[galaxy-dev] How to remove a broken toolshed install

[Clare Sloggett]

Hi all,

I managed to break a toolshed-installed tool by fiddling with the
files under shed_tools. This led to a situation in which the Galaxy
admin interface claims the tool is still installed, but can't find any
files for it. I manually put the repository files where I think they
should go, but this didn't fix the situation, so what I really want to
do is just get rid of it altogether and reinstall cleanly. I'm not
certain that the tool was working properly before I fiddled with it,
either.

Galaxy won't let me uninstall, deactivate or update it (because it
can't find it properly) and it won't let me install it (because it
thinks it's installed). It also seems (judging by the last of the
errors below) to be unable to find some config information that it
expects, but I don't really understand what's going on there.

So my question is: given a messy, screwed up install, how can I
completely remove it and start from scratch? What are the different
components and config files I need to remove it from and are they all
manually accessible?

Thanks in advance for any help!


If it's relevant to my question, here are some of the behaviours I see
currently:

The tool appears as "Installed" under Admin -> Manage installed tool
shed repositories, but doesn't show up in the tools panel.

If I try Repository Actions -> Get repository updates , I get the error:
The directory containing the installed repository named
'bcftools_view' cannot be found.

But if I try Repository Actions -> Reset repository metadata , it
apparently works, I get
Metadata has been reset on repository bcftools_view.

And, if I try to 'Deactivate or uninstall' the apparently-installed
repository, I get:

URL: 
http://galaxy-tut.genome.edu.au/admin_toolshed/deactivate_or_uninstall_repository?id=a25e134c184d6e4b
Module paste.exceptions.errormiddleware:144 in __call__
>>  app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
>>  environ, self.app)
Module paste.wsgilib:543 in intercept_output
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:84 in __call__
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
>>  body = method( trans, **kwargs )
Module galaxy.web.framework:205 in decorator
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:452 in
deactivate_or_uninstall_repository
>>  remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, 
>> uninstall=remove_from_disk_checked )
Module galaxy.util.shed_util:1781 in remove_from_tool_panel
>>  tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( 
>> trans, repository )
Module galaxy.util.shed_util:942 in
generate_tool_panel_dict_from_shed_tool_conf_entries
>>  tree = util.parse_xml( shed_tool_conf )
Module galaxy.util:135 in parse_xml
>>  tree = ElementTree.parse(fname)
Module elementtree.ElementTree:859 in parse
Module elementtree.ElementTree:576 in parse
TypeError: coercing to Unicode: need string or buffer, NoneType found



Thanks,
Clare

-- 

Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357  M: 0414 854 759
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Re: [galaxy-dev] pass more information on a dataset merge

[Alex.Khassapov]

Hi John,

I tried your galaxy-central-homogeneous-composite-datatypes implementation, 
works great thank you (and Jorrit).

A couple of fixes:

1. Add multi_upload.xml to too_conf.xml
2. lib/galaxy/tools/parameters/grouping.py line 322 (in get_filenames( context 
)) - 
"if ftp_files is not None:"
   Remove "is not None" as ftp_files is empty [], but not None, then line 331 
"user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email 
)" throws an exeption if ftp_upload_dir isn't set.

Alex

-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John Chilton
Sent: Tuesday, 16 October 2012 1:07 AM
To: Jorrit Boekel
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] pass more information on a dataset merge

Here is an implementation of the implicit multi-file composite datatypes piece 
of that idea. I think the implicit parallelism may be harder.

https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes/compare

Jorrit do you have any objection to me trying to get this included in 
galaxy-central (this is 95% code I stole from you)? I made the changes against 
a clean galaxy-central fork and included nothing proteomics specific in 
anticipation of trying to do that. I have talked with Jim Johnson about the 
idea and he believes it would be useful his mothur metagenomics tools, so the 
idea is valuable outside of proteomics.

Galaxy team, would you be okay with including this and if so is there anything 
you would like to see either at a high level or at the level of the actual 
implementation.

-John


John Chilton
Senior Software Developer
University of Minnesota Supercomputing Institute
Office: 612-625-0917
Cell: 612-226-9223
Bitbucket: https://bitbucket.org/jmchilton
Github: https://github.com/jmchilton
Web: http://jmchilton.net

On Mon, Oct 8, 2012 at 9:24 AM, John Chilton  wrote:
> Jim Johnson and I have been discussing that approach to handling 
> fractionated proteomics samples as well (composite datatypes, not the 
> specifics of the interface for parallelizing).
>
> My perspective has been that Galaxy should be augmented with better 
> native mechanisms for grouping objects in histories, operating over 
> those groups, building workflows that involve arbitrary numbers of 
> inputs, etc... Composite data types are kindof a kludge, I think they 
> are more useful for grouping HTML files together when you don't care 
> about operating on the constituent parts you just want to view pages a 
> as a report or something. With this proteomic data we are working 
> with, the individual pieces are really interesting right? You want to 
> operate on the individual pieces with the full array of tools (not 
> just these special tools that have the logic for dealing with the 
> composite datatypes), you want to visualize the files, etc... Putting 
> these component pieces in the composite data type extra_files path 
> really limits what you can do with the pieces in Galaxy.
>
> I have a vague idea of something that I think could bridge some of the 
> gaps between the approaches (though I have no clue on the 
> feasibility). Looking through your implementation on bitbucket it 
> looks like you are defining your core datatypes (MS2, CruxSequest) as 
> subclasses of this composite data type (CompositeMultifile). My 
> recommendation would be to try to define plain datatypes for these 
> core datatype (MS2, CruxSequest) and then have the separate composite 
> datatype sort of delegate to the plain datatypes.
>
> You could then continue to explicitly declare subclasses of the 
> composite datatype (maybe MS2Set, CruxSequestSet), but also maybe 
> augement the tool xml so you can do implicit data type instances the 
> way you can with tabular data for instance (instead of defining 
> columns you would define the datatype to delegate to).
>
> The next step would be to make the parallelism implicit (i.e pull it 
> out of the tool wrapper). Your tool wrappers wouldn't reference the 
> composite datatypes, they would reference the simple datatypes, but 
> you could add a little icon next to any input that let you replace a 
> single input with a composite input for that type. It would be kind of 
> like the run workflow page where you can replace an input with a 
> multiple inputs. If a composite input (or inputs) are selected the 
> tool would then produce composite outputs.
>
> For the steps that actually combine multiple inputs, I think in your 
> case this is perculator maybe (a tool like interprophet or Scaffold 
> that merges peptide probabilities across runs and groups proteins), 
> then you could have the same sort of implicit replacement but instead 
> of for single inputs it could do that for multi-inputs (assuming the 
> Galaxy powers that be accept my fixes for multi-input tool parameters:
> https://bitbucket.org/galaxy/galaxy-central/pull

[galaxy-dev] picard bug in Add or Replace Groups

[David Hoover]

In the Add or Replace Groups tool for picard, if the read group platform unit 
is left blank, the read group sample name is lost as well.  Must all the read 
group tags be set with this tool?  Can some of them remain blank?

David Hoover
Helix Systems Staff, CIT/NIH
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Re: [galaxy-dev] CCAT Tool Error

[Kyle Chessman]

I managed to fix my problem.

I modified the CCAT wrapper to output the CCAT log file to Galaxy,
then got this at the end:

reading tag files..
0 tags in L1, 0 tags in L2.
tag file error!

So there was an error when running the CCAT binary, but the CCAT
wrapper thinks it succeeded and tries to move the output files.
I looked at the CCAT source and it turns out it is returning 0 on
error, which seems bizarre.

The cause of the real error was my chromosome names were "1", "2",
"Y", etc. instead of "chr1", "chr2", "chrY", etc.

Kyle

On Fri, Oct 12, 2012 at 3:59 PM, Kyle Chessman  wrote:
> When running CCAT I get:
>
> Error running CCAT.
> Traceback (most recent call last):
>   File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 44, in 
> if __name__ == "__main__": main()
>   File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 41, in main
> return stop_err( tmp_dir, e )
>   File "/opt/Galaxy/tools/peak_calling/ccat_wrapper.py", line 15, in stop_err
> raise exception
> IOError: [Errno 2] No such file or directory: '/tmp/tmpc3sfYR/CCAT in
> Galaxy.significant.peak'
>
> I'm using the latest galaxy-dist and have the CCAT binary in
> /usr/local/bin. Nothing gets put into the temp directory while CCAT is
> running.
>
> Any ideas?
>
> Thanks,
> Kyle
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[galaxy-dev] [Patch] ToolShed support for included tools

[Björn Grüning]

Hi,

i'm writing a galaxy wrapper for bismark and trim-galore. Both are plain
perl scripts, that wraps around other dependencies (e.g. Bowtie). The
idea was to include the perl-scripts directly in the galaxy-wrapper and
update the PATH to the REPOSITORY_INSTALL_DIR in the tool_dependency.xml
file.






$REPOSITORY_INSTALL_DIR


   
   
bismark, bismark_genome_preparation and bismark_methylation_extractor
are shipped with that wrapper
   



Unfortunately, that was not supported because the toolshed expected at
least one "action_type". The attached patch should add that feature.

Furthermore, bowtie2 is only available as zip archive and afaik that was
not handled in the toolshed. The attached patch also added
check_zipfile(), extract_zip() and zip_extraction_directory() to fully
support zip archives.

Thanks!
Bjoern

diff -r cc45bdf57b66 lib/galaxy/tool_shed/tool_dependencies/common_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py	Fri Oct 12 17:22:51 2012 -0400
+++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py	Mon Oct 15 18:30:58 2012 +0200
@@ -1,12 +1,13 @@
 import os, shutil, tarfile, urllib2
 from galaxy.datatypes.checkers import *
+from zipfile import ZipFile
 
 def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ):
 env_var_name = elem.get( 'name', 'PATH' )
 env_var_action = elem.get( 'action', 'prepend_to' )
 env_var_text = None
 if elem.text and elem.text.find( 'REPOSITORY_INSTALL_DIR' ) >= 0:
-if tool_shed_repository_install_dir:
+if tool_shed_repository_install_dir and elem.text.find( '$REPOSITORY_INSTALL_DIR' ) != -1:
 env_var_text = elem.text.replace( '$REPOSITORY_INSTALL_DIR', tool_shed_repository_install_dir )
 return dict( name=env_var_name, action=env_var_action, value=env_var_text )
 else:
@@ -50,6 +51,27 @@
 tar = tarfile.open( file_name )
 tar.extractall( path=file_path )
 tar.close()
+def check_zipfile( archive_name ):
+"""
+This function is a bit pedantic and not functionally necessary.
+It checks whether there is no file pointing outside of the extraction, 
+because ZipFile.extractall() has some potential security holes.
+See python zipfile documentation for more details.
+"""
+basename = os.path.normcase( os.path.realpath( os.path.dirname( archive_name ) ) )
+with ZipFile( archive_name ) as zip:
+for member in ZipFile.namelist(zip):
+member_path = os.path.normcase( os.path.realpath( os.path.join(basename, member) ) )
+if not member_path.startswith( basename ):
+return False
+return True
+def extract_zip( archive_path, extraction_path ):
+if not check_zipfile( archive_path ):
+return False
+zip = ZipFile( archive_path )
+zip.extractall( extraction_path )
+zip.close()
+return True
 def isbz2( file_path ):
 return is_bz2( file_path )
 def isgzip( file_path ):
@@ -87,6 +109,21 @@
 if os.path.exists( os.path.abspath( os.path.join( file_path, file_name ) ) ):
 return os.path.abspath( os.path.join( file_path, file_name ) )
 raise ValueError( 'Could not find directory %s' % os.path.abspath( os.path.join( file_path, file_name[ :-len( extension ) ] ) ) )
+def zip_extraction_directory( file_path, file_name ):
+"""
+Try to guess the extraction directory.
+1. Is there one folder inside the working directory.
+2. Are there more than one folder/files return working directory.
+"""
+files = [filename for filename in os.listdir( file_path ) if not filename.endswith('.zip')]
+if len(files) > 1:
+return os.path.abspath( file_path )
+elif len(files) == 1:
+# if there is only on file it should be a folder
+if os.path.isdir( os.path.join( file_path, files[0] ) ):
+return os.path.abspath( os.path.join( file_path, files[0] ) )
+# otherwise we assume that the download or something else went wrong
+raise ValueError( 'Could not find directory for the extracted file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) )
 def url_download( install_dir, downloaded_file_name, download_url ):
 file_path = os.path.join( install_dir, downloaded_file_name )
 src = None
diff -r cc45bdf57b66 lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py	Fri Oct 12 17:22:51 2012 -0400
+++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py	Mon Oct 15 18:30:58 2012 +0200
@@ -58,6 +58,9 @@
 # The first action in the list of actions will be the one that defines the installation process.  There
 # are currently only two supported processes; download_by_url and clone via a "shell_command" action type.
 action_type, action_dict = actions[ 0 ]
+   

Re: [galaxy-dev] Group parameters

[James Taylor]

Be aware that this may not work in future versions of Galaxy, and
probably won't work in some places already (e.g. trackster).

If this is a common need, one option would be to create a new type of
grouping construct that would simply be a labeled group. In the config
this would be:


  ...
  ...


(collapsed/collapsable would configure whether the group can be hidden
and is hidden by default, this would be a more natural way to define
commonly used vs all parameters for example).

-- jt


On Mon, Oct 15, 2012 at 10:11 AM, Joachim Jacob  wrote:
> You might have a look to the GMAP aligner wrapper in the toolshed
> http://toolshed.g2.bx.psu.edu/. Apparently you have to use the html codes
> for the symbols, instead of the symbols themselves
> GMAP example:
>
> label="
Input Sequences
Select an mRNA or EST dataset to
> map" />
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[galaxy-dev] How to get a shedtool to run locally

[Liisa Koski]

Hello,
I've installed a tool to my local Galaxy installation via my local 
ToolShed. I would like to run this tool locally, and not have it submitted 
to the grid.

I have tried two ids in the universe_wsgi.ini [galaxy:tool_runners] 
section.

The tool id directly from the tool.xml file and the id from the 
shed_tool_conf.xml (same id found in the integrated_tool_panel.xml)

tool = local:///
galaxy.server:9009/repos/user/tool/1.0 = local:///


My job still gets submitted to the grid.

Any help would be much appreciated.

Thanks,
Liisa

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[galaxy-dev] BOSC/Broad Interoperability Hackathon: potential dates

[Brad Chapman]

Hi all;
Open Bio regularly organizes hackathon coding sessions in conjunction
with the Bioinformatics Open Source Conference. The goal is to get
together biologists writing open source code, provide a room and
internet, and encourage fun collaborative coding. We've had successful
two day Codefests the past three years:

http://www.open-bio.org/wiki/Codefest_2012

This year, the Broad Institute kindly offered to host a two day
Hackathon in Boston during April. We've proposed three sets of dates:

April 4-5th, Thursday and Friday before Bio-IT
April 7-8th, Sunday and Monday before Bio-IT
April 22-23rd, Monday and Tuesday

If you have interest in attending, please fill out this Doodle poll to
let us know which dates work best:

http://doodle.com/aapy694g43e6ya4f

If you can find funds for travel and hotel (or are local to Boston), the
event is free and everyone is welcome. As we finalize dates, we'll send
around additional details. Thanks everyone,
Brad
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Re: [galaxy-dev] Group parameters

[Alfredo Guilherme Silva Souza]

Very Good!

It worked, it helped me a lot.

Thank you.



2012/10/15 Joachim Jacob 

> Hi,
>
> You might have a look to the GMAP aligner wrapper in the toolshed
> http://toolshed.g2.bx.psu.edu/**. Apparently you have to use the html
> codes for the symbols, instead of the symbols themselves
> GMAP example:
>
> label="
Input Sequences
Select an mRNA or EST dataset
> to map" />
>
> Cheers,
> Joachim
>
>
> Joachim Jacob, PhD
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> On 10/15/2012 03:41 PM, Alfredo Guilherme Silva Souza wrote:
>
>>
>>
>> Hello Joachim,
>>
>> I did the test here, but there appears no effect when I add tags to label
>> the value you entered.
>>
>> Do you have any examples?
>> Maybe I might be doing wrong.
>>
>>
>> Hugs.
>>
>>
>> 2012/10/15 Joachim Jacob > joachim.ja...@vib.be>>
>>
>>
>> Hi,
>>
>> I assume you mean to group the parameters visually. What I have
>> seen people doing is adding HTML code to the value of the label
>> attribute of a  tag set, like ending the label with e.g.
>> "".
>>
>> Otherwise, if the two groups of parameters are mutually exclusive,
>> you can use the  tag set.
>>
>>
>> cheers,
>> Joachim
>>
>>
>> Message: 10
>> Date: Sat, 13 Oct 2012 12:07:03 -0300
>> From: Alfredo Guilherme Silva
>> 
>> Souza
>> 
>> > >>
>> To:galaxy-dev@lists.bx.psu.edu
>> 
>> > >
>>
>> Subject: [galaxy-dev] Group parameters
>> Message-ID:
>>> 2xqdis5u+...@mail.gmail.com> CAL39R3o%**2BJupW225QZ7q4mqf8wMX3MbsmjtnL**zA2XqDis5U%2BZCg@mail.gmail.**
>> com
>> >>
>>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> Hello
>>
>> I'm needing some grouping parameters into a tool that I'm
>> developing, so I
>> did not find any answers in the wiki galaxy.
>>
>> Attached is a picture with the example of the way that the
>> parameters are
>> in my tool currently, and the manner in which I need to leave.
>>
>> Thank you.
>>
>>
>> -- Joachim Jacob, PhD
>>
>> Rijvisschestraat 120, 9052 Zwijnaarde
>> Tel: +32 9 244.66.34 
>>
>> Bioinformatics Training and Services (BITS)
>> http://www.bits.vib.be
>> @bitsatvib
>>
>>
>>
>>
>> --
>>
>> /*Alfredo Guilherme*/
>>
>> /*
>> */
>>
>>
>>
>


-- 

*Alfredo Guilherme*

*
*
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Re: [galaxy-dev] Anybody knows how to disable daily digest for this email list?

[Joachim Jacob]

Thanks! Now I wonder of course how I missed it. But I was stuck 
apparently at http://dev.list.galaxyproject.org/


Thanks again for your time,
Joachim

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 10/15/2012 04:30 PM, Carlos Borroto wrote:

On Mon, Oct 15, 2012 at 5:12 AM, Joachim Jacob  wrote:

I really could not find this. Anybody willing to show me? :-)


Sure, go here:
http://lists.bx.psu.edu/options/galaxy-dev

After entering your credentials, "Set Digest Mode" is the second
option from the top.

Hope it helps,
Carlos


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Re: [galaxy-dev] Anybody knows how to disable daily digest for this email list?

[Carlos Borroto]

On Mon, Oct 15, 2012 at 5:12 AM, Joachim Jacob  wrote:
> I really could not find this. Anybody willing to show me? :-)
>

Sure, go here:
http://lists.bx.psu.edu/options/galaxy-dev

After entering your credentials, "Set Digest Mode" is the second
option from the top.

Hope it helps,
Carlos
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Re: [galaxy-dev] pass more information on a dataset merge

[John Chilton]

Here is an implementation of the implicit multi-file composite
datatypes piece of that idea. I think the implicit parallelism may be
harder.

https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes/compare

Jorrit do you have any objection to me trying to get this included in
galaxy-central (this is 95% code I stole from you)? I made the changes
against a clean galaxy-central fork and included nothing proteomics
specific in anticipation of trying to do that. I have talked with Jim
Johnson about the idea and he believes it would be useful his mothur
metagenomics tools, so the idea is valuable outside of proteomics.

Galaxy team, would you be okay with including this and if so is there
anything you would like to see either at a high level or at the level
of the actual implementation.

-John


John Chilton
Senior Software Developer
University of Minnesota Supercomputing Institute
Office: 612-625-0917
Cell: 612-226-9223
Bitbucket: https://bitbucket.org/jmchilton
Github: https://github.com/jmchilton
Web: http://jmchilton.net

On Mon, Oct 8, 2012 at 9:24 AM, John Chilton  wrote:
> Jim Johnson and I have been discussing that approach to handling
> fractionated proteomics samples as well (composite datatypes, not the
> specifics of the interface for parallelizing).
>
> My perspective has been that Galaxy should be augmented with better
> native mechanisms for grouping objects in histories, operating over
> those groups, building workflows that involve arbitrary numbers of
> inputs, etc... Composite data types are kindof a kludge, I think they
> are more useful for grouping HTML files together when you don't care
> about operating on the constituent parts you just want to view pages a
> as a report or something. With this proteomic data we are working
> with, the individual pieces are really interesting right? You want to
> operate on the individual pieces with the full array of tools (not
> just these special tools that have the logic for dealing with the
> composite datatypes), you want to visualize the files, etc... Putting
> these component pieces in the composite data type extra_files path
> really limits what you can do with the pieces in Galaxy.
>
> I have a vague idea of something that I think could bridge some of the
> gaps between the approaches (though I have no clue on the
> feasibility). Looking through your implementation on bitbucket it
> looks like you are defining your core datatypes (MS2, CruxSequest) as
> subclasses of this composite data type (CompositeMultifile). My
> recommendation would be to try to define plain datatypes for these
> core datatype (MS2, CruxSequest) and then have the separate composite
> datatype sort of delegate to the plain datatypes.
>
> You could then continue to explicitly declare subclasses of the
> composite datatype (maybe MS2Set, CruxSequestSet), but also maybe
> augement the tool xml so you can do implicit data type instances the
> way you can with tabular data for instance (instead of defining
> columns you would define the datatype to delegate to).
>
> The next step would be to make the parallelism implicit (i.e pull it
> out of the tool wrapper). Your tool wrappers wouldn't reference the
> composite datatypes, they would reference the simple datatypes, but
> you could add a little icon next to any input that let you replace a
> single input with a composite input for that type. It would be kind of
> like the run workflow page where you can replace an input with a
> multiple inputs. If a composite input (or inputs) are selected the
> tool would then produce composite outputs.
>
> For the steps that actually combine multiple inputs, I think in your
> case this is perculator maybe (a tool like interprophet or Scaffold
> that merges peptide probabilities across runs and groups proteins),
> then you could have the same sort of implicit replacement but instead
> of for single inputs it could do that for multi-inputs (assuming the
> Galaxy powers that be accept my fixes for multi-input tool parameters:
> https://bitbucket.org/galaxy/galaxy-central/pull-request/76/multi-input-data-tool-parameter-fixes).
>
> The upshot of all of that would be that then even if these composites
> datatypes aren't used widely, other people could still use your
> proteomics tools (my users are definitely interested in Crux for
> instance) and you could then use other developers' proteomic tools
> with your composite datatypes even though they weren't designed with
> that use case in mind (I have msconvert, myrimatch, idpicker,
> proteinpilot, Ira Cooke has X! Tandem, OMSSA, TPP, and NBIC has an
> entire suite of label free quant tools). A third benefit would be that
> people working in other -omicses could make use of the homogenous
> composite datatype implementation without needing to rewrite their
> wrappers and datatypes.
>
> There is probably something that I am missing that makes this very
> difficult, let me know if 

Re: [galaxy-dev] Group parameters

[Joachim Jacob]

Hi,

You might have a look to the GMAP aligner wrapper in the toolshed 
http://toolshed.g2.bx.psu.edu/. Apparently you have to use the html 
codes for the symbols, instead of the symbols themselves

GMAP example:

label="
Input Sequences
Select an mRNA or EST dataset 
to map" />


Cheers,
Joachim

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 10/15/2012 03:41 PM, Alfredo Guilherme Silva Souza wrote:



Hello Joachim,

I did the test here, but there appears no effect when I add tags to 
label the value you entered.


Do you have any examples?
Maybe I might be doing wrong.


Hugs.


2012/10/15 Joachim Jacob >


Hi,

I assume you mean to group the parameters visually. What I have
seen people doing is adding HTML code to the value of the label
attribute of a  tag set, like ending the label with e.g.
"".

Otherwise, if the two groups of parameters are mutually exclusive,
you can use the  tag set.


cheers,
Joachim


Message: 10
Date: Sat, 13 Oct 2012 12:07:03 -0300
From: Alfredo Guilherme Silva
Souzamailto:alfredo.bioinformat...@gmail.com>>
To:galaxy-dev@lists.bx.psu.edu

Subject: [galaxy-dev] Group parameters
Message-ID:
   
mailto:cal39r3o%2bjupw225qz7q4mqf8wmx3mbsmjtnlza2xqdis5u%2b...@mail.gmail.com>>

Content-Type: text/plain; charset="iso-8859-1"


Hello

I'm needing some grouping parameters into a tool that I'm
developing, so I
did not find any answers in the wiki galaxy.

Attached is a picture with the example of the way that the
parameters are
in my tool currently, and the manner in which I need to leave.

Thank you.


-- 
Joachim Jacob, PhD


Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib




--

/*Alfredo Guilherme*/

/*
*/




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Re: [galaxy-dev] Group parameters

[Alfredo Guilherme Silva Souza]

Hello Joachim,

I did the test here, but there appears no effect when I add tags to label
the value you entered.

Do you have any examples?
Maybe I might be doing wrong.


Hugs.


2012/10/15 Joachim Jacob 

> Hi,
>
> I assume you mean to group the parameters visually. What I have seen
> people doing is adding HTML code to the value of the label attribute of a
>  tag set, like ending the label with e.g. "".
>
> Otherwise, if the two groups of parameters are mutually exclusive, you can
> use the  tag set.
>
>
> cheers,
> Joachim
>
>
> Message: 10
> Date: Sat, 13 Oct 2012 12:07:03 -0300
> From: Alfredo Guilherme Silva 
> Souza
> >
> To:galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] Group parameters
> Message-ID:
>  2xqdis5u+...@mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hello
>
> I'm needing some grouping parameters into a tool that I'm developing, so I
> did not find any answers in the wiki galaxy.
>
> Attached is a picture with the example of the way that the parameters are
> in my tool currently, and the manner in which I need to leave.
>
> Thank you.
>
>
> --
> Joachim Jacob, PhD
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
>


-- 

*Alfredo Guilherme*

*
*
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Re: [galaxy-dev] stack track on attempt to kill job from admin manage jobs page

[Daniel Blankenberg]

Hi Brad,

Thanks for reporting this error, it has been fixed in changeset 
7902:2d12f10c87c7 and will be available in the next distribution.

Thanks for using Galaxy,

Dan


On Oct 13, 2012, at 10:30 PM, Langhorst, Brad wrote:

> Error - : global name 'string' is not defined
> URL: http://galaxy.neb.com/admin/jobs
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
>  line 143 in __call__
>   app_iter = self.application(environ, start_response)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
>  line 80 in __call__
>   return self.application(environ, start_response)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>  line 91 in __call__
>   return self.app( environ, start_response )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
>  line 632 in __call__
>   return self.application(environ, start_response)
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 
> 160 in __call__
>   body = method( trans, **kwargs )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', 
> line 205 in decorator
>   return func( self, trans, *args, **kwargs )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', 
> line 1019 in jobs
>   if stop_msg[-1] not in string.punctuation:
> NameError: global name 'string' is not defined
> 
> 
> 
> Brad
> --
> Brad Langhorst
> langho...@neb.com
> 
> 
> 
> 
> 
> ___
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>  http://lists.bx.psu.edu/

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[galaxy-dev] Fwd: Galaxy data upload

[Greg Von Kuster]

Hello Oliver,

I've forwarded this to the galaxy-dev mail list since it is the contact point 
for issues like this.  Please send questions like this to the Galaxy mail lists 
(galaxy-dev, galaxy-user) in the future as there is no guarantee you'll get 
timely answers from individual contacts.

Thanks very much,

Greg Von Kuster

Begin forwarded message:

> From: "Oliver Berkowitz" 
> Date: October 14, 2012 11:47:13 PM EDT
> To: 
> Subject: Galaxy data upload
> 
> Dear Greg,
>  
> not sure if you are the right person to contact…
>  
> I have tried several times to upload data to the galaxy server via ftp. 
> Trying to connect leads to error 530, max number of clients already 
> connected, like this:
>  
> Status: Resolving address of main.g2.bx.psu.edu
> Status: Connecting to .
> Status: Connection established, waiting for welcome message...
> Response:220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) 
> [:::128.118.250.4]
> Command:  USER xx
> Response:331 Password required for xxx
> Command:  PASS ***
> Response:530 Sorry, the maximum number of clients (3) for this user 
> are already connected.
> Error:   Critical error
> Error:   Could not connect to server
>  
>  
> Do you have an idea what I am doing wrong  (or the server J) ?
>  
> Cheers
> Oliver
>  
>  
> 
> Dr. Oliver Berkowitz
> Murdoch University
> Centre for Phytophthora Science and Management
> School of Biological Sciences and Biotechnology
> 90 South Street, Murdoch WA 6150, Australia
> P: 61 - (0)8 9360 6335
> E: o.berkow...@murdoch.edu.au
> W: http://profiles.murdoch.edu.au/myprofile/oliver-berkowitz/
>  

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Re: [galaxy-dev] Param Tag

[Kohler Manuel]

Hi Alfredo,
I also asked the same question before without any response:
http://dev.list.galaxyproject.org/Reserved-variables-in-param-tags-td465640
2.html

But I met Dannon Baker on the Swiss galaxy workshop in Bern and explained
this problem to him. He said it should not be a big problem to fix this.
He gave me no date until it will be fixed but I hope it will be done
within the next weeks. Let's see when this will be possible.

Cheers
Manuel

-- 
Manuel Kohler
Center for Information Sciences and Databases (C-ISD)
Department of Biosystems Science & Engineering (D-BSSE)
SIB Swiss Institute of Bioinformatics
ETH Zurich, Mattenstr. 26 (1078 1.02), CH-4058 Basel, +41 61 387 3132




On 10. October 2012 5:34 AM, "Alfredo Guilherme Silva Souza"
 wrote:

>
>
>Hi,
>I have a question about param tag. I need to pass the parameter $
>__user_email__ part of the galaxy variables reserved for the default
>value of a parameter that I am creating
>
>
>example:
>name="email" /> 
>
>Has someone done this before?
>
>
>Thank you !
>-- 
>Alfredo Guilherme
>
>
>


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[galaxy-dev] Anybody knows how to disable daily digest for this email list?

[Joachim Jacob]

I really could not find this. Anybody willing to show me? :-)

Cheers,
Joachim

BTW: pity that they disabled the issue tracker on BitBucket... Hope it 
will be replaced by something similar soon. I feel like this community 
needs an issue tracker, besides a help communication channel like this 
email list.


--
Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: [galaxy-dev] Group parameters

[Joachim Jacob]

Hi,

I assume you mean to group the parameters visually. What I have seen 
people doing is adding HTML code to the value of the label attribute of 
a  tag set, like ending the label with e.g. "".


Otherwise, if the two groups of parameters are mutually exclusive, you 
can use the  tag set.



cheers,
Joachim


Message: 10
Date: Sat, 13 Oct 2012 12:07:03 -0300
From: Alfredo Guilherme Silva Souza
To:galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Group parameters
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hello

I'm needing some grouping parameters into a tool that I'm developing, so I
did not find any answers in the wiki galaxy.

Attached is a picture with the example of the way that the parameters are
in my tool currently, and the manner in which I need to leave.

Thank you.


--
Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: [galaxy-dev] Empty TopHat output

[Joachim Jacob]

The same here.

Cheers,
Joachim

--
Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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[galaxy-dev] Avoiding same dataset selection

[Lukasse, Pieter]

Hi,

Is there a way to use  or perhaps  options to avoid the 
selection of the same dataset twice in different parameters of a tool.

E.g. a tool has 2 "data" type parameters of the same type, but it should not be 
possible for the user to set both parameters to the same dataset. So if his 
history contains files A,B, and C and he selects A in his first parameter, then 
the second parameter should display only the options B and C.

Thanks and regards,

Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
http://www.pri.wur.nl

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