local job runner (as the test framework likely does), I
believe samtools needs to be on Galaxy's path. I don't think it is
enough to just have it available as a "tool dependency" (installed via
tool shed or not).

As workarounds Dave could either install the samtools OS package or
place the tool shed install of this on Galaxy's path before starting?
.Alternatively, I guess the underlying problem could be solved -
though it is not entirely clear the best path forward on that, only
that is a real problem.

-John


On Tue, Nov 12, 2013 at 6:07 AM, Peter Cock  wrote:
> Hi guys,
>
> I have a new wrapper for samtools idxstats with a working
> unit test via run_functional_tests.sh run locally or on TravisCI:
> https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html
>
> However, this tool's test is failing on the Test Tool Shed:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/6564815949e0
>
> Tool test results
> Automated test environment
> Time tested: ~ 11 hours ago
> System: Linux 3.8.0-30-generic
> Architecture: x86_64
> Python version: 2.7.4
> Galaxy revision: 11284:28469a503b56
> Galaxy database version: 117
> Tool shed revision:
> Tool shed database version:
> Tool shed mercurial version:
> Tests that failed
> Tool id: samtools_idxstats
> Tool version: samtools_idxstats
> Test: test_tool_00
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_idxstats/samtools_idxstats/0.0.1)
> Stderr:
> Fatal error: Exit code 1 ()
> Input BAI file not found: None
> Traceback:
> Traceback (most recent call last):
>   File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 216, in test_tool
> self.do_it( td, shed_tool_id=shed_tool_id )
>   File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 28, in do_it
> self.__verify_outputs( testdef, shed_tool_id, data_list )
>   File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 134, in __verify_outputs
> self.__verify_output( output_tuple, shed_tool_id, elem,
> maxseconds=maxseconds )
>   File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 141, in __verify_output
> self.verify_dataset_correctness( outfile, hid=elem_hid,
> attributes=attributes, shed_tool_id=shed_tool_id )
>   File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> line 782, in verify_dataset_correctness
> self._assert_dataset_state( elem, 'ok' )
>   File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> line 606, in _assert_dataset_state
> raise AssertionError( errmsg )
> AssertionError: Expecting dataset state 'ok', but state is 'error'.
> Dataset blurb: error
>
> It appears that the upload has not generated the *.bai index and
> assigned it to the variable input_bam.metadata.bam_index
> (but this works via run_functional_tests.sh for me):
>
> $ ls test-data/ex1.*
> test-data/ex1.bam  test-data/ex1.idxstats.tabular
>
> $ ./run_functional_tests.sh -id samtools_idxstats
> ...
> Ran 1 test in 32.400s
>
> OK
> ...
> (all fine)
>
> (Note that the bai file does not seem to be needed)
>
> Tested with this revision, which works:
>
> $ hg branch
> default
> $ hg log | head
> changeset:   12309:1df960b4892a
> tag: tip
> user:John Chilton 
> date:Sun Nov 10 23:37:56 2013 -0600
> summary: PEP-8 cleanups of lib/galaxy/security/__init__.py.
>
> Updated to current tip, also works:
>
> $ hg branch
> default
> [galaxy@ppserver galaxy-central]$ hg log | head
> changeset:   12321:e12a10e5418d
> tag: tip
> user:guerler
> date:Mon Nov 11 16:00:10 2013 -0500
> summary: UI: Fix tooltip placement for masthead icons
>
> Are there anyone known differences on the Test Tool Shed
> which could explain this failure?
>
> Thanks,
>
> Peter
> ___
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> in your mail client.  To manage your subscriptions to this
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>
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Re: [galaxy-dev] BAM/BAI index file test problem on (Test) Tool Shed

[Greg Von Kuster]

Hello Peter,

Thanks for reporting this - I've added the following Trello card for this issue.

https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1

Greg Von Kuster

On Nov 12, 2013, at 7:07 AM, Peter Cock  wrote:

> Hi guys,
> 
> I have a new wrapper for samtools idxstats with a working
> unit test via run_functional_tests.sh run locally or on TravisCI:
> https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html
> 
> However, this tool's test is failing on the Test Tool Shed:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/6564815949e0
> 
> Tool test results
> Automated test environment
> Time tested: ~ 11 hours ago
> System: Linux 3.8.0-30-generic
> Architecture: x86_64
> Python version: 2.7.4
> Galaxy revision: 11284:28469a503b56
> Galaxy database version: 117
> Tool shed revision:
> Tool shed database version:
> Tool shed mercurial version:
> Tests that failed
> Tool id: samtools_idxstats
> Tool version: samtools_idxstats
> Test: test_tool_00
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_idxstats/samtools_idxstats/0.0.1)
> Stderr:
> Fatal error: Exit code 1 ()
> Input BAI file not found: None
> Traceback:
> Traceback (most recent call last):
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 216, in test_tool
>self.do_it( td, shed_tool_id=shed_tool_id )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 28, in do_it
>self.__verify_outputs( testdef, shed_tool_id, data_list )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 134, in __verify_outputs
>self.__verify_output( output_tuple, shed_tool_id, elem,
> maxseconds=maxseconds )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 141, in __verify_output
>self.verify_dataset_correctness( outfile, hid=elem_hid,
> attributes=attributes, shed_tool_id=shed_tool_id )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> line 782, in verify_dataset_correctness
>self._assert_dataset_state( elem, 'ok' )
>  File 
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> line 606, in _assert_dataset_state
>raise AssertionError( errmsg )
> AssertionError: Expecting dataset state 'ok', but state is 'error'.
> Dataset blurb: error
> 
> It appears that the upload has not generated the *.bai index and
> assigned it to the variable input_bam.metadata.bam_index
> (but this works via run_functional_tests.sh for me):
> 
> $ ls test-data/ex1.*
> test-data/ex1.bam  test-data/ex1.idxstats.tabular
> 
> $ ./run_functional_tests.sh -id samtools_idxstats
> ...
> Ran 1 test in 32.400s
> 
> OK
> ...
> (all fine)
> 
> (Note that the bai file does not seem to be needed)
> 
> Tested with this revision, which works:
> 
> $ hg branch
> default
> $ hg log | head
> changeset:   12309:1df960b4892a
> tag: tip
> user:John Chilton 
> date:Sun Nov 10 23:37:56 2013 -0600
> summary: PEP-8 cleanups of lib/galaxy/security/__init__.py.
> 
> Updated to current tip, also works:
> 
> $ hg branch
> default
> [galaxy@ppserver galaxy-central]$ hg log | head
> changeset:   12321:e12a10e5418d
> tag: tip
> user:guerler
> date:Mon Nov 11 16:00:10 2013 -0500
> summary: UI: Fix tooltip placement for masthead icons
> 
> Are there anyone known differences on the Test Tool Shed
> which could explain this failure?
> 
> Thanks,
> 
> Peter
> ___
> 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:
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> 
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[galaxy-dev] BAM/BAI index file test problem on (Test) Tool Shed

[Peter Cock]

Hi guys,

I have a new wrapper for samtools idxstats with a working
unit test via run_functional_tests.sh run locally or on TravisCI:
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html

However, this tool's test is failing on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/6564815949e0

Tool test results
Automated test environment
Time tested: ~ 11 hours ago
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 11284:28469a503b56
Galaxy database version: 117
Tool shed revision:
Tool shed database version:
Tool shed mercurial version:
Tests that failed
Tool id: samtools_idxstats
Tool version: samtools_idxstats
Test: test_tool_00
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_idxstats/samtools_idxstats/0.0.1)
Stderr:
Fatal error: Exit code 1 ()
Input BAI file not found: None
Traceback:
Traceback (most recent call last):
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 216, in test_tool
self.do_it( td, shed_tool_id=shed_tool_id )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 28, in do_it
self.__verify_outputs( testdef, shed_tool_id, data_list )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 134, in __verify_outputs
self.__verify_output( output_tuple, shed_tool_id, elem,
maxseconds=maxseconds )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 141, in __verify_output
self.verify_dataset_correctness( outfile, hid=elem_hid,
attributes=attributes, shed_tool_id=shed_tool_id )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 782, in verify_dataset_correctness
self._assert_dataset_state( elem, 'ok' )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 606, in _assert_dataset_state
raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'.
Dataset blurb: error

It appears that the upload has not generated the *.bai index and
assigned it to the variable input_bam.metadata.bam_index
(but this works via run_functional_tests.sh for me):

$ ls test-data/ex1.*
test-data/ex1.bam  test-data/ex1.idxstats.tabular

$ ./run_functional_tests.sh -id samtools_idxstats
...
Ran 1 test in 32.400s

OK
...
(all fine)

(Note that the bai file does not seem to be needed)

Tested with this revision, which works:

$ hg branch
default
$ hg log | head
changeset:   12309:1df960b4892a
tag: tip
user:John Chilton 
date:Sun Nov 10 23:37:56 2013 -0600
summary: PEP-8 cleanups of lib/galaxy/security/__init__.py.

Updated to current tip, also works:

$ hg branch
default
[galaxy@ppserver galaxy-central]$ hg log | head
changeset:   12321:e12a10e5418d
tag: tip
user:guerler
date:Mon Nov 11 16:00:10 2013 -0500
summary: UI: Fix tooltip placement for masthead icons

Are there anyone known differences on the Test Tool Shed
which could explain this failure?

Thanks,

Peter
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[galaxy-dev] dynamic_options selected value as input for second dynamic_options function call

[Hans van Leeuwen]

Hello,

I would like to have a tool form with a two parameters:

1. Select State
2. Select Town

The options for 'Select State' are dynamically generated with
dynamic_options which calls a python function, which connects to a database
and returns the list of States. This works fine in my form xml code:

 label="Select State" display="radio" multiple="false">


Now I want to dynamically create the options for '2. Select Town'. To make
this work I need to take the selected option from '1. Select State', pass
it as an argument to a dynamic_options function call that would then
connect to a database and retrieve the Towns for the provided State. These
Towns would then be the options for '2. Select Town'. So, the second
parameter '2. Select Town' should do something like this:

 multiple="false">


The part in square brackets is pseudo code; this is the part that I cannot
get to work . That part should also be automatically refreshed if the user
changes the selection in '1. Select State'.

I looked into the use of  but I don't see how I can use that
if I don't know beforehand what values I can have (determined in real time
based on content of database), so I cannot code the  tags.

Any help is greatly appreciated.

Thank you in advance,

Hans
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Re: [galaxy-dev] Error editing users associated with a quota

[Peter Cock]

On Mon, Nov 11, 2013 at 6:55 PM, John Chilton  wrote:
> Hey Peter,
>
>   Does your universe_wsgi.ini have "enable_quotas = True" set?
>
> -John

No,

$ grep enable_quotas universe_wsgi.ini
(nothing)

I had suspected the quotas might not be working...

If the default is not to enable quotas, then the "Manage quotas"
entry of the "Admin" page ought perhaps to be disabled?

Peter
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