[galaxy-dev] How to unsubscribe - was: Re: RFC: Citations for tools

[Hans-Rudolf Hotz]

Hi Shari

Have a look at the last few lines of the e-mail:

"... To manage your subscriptions to this
 and other Galaxy lists, please use the interface
 at: http://lists.bx.psu.edu/"



Hans-Rudolf


On 05/28/2014 03:56 AM, Shari Javadiyan wrote:

Hi all,
Is there any way to unsubscribes from mail lists?
Cheers,
Shari


On Wednesday, 28 May 2014 2:52 AM, Jim McCusker
 wrote:


I would suggest using as much as possible from PROV, especially since
other workflow engines (Taverna and Pegasus come to mind) already
support it. Rather than looking for bibtex mappings in XML, we should be
looking for vocabularies that represent the elements we need to
represent, and the relevant bibtex should be generated from that. PROV
and Dublin Core Terms can get us most of the way there, I think.

Jim


On Tue, May 27, 2014 at 1:09 PM, Peter Cock mailto:p.j.a.c...@googlemail.com>> wrote:

Hi Eric,

I was sure there was a Trello card for this, but I can't find it
right now...

I've pushed this idea on the mailing list before, and in person at
the Galaxy Community Conference too. See also these threads:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html

http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html

Are you familiar enough with the area of semantic web/linked
data to know what would be the best XML based markup to
use for embedding the citations?

i.e. We should not reinvent the wheel here ;)

Peter


On Tue, May 27, 2014 at 5:54 PM, James Taylor mailto:ja...@jamestaylor.org>> wrote:
 > Eric, I'm very much in favor of this feature, and particularly the
 > idea of generating a list of citations from a history or workflow. I
 > imagine the only thing to quibble about will be the syntax. There are
 > already some efforts to represent bibtex in xml (e.g.
 > https://github.com/Zearin/BibTeXML), however they have always struck
 > me as overly verbose.
 >
 > -- jt
 >
 >
 > On Tue, May 27, 2014 at 12:45 PM, Eric Rasche
mailto:rasche.e...@yandex.ru>> wrote:
 >> -BEGIN PGP SIGNED MESSAGE-
 >> Hash: SHA1
 >>
 >> I'd want to open up discussion on a feature I'd like to see.
I'll try
 >> and implement it if I can find time this summer. I didn't see a
trello
 >> card for anything like this yet, but please feel free to direct
me there
 >> if I missed it.
 >>
 >>
 >> I'd like to see citations as a part of every tool.
 >>
 >> This would happen in the form of a  block in the XML,
which
 >> would contain sub-elements with text. These sub-elements could
be based
 >> off of BibTeX, since they have existing specs for citing things:
 >> https://en.wikipedia.org/wiki/BibTeX
 >>
 >> These citations would then be accessible in the HTML generated tool
 >> pages, or via a View/Download button somewhere on the tool page. By
 >> storing as an XML tree, we could render these citations as BibTeX
 >> entries for the LaTeX users, and I believe there are ways to convert
 >> BibTeX to EndNote XML and so on.
 >>
 >> This could be extended for use in workflows so that when you run
 >> workflows, somehow a list of citations for all tools used could be
 >> generated.
 >>
 >> Anyone have thoughts or opinions on this?
 >>
 >>
 >>
 >>
 >> Using the example bibtex entry from the wikipedia page:
 >>
 >> @Book{abramowitz+stegun,
 >>  author= "Milton {Abramowitz} and Irene A. {Stegun}",
 >>  title = "Handbook of Mathematical Functions with
 >>   Formulas, Graphs, and Mathematical Tables",
 >>  publisher = "Dover",
 >>  year  =  1964,
 >>  address   = "New York",
 >>  edition   = "ninth Dover printing, tenth GPO printing"
 >> }
 >>
 >> I imagine it'd look like the following in a real-life tool:
 >>
 >> 
 >>   ...
 >>   
 >> Milton Abramowitz and Irene A. Stegun"
 >> Handbook of Mathematical Functions with Formulas,
Graphs, and
 >> Mathematical Tables
 >> Dover
 >> 1964
 >> New York
 >> ninth Dover printing, tenth GPO printing
 >>   
 >> 
 >>
 >>
 >> Cheers,
 >> Eric
 >> - --
 >> Eric Rasche
 >> Programmer II
 >> Center for Phage Technology
 >> Texas A&M University
 >> College Station, TX 77843
 >> 404-692-2048
 >> e...@tamu.edu 
 >> rasche.e...@yandex.ru 
 >> -BEGIN PGP SIGNATURE-
 >> Version: GnuPG v2.0.17 (GNU/Linux)
 >>
 >> iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC
 >> jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU
 >> IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a
 >> FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgi

Re: [galaxy-dev] RFC: Citations for tools

[Shari Javadiyan]

Hi all,
Is there any way to unsubscribes from mail lists? 

Cheers,
Shari



On Wednesday, 28 May 2014 2:52 AM, Jim McCusker  
wrote:
 


I would suggest using as much as possible from PROV, especially since other 
workflow engines (Taverna and Pegasus come to mind) already support it. Rather 
than looking for bibtex mappings in XML, we should be looking for vocabularies 
that represent the elements we need to represent, and the relevant bibtex 
should be generated from that. PROV and Dublin Core Terms can get us most of 
the way there, I think.

Jim



On Tue, May 27, 2014 at 1:09 PM, Peter Cock  wrote:

Hi Eric,
>
>I was sure there was a Trello card for this, but I can't find it right now...
>
>I've pushed this idea on the mailing list before, and in person at
>the Galaxy Community Conference too. See also these threads:
>
>http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html
>
>http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html
>
>Are you familiar enough with the area of semantic web/linked
>data to know what would be the best XML based markup to
>use for embedding the citations?
>
>i.e. We should not reinvent the wheel here ;)
>
>Peter
>
>
>
>On Tue, May 27, 2014 at 5:54 PM, James Taylor  wrote:
>> Eric, I'm very much in favor of this feature, and particularly the
>> idea of generating a list of citations from a history or workflow. I
>> imagine the only thing to quibble about will be the syntax. There are
>> already some efforts to represent bibtex in xml (e.g.
>> https://github.com/Zearin/BibTeXML), however they have always struck
>> me as overly verbose.
>>
>> -- jt
>>
>>
>> On Tue, May 27, 2014 at 12:45 PM, Eric Rasche  wrote:
>>> -BEGIN PGP SIGNED MESSAGE-
>>> Hash: SHA1
>>>
>>> I'd want to open up discussion on a feature I'd like to see. I'll try
>>> and implement it if I can find time this summer. I didn't see a trello
>>> card for anything like this yet, but please feel free to direct me there
>>> if I missed it.
>>>
>>>
>>> I'd like to see citations as a part of every tool.
>>>
>>> This would happen in the form of a  block in the XML, which
>>> would contain sub-elements with text. These sub-elements could be based
>>> off of BibTeX, since they have existing specs for citing things:
>>> https://en.wikipedia.org/wiki/BibTeX
>>>
>>> These citations would then be accessible in the HTML generated tool
>>> pages, or via a View/Download button somewhere on the tool page. By
>>> storing as an XML tree, we could render these citations as BibTeX
>>> entries for the LaTeX users, and I believe there are ways to convert
>>> BibTeX to EndNote XML and so on.
>>>
>>> This could be extended for use in workflows so that when you run
>>> workflows, somehow a list of citations for all tools used could be
>>> generated.
>>>
>>> Anyone have thoughts or opinions on this?
>>>
>>>
>>>
>>>
>>> Using the example bibtex entry from the wikipedia page:
>>>
>>> @Book{abramowitz+stegun,
>>>  author    = "Milton {Abramowitz} and Irene A. {Stegun}",
>>>  title     = "Handbook of Mathematical Functions with
>>>               Formulas, Graphs, and Mathematical Tables",
>>>  publisher = "Dover",
>>>  year      =  1964,
>>>  address   = "New York",
>>>  edition   = "ninth Dover printing, tenth GPO printing"
>>> }
>>>
>>> I imagine it'd look like the following in a real-life tool:
>>>
>>> 
>>>   ...
>>>   
>>>     Milton Abramowitz and Irene A. Stegun"
>>>     Handbook of Mathematical Functions with Formulas, Graphs, and
>>> Mathematical Tables
>>>     Dover
>>>     1964
>>>     New York
>>>     ninth Dover printing, tenth GPO printing
>>>   
>>> 
>>>
>>>
>>> Cheers,
>>> Eric
>>> - --
>>> Eric Rasche
>>> Programmer II
>>> Center for Phage Technology
>>> Texas A&M University
>>> College Station, TX 77843
>>> 404-692-2048
>>> e...@tamu.edu
>>> rasche.e...@yandex.ru
>>> -BEGIN PGP SIGNATURE-
>>> Version: GnuPG v2.0.17 (GNU/Linux)
>>>
>>> iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC
>>> jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU
>>> IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a
>>> FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgiogi
>>> 0SWGIGZ6OJdqX60h2hOjJ06NhzBcTsjQea+AwTo5wAkyGPFJy4DV78jKOvsd5PMG
>>> qkk4U6gBcmcFolCeItlLPa/C4uiyOK2wVWHyTnEeKjdpD6dwLuemRmwtZrModbQu
>>> PPPFkKzQhUnh5Wgq8TIP4kSc2t1/jSpdV8MHqM0piqOFnR52fExPrwLn82WEFcp8
>>> tXfHHTaZj+6gL+IGswdAgqvxk1V+6QTjH57igWmYtcENpIDbhZVBh+HOD8SS2qdv
>>> ohwFg/Vn8VrCeTGGehNSBvkam0HXjXXq7mZ8W4xrOS8vxv8HPAFZHze2sPlUG/Ob
>>> WeOdiLgD2HCH95SXYDDBNFG6HwFkLETA3DjpfvgHqPdaLmEfIZW+ks1WF9RG+Pmo
>>> jhbWH8OmtTk5A/Zh63uRowMaDe7QSCruPIfIwlrgqLozOj8htMyJPBIW9oZGGkqC
>>> 7Vu5UFeL8gcigRmQv5NA
>>> =ceAo
>>> -END PGP SIGNATURE-
>>> ___
>>> 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:

Re: [galaxy-dev] complex help for conditional param

[Jun Fan]

Hi Peter,

 I am afraid that the link you gave me could not solve the problem. The 
question I asked is about the help element, not the label attribute for data 
element.
 To clarify my question, here is the code which does not work, but shows 
what I intend to do:


BLASTN
BLASTP


BLAST DNA against DNA



BLAST protein against protein



  I tried to set the help content according to the selected type, which 
works like a section header to the following param list.
  Obviously this does not work. Then I tried a less-fancy way by providing 
static help context by adding  under select param like

BLASTN: BLAST DNA against DNA, BLASTP: BLAST protein 
against protein
BLASTN
  Of course it works but in an ugly formatting text. Is there any document 
to format it nicely, e.g. a list?

Best regards!
Jun 

-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Sent: Tuesday, May 27, 2014 4:40 PM
To: Jun Fan
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] complex help for conditional param

On Tue, May 27, 2014 at 4:32 PM, Jun Fan  wrote:
> Hi all,
>
>
>
>In the conditional param, when sub-element allows you to write 
> specific parameters for a particular value selected. I am wondering 
> how to write the help context according to the value selection. For 
> example, if there is a conditional param called blast_type, when 
> “blastn” is selected, the help context will be “blast dna against dna” 
> and when “blastp” is selected, the help context will be “blast protein 
> against protein”.
> Basically this selection-based help text provides a general 
> description of the selection, which could help to set up the corresponding 
> parameters.
>
>   By the way, is there any document about formatting text in the 
> help element?
>
> Best regards!
>
> Jun

You can do this kind of thing with one-line Cheetah syntax within the output 
XML tag, but it quickly gets very complicated. e.g.

https://github.com/peterjc/pico_galaxy/commit/3991893c6ee2cc69c33aaa391bbed412c85fa9db

Peter

___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] RFC: Citations for tools

[Jim McCusker]

I'm a semantic web folk (I'm on the PROV Data Model), and I'm willing to
advise as needed. PROV is very generalized, but workflow provenance was one
of the primary use cases for its design (it descends from OPM, which was
almost entirely workflow provenance-oriented).

Workflow tools probably should be prov:Plan, a subclass of prov:Entity.
PROV can cover attribution of things, agents (people and orgs) acting on
behalf of other agents, and virtual and physical locations
(prov:atLocation). Tool provenance is a little smaller-scoped than workflow
invocation provenance, but obviously we want the two to mesh neatly.

Below I'm going to use Turtle to write out an example, but the tool XML can
obviously embed RDF-XML instead.

We would need to supply a little bit of our own vocabulary:

galaxy:Tool rdfs:subClassOf prov:Plan.

Citing a book in a tool might look like this:

:mytool a galaxy:Tool;
   prov:wasDerivedFrom  ; # For DOI-able
references. [1]
   dc:creator .


[1] dx.doi.org will return RDF for the document if you ask for it. We can
use their vocabulary within our own RDF if there is no DOI for it.

@prefix doi: .
@prefix prism: .
@prefix xsd: .
@prefix foaf: .
@prefix dc: .
@prefix bibo: .
@prefix owl: .

 a
 foaf:Person> ;
  foaf:familyName "Abramowitz" ;
  foaf:givenName "Milton" ;
  foaf:name "Milton Abramowitz" .

doi:10.1119/1.15378
  prism:doi "10.1119/1.15378" ;
  prism:startingPage "958" ;
  prism:volume "56" ;
  dc:creator <
http://id.crossref.org/contributor/milton-abramowitz-1hbgxt653tpie> ;
  dc:date "1988"^^ ;
  dc:identifier "10.1119/1.15378" ;
  dc:isPartOf  ;
  dc:publisher "American Association of Physics Teachers (AAPT)" ;
  dc:title "Handbook of Mathematical Functions with Formulas, Graphs,
and Mathematical Tables" ;
  bibo:doi "10.1119/1.15378" ;
  bibo:pageStart "958" ;
  bibo:volume "56" ;
  owl:sameAs  ,  .

 a bibo:Journal ;
  prism:issn "0002-9505" ;
  dc:title "American Journal of Physics" ;
  bibo:issn "0002-9505" ;
  owl:sameAs  .

Jim


On Tue, May 27, 2014 at 2:17 PM, Peter Cock wrote:

> On Tue, May 27, 2014 at 6:21 PM, Jim McCusker
>  wrote:
> > I would suggest using as much as possible from PROV, especially since
> other
> > workflow engines (Taverna and Pegasus come to mind) already support it.
> > Rather than looking for bibtex mappings in XML, we should be looking for
> > vocabularies that represent the elements we need to represent, and the
> > relevant bibtex should be generated from that. PROV and Dublin Core Terms
> > can get us most of the way there, I think.
> >
> > Jim
>
> This PROV ontology? http://www.w3.org/TR/prov-o/
> http://www.taverna.org.uk/documentation/taverna-2-x/provenance/
> https://github.com/wf4ever/taverna-prov
>
> It looks potentially relevant, but tackling a wider issue.
> Are you aware of specific examples covering tool
> citation within the context of workflow provenance?
> I think many people (myself included) would find that
> useful - a basic example for what might go into a
> Galaxy Tool's XML file?
>
> Maybe we need to CC some semantic web folk to advise...
> or schedule a get together as a BoF at GCC2014? It
> seems once a format is agreed, there is willingness
> on the Galaxy side to start coding :)
>
> Peter
>
___
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Re: [galaxy-dev] RFC: Citations for tools

[Peter Cock]

On Tue, May 27, 2014 at 6:21 PM, Jim McCusker
 wrote:
> I would suggest using as much as possible from PROV, especially since other
> workflow engines (Taverna and Pegasus come to mind) already support it.
> Rather than looking for bibtex mappings in XML, we should be looking for
> vocabularies that represent the elements we need to represent, and the
> relevant bibtex should be generated from that. PROV and Dublin Core Terms
> can get us most of the way there, I think.
>
> Jim

This PROV ontology? http://www.w3.org/TR/prov-o/
http://www.taverna.org.uk/documentation/taverna-2-x/provenance/
https://github.com/wf4ever/taverna-prov

It looks potentially relevant, but tackling a wider issue.
Are you aware of specific examples covering tool
citation within the context of workflow provenance?
I think many people (myself included) would find that
useful - a basic example for what might go into a
Galaxy Tool's XML file?

Maybe we need to CC some semantic web folk to advise...
or schedule a get together as a BoF at GCC2014? It
seems once a format is agreed, there is willingness
on the Galaxy side to start coding :)

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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] RFC: Citations for tools

[Eric Rasche]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Will,

Nice! I follow the tex.SE and missed that one. That's incredibly useful.
I believe the final implementation will include both options (doi/citation)

Jim,

Great, agreed. I want to represent non-published/non-DOI materials, so
this is better than restricting to DOI-only materials. PROV + dublin
core would be good for a reference implementation and we can build
outwards from there if we need special entries. My background of LaTeX
pushed me in BibTeX, but these are definitely better options in terms of
generalising the implementation.

Cheers,
Eric

On 05/27/2014 12:21 PM, Will Holtz wrote:
> As hinted at in the Trello card Greg posted, it could be much simpler if
> the citation tag just took a DOI. It appears that the DOI to bibtex
> conversion can be done by
> Crossref: 
> http://tex.stackexchange.com/questions/6848/automatically-dereference-doi-to-bib
> 
> -Will
> 
> 
> 
> On Tue, May 27, 2014 at 10:16 AM, Greg Von Kuster  > wrote:
> 
> Peter, this may be the Trello card you were thinking of.
> 
> https://trello.com/c/kY7RCnd0/95-tool-shed-citation-for-tools-dois
> 
> Greg Von Kuster
> 
> 
> On May 27, 2014, at 1:09 PM, Peter Cock  > wrote:
> 
> > Hi Eric,
> >
> > I was sure there was a Trello card for this, but I can't find it
> right now...
> >
> > I've pushed this idea on the mailing list before, and in person at
> > the Galaxy Community Conference too. See also these threads:
> >
> > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html
> >
> > http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html
> >
> > Are you familiar enough with the area of semantic web/linked
> > data to know what would be the best XML based markup to
> > use for embedding the citations?
> >
> > i.e. We should not reinvent the wheel here ;)
> >
> > Peter
> >
> >
> > On Tue, May 27, 2014 at 5:54 PM, James Taylor
> mailto:ja...@jamestaylor.org>> wrote:
> >> Eric, I'm very much in favor of this feature, and particularly the
> >> idea of generating a list of citations from a history or workflow. I
> >> imagine the only thing to quibble about will be the syntax. There are
> >> already some efforts to represent bibtex in xml (e.g.
> >> https://github.com/Zearin/BibTeXML), however they have always struck
> >> me as overly verbose.
> >>
> >> -- jt
> >>
> >>
> >> On Tue, May 27, 2014 at 12:45 PM, Eric Rasche
> mailto:rasche.e...@yandex.ru>> wrote:
> I'd want to open up discussion on a feature I'd like to see.
>> I'll try
> and implement it if I can find time this summer. I didn't see a
>> trello
> card for anything like this yet, but please feel free to direct
>> me there
> if I missed it.
> 
> 
> I'd like to see citations as a part of every tool.
> 
> This would happen in the form of a  block in the XML,
>> which
> would contain sub-elements with text. These sub-elements could
>> be based
> off of BibTeX, since they have existing specs for citing things:
> https://en.wikipedia.org/wiki/BibTeX
> 
> These citations would then be accessible in the HTML generated tool
> pages, or via a View/Download button somewhere on the tool page. By
> storing as an XML tree, we could render these citations as BibTeX
> entries for the LaTeX users, and I believe there are ways to convert
> BibTeX to EndNote XML and so on.
> 
> This could be extended for use in workflows so that when you run
> workflows, somehow a list of citations for all tools used could be
> generated.
> 
> Anyone have thoughts or opinions on this?
> 
> 
> 
> 
> Using the example bibtex entry from the wikipedia page:
> 
> @Book{abramowitz+stegun,
> author= "Milton {Abramowitz} and Irene A. {Stegun}",
> title = "Handbook of Mathematical Functions with
>  Formulas, Graphs, and Mathematical Tables",
> publisher = "Dover",
> year  =  1964,
> address   = "New York",
> edition   = "ninth Dover printing, tenth GPO printing"
> }
> 
> I imagine it'd look like the following in a real-life tool:
> 
> 
>  ...
>  
>Milton Abramowitz and Irene A. Stegun"
>Handbook of Mathematical Functions with Formulas,
>> Graphs, and
> Mathematical Tables
>Dover
>1964
>New York
>ninth Dover printing, tenth GPO printing
>  
> 
> 
> 
> Cheers,
> Eric
> >>> ___
> >>> 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/
> >>>
> >>> To search Galaxy mailing lists use the unified search at:
> >>>  http://galaxyproject.org/search/mailinglists/
> >> ___

Re: [galaxy-dev] RFC: Citations for tools

[Eric Rasche]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Peter,

What do you know, it has! I should've searched for those emails first.
Nevertheless, I'd like to see this implemented, and may take it on since
there's obviously a need for it.

You raise a good point, I am not familiar with semantic web/linked data
enough to know the best markup for citations. I come from a LaTeX
background, so embedding citations as close to BibTeX as possible seemed
like the simplest/most obvious solution to me.

I'm open to suggestions if anyone would like to bring them to the table!

James,

Good to know about BibTeXML, thanks for that link. If people will
generally support something along those lines, that'll come in handy.



Cheers,
Eric


On 05/27/2014 12:09 PM, Peter Cock wrote:
> Hi Eric,
> 
> I was sure there was a Trello card for this, but I can't find it right now...
> 
> I've pushed this idea on the mailing list before, and in person at
> the Galaxy Community Conference too. See also these threads:
> 
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html
> 
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html
> 
> Are you familiar enough with the area of semantic web/linked
> data to know what would be the best XML based markup to
> use for embedding the citations?
> 
> i.e. We should not reinvent the wheel here ;)
> 
> Peter
> 
> 
> On Tue, May 27, 2014 at 5:54 PM, James Taylor  wrote:
>> Eric, I'm very much in favor of this feature, and particularly the
>> idea of generating a list of citations from a history or workflow. I
>> imagine the only thing to quibble about will be the syntax. There are
>> already some efforts to represent bibtex in xml (e.g.
>> https://github.com/Zearin/BibTeXML), however they have always struck
>> me as overly verbose.
>>
>> -- jt
>>
>>
>> On Tue, May 27, 2014 at 12:45 PM, Eric Rasche  wrote:
> I'd want to open up discussion on a feature I'd like to see. I'll try
> and implement it if I can find time this summer. I didn't see a trello
> card for anything like this yet, but please feel free to direct me there
> if I missed it.
> 
> 
> I'd like to see citations as a part of every tool.
> 
> This would happen in the form of a  block in the XML, which
> would contain sub-elements with text. These sub-elements could be based
> off of BibTeX, since they have existing specs for citing things:
> https://en.wikipedia.org/wiki/BibTeX
> 
> These citations would then be accessible in the HTML generated tool
> pages, or via a View/Download button somewhere on the tool page. By
> storing as an XML tree, we could render these citations as BibTeX
> entries for the LaTeX users, and I believe there are ways to convert
> BibTeX to EndNote XML and so on.
> 
> This could be extended for use in workflows so that when you run
> workflows, somehow a list of citations for all tools used could be
> generated.
> 
> Anyone have thoughts or opinions on this?
> 
> 
> 
> 
> Using the example bibtex entry from the wikipedia page:
> 
> @Book{abramowitz+stegun,
>  author= "Milton {Abramowitz} and Irene A. {Stegun}",
>  title = "Handbook of Mathematical Functions with
>   Formulas, Graphs, and Mathematical Tables",
>  publisher = "Dover",
>  year  =  1964,
>  address   = "New York",
>  edition   = "ninth Dover printing, tenth GPO printing"
> }
> 
> I imagine it'd look like the following in a real-life tool:
> 
> 
>   ...
>   
> Milton Abramowitz and Irene A. Stegun"
> Handbook of Mathematical Functions with Formulas, Graphs, and
> Mathematical Tables
> Dover
> 1964
> New York
> ninth Dover printing, tenth GPO printing
>   
> 
> 
> 
> Cheers,
> Eric
>>> ___
>>> 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/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>> ___
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/

- -- 
Эрик Раше
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Version: GnuPG v2.0.17 (GNU/Linux)

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Re: [galaxy-dev] RFC: Citations for tools

[Jim McCusker]

I would suggest using as much as possible from PROV, especially since other
workflow engines (Taverna and Pegasus come to mind) already support it.
Rather than looking for bibtex mappings in XML, we should be looking for
vocabularies that represent the elements we need to represent, and the
relevant bibtex should be generated from that. PROV and Dublin Core Terms
can get us most of the way there, I think.

Jim


On Tue, May 27, 2014 at 1:09 PM, Peter Cock wrote:

> Hi Eric,
>
> I was sure there was a Trello card for this, but I can't find it right
> now...
>
> I've pushed this idea on the mailing list before, and in person at
> the Galaxy Community Conference too. See also these threads:
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html
>
> Are you familiar enough with the area of semantic web/linked
> data to know what would be the best XML based markup to
> use for embedding the citations?
>
> i.e. We should not reinvent the wheel here ;)
>
> Peter
>
>
> On Tue, May 27, 2014 at 5:54 PM, James Taylor 
> wrote:
> > Eric, I'm very much in favor of this feature, and particularly the
> > idea of generating a list of citations from a history or workflow. I
> > imagine the only thing to quibble about will be the syntax. There are
> > already some efforts to represent bibtex in xml (e.g.
> > https://github.com/Zearin/BibTeXML), however they have always struck
> > me as overly verbose.
> >
> > -- jt
> >
> >
> > On Tue, May 27, 2014 at 12:45 PM, Eric Rasche 
> wrote:
> >> -BEGIN PGP SIGNED MESSAGE-
> >> Hash: SHA1
> >>
> >> I'd want to open up discussion on a feature I'd like to see. I'll try
> >> and implement it if I can find time this summer. I didn't see a trello
> >> card for anything like this yet, but please feel free to direct me there
> >> if I missed it.
> >>
> >>
> >> I'd like to see citations as a part of every tool.
> >>
> >> This would happen in the form of a  block in the XML, which
> >> would contain sub-elements with text. These sub-elements could be based
> >> off of BibTeX, since they have existing specs for citing things:
> >> https://en.wikipedia.org/wiki/BibTeX
> >>
> >> These citations would then be accessible in the HTML generated tool
> >> pages, or via a View/Download button somewhere on the tool page. By
> >> storing as an XML tree, we could render these citations as BibTeX
> >> entries for the LaTeX users, and I believe there are ways to convert
> >> BibTeX to EndNote XML and so on.
> >>
> >> This could be extended for use in workflows so that when you run
> >> workflows, somehow a list of citations for all tools used could be
> >> generated.
> >>
> >> Anyone have thoughts or opinions on this?
> >>
> >>
> >>
> >>
> >> Using the example bibtex entry from the wikipedia page:
> >>
> >> @Book{abramowitz+stegun,
> >>  author= "Milton {Abramowitz} and Irene A. {Stegun}",
> >>  title = "Handbook of Mathematical Functions with
> >>   Formulas, Graphs, and Mathematical Tables",
> >>  publisher = "Dover",
> >>  year  =  1964,
> >>  address   = "New York",
> >>  edition   = "ninth Dover printing, tenth GPO printing"
> >> }
> >>
> >> I imagine it'd look like the following in a real-life tool:
> >>
> >> 
> >>   ...
> >>   
> >> Milton Abramowitz and Irene A. Stegun"
> >> Handbook of Mathematical Functions with Formulas, Graphs, and
> >> Mathematical Tables
> >> Dover
> >> 1964
> >> New York
> >> ninth Dover printing, tenth GPO printing
> >>   
> >> 
> >>
> >>
> >> Cheers,
> >> Eric
> >> - --
> >> Eric Rasche
> >> Programmer II
> >> Center for Phage Technology
> >> Texas A&M University
> >> College Station, TX 77843
> >> 404-692-2048
> >> e...@tamu.edu
> >> rasche.e...@yandex.ru
> >> -BEGIN PGP SIGNATURE-
> >> Version: GnuPG v2.0.17 (GNU/Linux)
> >>
> >> iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC
> >> jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU
> >> IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a
> >> FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgiogi
> >> 0SWGIGZ6OJdqX60h2hOjJ06NhzBcTsjQea+AwTo5wAkyGPFJy4DV78jKOvsd5PMG
> >> qkk4U6gBcmcFolCeItlLPa/C4uiyOK2wVWHyTnEeKjdpD6dwLuemRmwtZrModbQu
> >> PPPFkKzQhUnh5Wgq8TIP4kSc2t1/jSpdV8MHqM0piqOFnR52fExPrwLn82WEFcp8
> >> tXfHHTaZj+6gL+IGswdAgqvxk1V+6QTjH57igWmYtcENpIDbhZVBh+HOD8SS2qdv
> >> ohwFg/Vn8VrCeTGGehNSBvkam0HXjXXq7mZ8W4xrOS8vxv8HPAFZHze2sPlUG/Ob
> >> WeOdiLgD2HCH95SXYDDBNFG6HwFkLETA3DjpfvgHqPdaLmEfIZW+ks1WF9RG+Pmo
> >> jhbWH8OmtTk5A/Zh63uRowMaDe7QSCruPIfIwlrgqLozOj8htMyJPBIW9oZGGkqC
> >> 7Vu5UFeL8gcigRmQv5NA
> >> =ceAo
> >> -END PGP SIGNATURE-
> >> ___
> >> 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

Re: [galaxy-dev] RFC: Citations for tools

[Will Holtz]

As hinted at in the Trello card Greg posted, it could be much simpler if
the citation tag just took a DOI. It appears that the DOI to bibtex
conversion can be done by Crossref:
http://tex.stackexchange.com/questions/6848/automatically-dereference-doi-to-bib

-Will



On Tue, May 27, 2014 at 10:16 AM, Greg Von Kuster  wrote:

> Peter, this may be the Trello card you were thinking of.
>
> https://trello.com/c/kY7RCnd0/95-tool-shed-citation-for-tools-dois
>
> Greg Von Kuster
>
>
> On May 27, 2014, at 1:09 PM, Peter Cock  wrote:
>
> > Hi Eric,
> >
> > I was sure there was a Trello card for this, but I can't find it right
> now...
> >
> > I've pushed this idea on the mailing list before, and in person at
> > the Galaxy Community Conference too. See also these threads:
> >
> > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html
> >
> > http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html
> >
> > Are you familiar enough with the area of semantic web/linked
> > data to know what would be the best XML based markup to
> > use for embedding the citations?
> >
> > i.e. We should not reinvent the wheel here ;)
> >
> > Peter
> >
> >
> > On Tue, May 27, 2014 at 5:54 PM, James Taylor 
> wrote:
> >> Eric, I'm very much in favor of this feature, and particularly the
> >> idea of generating a list of citations from a history or workflow. I
> >> imagine the only thing to quibble about will be the syntax. There are
> >> already some efforts to represent bibtex in xml (e.g.
> >> https://github.com/Zearin/BibTeXML), however they have always struck
> >> me as overly verbose.
> >>
> >> -- jt
> >>
> >>
> >> On Tue, May 27, 2014 at 12:45 PM, Eric Rasche 
> wrote:
> >>> -BEGIN PGP SIGNED MESSAGE-
> >>> Hash: SHA1
> >>>
> >>> I'd want to open up discussion on a feature I'd like to see. I'll try
> >>> and implement it if I can find time this summer. I didn't see a trello
> >>> card for anything like this yet, but please feel free to direct me
> there
> >>> if I missed it.
> >>>
> >>>
> >>> I'd like to see citations as a part of every tool.
> >>>
> >>> This would happen in the form of a  block in the XML, which
> >>> would contain sub-elements with text. These sub-elements could be based
> >>> off of BibTeX, since they have existing specs for citing things:
> >>> https://en.wikipedia.org/wiki/BibTeX
> >>>
> >>> These citations would then be accessible in the HTML generated tool
> >>> pages, or via a View/Download button somewhere on the tool page. By
> >>> storing as an XML tree, we could render these citations as BibTeX
> >>> entries for the LaTeX users, and I believe there are ways to convert
> >>> BibTeX to EndNote XML and so on.
> >>>
> >>> This could be extended for use in workflows so that when you run
> >>> workflows, somehow a list of citations for all tools used could be
> >>> generated.
> >>>
> >>> Anyone have thoughts or opinions on this?
> >>>
> >>>
> >>>
> >>>
> >>> Using the example bibtex entry from the wikipedia page:
> >>>
> >>> @Book{abramowitz+stegun,
> >>> author= "Milton {Abramowitz} and Irene A. {Stegun}",
> >>> title = "Handbook of Mathematical Functions with
> >>>  Formulas, Graphs, and Mathematical Tables",
> >>> publisher = "Dover",
> >>> year  =  1964,
> >>> address   = "New York",
> >>> edition   = "ninth Dover printing, tenth GPO printing"
> >>> }
> >>>
> >>> I imagine it'd look like the following in a real-life tool:
> >>>
> >>> 
> >>>  ...
> >>>  
> >>>Milton Abramowitz and Irene A. Stegun"
> >>>Handbook of Mathematical Functions with Formulas, Graphs, and
> >>> Mathematical Tables
> >>>Dover
> >>>1964
> >>>New York
> >>>ninth Dover printing, tenth GPO printing
> >>>  
> >>> 
> >>>
> >>>
> >>> Cheers,
> >>> Eric
> >>> - --
> >>> Eric Rasche
> >>> Programmer II
> >>> Center for Phage Technology
> >>> Texas A&M University
> >>> College Station, TX 77843
> >>> 404-692-2048
> >>> e...@tamu.edu
> >>> rasche.e...@yandex.ru
> >>> -BEGIN PGP SIGNATURE-
> >>> Version: GnuPG v2.0.17 (GNU/Linux)
> >>>
> >>> iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC
> >>> jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU
> >>> IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a
> >>> FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgiogi
> >>> 0SWGIGZ6OJdqX60h2hOjJ06NhzBcTsjQea+AwTo5wAkyGPFJy4DV78jKOvsd5PMG
> >>> qkk4U6gBcmcFolCeItlLPa/C4uiyOK2wVWHyTnEeKjdpD6dwLuemRmwtZrModbQu
> >>> PPPFkKzQhUnh5Wgq8TIP4kSc2t1/jSpdV8MHqM0piqOFnR52fExPrwLn82WEFcp8
> >>> tXfHHTaZj+6gL+IGswdAgqvxk1V+6QTjH57igWmYtcENpIDbhZVBh+HOD8SS2qdv
> >>> ohwFg/Vn8VrCeTGGehNSBvkam0HXjXXq7mZ8W4xrOS8vxv8HPAFZHze2sPlUG/Ob
> >>> WeOdiLgD2HCH95SXYDDBNFG6HwFkLETA3DjpfvgHqPdaLmEfIZW+ks1WF9RG+Pmo
> >>> jhbWH8OmtTk5A/Zh63uRowMaDe7QSCruPIfIwlrgqLozOj8htMyJPBIW9oZGGkqC
> >>> 7Vu5UFeL8gcigRmQv5NA
> >>> =ceAo
> >>> -END PGP SIGNATURE-
> >>> ___
> >>> Please keep 

Re: [galaxy-dev] RFC: Citations for tools

[Greg Von Kuster]

Peter, this may be the Trello card you were thinking of.

https://trello.com/c/kY7RCnd0/95-tool-shed-citation-for-tools-dois

Greg Von Kuster


On May 27, 2014, at 1:09 PM, Peter Cock  wrote:

> Hi Eric,
> 
> I was sure there was a Trello card for this, but I can't find it right now...
> 
> I've pushed this idea on the mailing list before, and in person at
> the Galaxy Community Conference too. See also these threads:
> 
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html
> 
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html
> 
> Are you familiar enough with the area of semantic web/linked
> data to know what would be the best XML based markup to
> use for embedding the citations?
> 
> i.e. We should not reinvent the wheel here ;)
> 
> Peter
> 
> 
> On Tue, May 27, 2014 at 5:54 PM, James Taylor  wrote:
>> Eric, I'm very much in favor of this feature, and particularly the
>> idea of generating a list of citations from a history or workflow. I
>> imagine the only thing to quibble about will be the syntax. There are
>> already some efforts to represent bibtex in xml (e.g.
>> https://github.com/Zearin/BibTeXML), however they have always struck
>> me as overly verbose.
>> 
>> -- jt
>> 
>> 
>> On Tue, May 27, 2014 at 12:45 PM, Eric Rasche  wrote:
>>> -BEGIN PGP SIGNED MESSAGE-
>>> Hash: SHA1
>>> 
>>> I'd want to open up discussion on a feature I'd like to see. I'll try
>>> and implement it if I can find time this summer. I didn't see a trello
>>> card for anything like this yet, but please feel free to direct me there
>>> if I missed it.
>>> 
>>> 
>>> I'd like to see citations as a part of every tool.
>>> 
>>> This would happen in the form of a  block in the XML, which
>>> would contain sub-elements with text. These sub-elements could be based
>>> off of BibTeX, since they have existing specs for citing things:
>>> https://en.wikipedia.org/wiki/BibTeX
>>> 
>>> These citations would then be accessible in the HTML generated tool
>>> pages, or via a View/Download button somewhere on the tool page. By
>>> storing as an XML tree, we could render these citations as BibTeX
>>> entries for the LaTeX users, and I believe there are ways to convert
>>> BibTeX to EndNote XML and so on.
>>> 
>>> This could be extended for use in workflows so that when you run
>>> workflows, somehow a list of citations for all tools used could be
>>> generated.
>>> 
>>> Anyone have thoughts or opinions on this?
>>> 
>>> 
>>> 
>>> 
>>> Using the example bibtex entry from the wikipedia page:
>>> 
>>> @Book{abramowitz+stegun,
>>> author= "Milton {Abramowitz} and Irene A. {Stegun}",
>>> title = "Handbook of Mathematical Functions with
>>>  Formulas, Graphs, and Mathematical Tables",
>>> publisher = "Dover",
>>> year  =  1964,
>>> address   = "New York",
>>> edition   = "ninth Dover printing, tenth GPO printing"
>>> }
>>> 
>>> I imagine it'd look like the following in a real-life tool:
>>> 
>>> 
>>>  ...
>>>  
>>>Milton Abramowitz and Irene A. Stegun"
>>>Handbook of Mathematical Functions with Formulas, Graphs, and
>>> Mathematical Tables
>>>Dover
>>>1964
>>>New York
>>>ninth Dover printing, tenth GPO printing
>>>  
>>> 
>>> 
>>> 
>>> Cheers,
>>> Eric
>>> - --
>>> Eric Rasche
>>> Programmer II
>>> Center for Phage Technology
>>> Texas A&M University
>>> College Station, TX 77843
>>> 404-692-2048
>>> e...@tamu.edu
>>> rasche.e...@yandex.ru
>>> -BEGIN PGP SIGNATURE-
>>> Version: GnuPG v2.0.17 (GNU/Linux)
>>> 
>>> iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC
>>> jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU
>>> IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a
>>> FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgiogi
>>> 0SWGIGZ6OJdqX60h2hOjJ06NhzBcTsjQea+AwTo5wAkyGPFJy4DV78jKOvsd5PMG
>>> qkk4U6gBcmcFolCeItlLPa/C4uiyOK2wVWHyTnEeKjdpD6dwLuemRmwtZrModbQu
>>> PPPFkKzQhUnh5Wgq8TIP4kSc2t1/jSpdV8MHqM0piqOFnR52fExPrwLn82WEFcp8
>>> tXfHHTaZj+6gL+IGswdAgqvxk1V+6QTjH57igWmYtcENpIDbhZVBh+HOD8SS2qdv
>>> ohwFg/Vn8VrCeTGGehNSBvkam0HXjXXq7mZ8W4xrOS8vxv8HPAFZHze2sPlUG/Ob
>>> WeOdiLgD2HCH95SXYDDBNFG6HwFkLETA3DjpfvgHqPdaLmEfIZW+ks1WF9RG+Pmo
>>> jhbWH8OmtTk5A/Zh63uRowMaDe7QSCruPIfIwlrgqLozOj8htMyJPBIW9oZGGkqC
>>> 7Vu5UFeL8gcigRmQv5NA
>>> =ceAo
>>> -END PGP SIGNATURE-
>>> ___
>>> 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/
>>> 
>>> To search Galaxy mailing lists use the unified search at:
>>>  http://galaxyproject.org/search/mailinglists/
>> ___
>> 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:
>>  htt

Re: [galaxy-dev] RFC: Citations for tools

[Peter Cock]

Hi Eric,

I was sure there was a Trello card for this, but I can't find it right now...

I've pushed this idea on the mailing list before, and in person at
the Galaxy Community Conference too. See also these threads:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html

http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html

Are you familiar enough with the area of semantic web/linked
data to know what would be the best XML based markup to
use for embedding the citations?

i.e. We should not reinvent the wheel here ;)

Peter


On Tue, May 27, 2014 at 5:54 PM, James Taylor  wrote:
> Eric, I'm very much in favor of this feature, and particularly the
> idea of generating a list of citations from a history or workflow. I
> imagine the only thing to quibble about will be the syntax. There are
> already some efforts to represent bibtex in xml (e.g.
> https://github.com/Zearin/BibTeXML), however they have always struck
> me as overly verbose.
>
> -- jt
>
>
> On Tue, May 27, 2014 at 12:45 PM, Eric Rasche  wrote:
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> I'd want to open up discussion on a feature I'd like to see. I'll try
>> and implement it if I can find time this summer. I didn't see a trello
>> card for anything like this yet, but please feel free to direct me there
>> if I missed it.
>>
>>
>> I'd like to see citations as a part of every tool.
>>
>> This would happen in the form of a  block in the XML, which
>> would contain sub-elements with text. These sub-elements could be based
>> off of BibTeX, since they have existing specs for citing things:
>> https://en.wikipedia.org/wiki/BibTeX
>>
>> These citations would then be accessible in the HTML generated tool
>> pages, or via a View/Download button somewhere on the tool page. By
>> storing as an XML tree, we could render these citations as BibTeX
>> entries for the LaTeX users, and I believe there are ways to convert
>> BibTeX to EndNote XML and so on.
>>
>> This could be extended for use in workflows so that when you run
>> workflows, somehow a list of citations for all tools used could be
>> generated.
>>
>> Anyone have thoughts or opinions on this?
>>
>>
>>
>>
>> Using the example bibtex entry from the wikipedia page:
>>
>> @Book{abramowitz+stegun,
>>  author= "Milton {Abramowitz} and Irene A. {Stegun}",
>>  title = "Handbook of Mathematical Functions with
>>   Formulas, Graphs, and Mathematical Tables",
>>  publisher = "Dover",
>>  year  =  1964,
>>  address   = "New York",
>>  edition   = "ninth Dover printing, tenth GPO printing"
>> }
>>
>> I imagine it'd look like the following in a real-life tool:
>>
>> 
>>   ...
>>   
>> Milton Abramowitz and Irene A. Stegun"
>> Handbook of Mathematical Functions with Formulas, Graphs, and
>> Mathematical Tables
>> Dover
>> 1964
>> New York
>> ninth Dover printing, tenth GPO printing
>>   
>> 
>>
>>
>> Cheers,
>> Eric
>> - --
>> Eric Rasche
>> Programmer II
>> Center for Phage Technology
>> Texas A&M University
>> College Station, TX 77843
>> 404-692-2048
>> e...@tamu.edu
>> rasche.e...@yandex.ru
>> -BEGIN PGP SIGNATURE-
>> Version: GnuPG v2.0.17 (GNU/Linux)
>>
>> iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC
>> jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU
>> IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a
>> FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgiogi
>> 0SWGIGZ6OJdqX60h2hOjJ06NhzBcTsjQea+AwTo5wAkyGPFJy4DV78jKOvsd5PMG
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>> PPPFkKzQhUnh5Wgq8TIP4kSc2t1/jSpdV8MHqM0piqOFnR52fExPrwLn82WEFcp8
>> tXfHHTaZj+6gL+IGswdAgqvxk1V+6QTjH57igWmYtcENpIDbhZVBh+HOD8SS2qdv
>> ohwFg/Vn8VrCeTGGehNSBvkam0HXjXXq7mZ8W4xrOS8vxv8HPAFZHze2sPlUG/Ob
>> WeOdiLgD2HCH95SXYDDBNFG6HwFkLETA3DjpfvgHqPdaLmEfIZW+ks1WF9RG+Pmo
>> jhbWH8OmtTk5A/Zh63uRowMaDe7QSCruPIfIwlrgqLozOj8htMyJPBIW9oZGGkqC
>> 7Vu5UFeL8gcigRmQv5NA
>> =ceAo
>> -END PGP SIGNATURE-
>> ___
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

[Paniagua, Eric]

Restarting the Galaxy server in multiple process mode appears to have helped.  
The test job is now running.

From: Paniagua, Eric
Sent: Tuesday, May 27, 2014 12:43 PM
To: Dannon Baker
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

Correction.  The job has entered the "waiting to run" phase, and doesn't appear 
to be leaving it.  There is nothing of note in the server log.

From: Paniagua, Eric
Sent: Tuesday, May 27, 2014 12:41 PM
To: Dannon Baker
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

I have created a fresh dump with

$ pg_dump -U galaxyprod galaxyprod

This time the import proceeded cleanly.

Further, using PostgreSQL 9.1, I no longer get the error regarding a read only 
database cursor and getting the next history item number.  I am currently 
running a test job to confirm that things are working as expected.  However, 
just the fact that this job is running is a very good sign.

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Tuesday, May 27, 2014 11:58 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

Since the database has lost consistency, I'd really try a fresh pg_dump / 
import if that's possible.  If there's an error this time around, note it and 
send it on over and we can figure out where to go from there.


On Tue, May 27, 2014 at 11:48 AM, Paniagua, Eric 
mailto:epani...@cshl.edu>> wrote:
The "dataset" table is populated.  I looked at the SQL dump file I used to copy 
the database, and it has create table and copy into statements for 
history_dataset_association, but it looks like there may have been an error 
while executing them.  Trying to figure out how to get  my data in...

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Tuesday, May 27, 2014 11:43 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric 
mailto:epani...@cshl.edu>>>
 wrote:
Thanks for pointing that out!  I missed it.  I am now connecting to the remote 
database.  I ran "sh manage_db.sh upgrade" and it upgraded from schema 114 to 
118 without error messages.  I then ran "sh 
./scripts/migrate_tools/0010_tools.sh install_dependencies" and received the 
following error:

line 35, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 
'gatk_picard_indexes'

I fixed this by adding the appropriate entries to tool_data_table_conf.xml.  I 
then reran the migrate_tools command successfully.  However, now my 
"history_dataset_association" table in the database was blown away at some 
point.  The table is now completely empty.  Have you ever seen this before?

I have not seen the tool migration issue before, but it seems harmless.  The 
fact that your history_dataset_association table is empty is concerning if 
there was ever anything in it.  Can you verify that there are datasets in the 
same database that *should* be associated to a history?  It sounds like this 
galaxy instance has been used with different databases, and my hope is that the 
wires are crossed up here and there actually should not be any.


___
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Re: [galaxy-dev] RFC: Citations for tools

[James Taylor]

Eric, I'm very much in favor of this feature, and particularly the
idea of generating a list of citations from a history or workflow. I
imagine the only thing to quibble about will be the syntax. There are
already some efforts to represent bibtex in xml (e.g.
https://github.com/Zearin/BibTeXML), however they have always struck
me as overly verbose.

-- jt


On Tue, May 27, 2014 at 12:45 PM, Eric Rasche  wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> I'd want to open up discussion on a feature I'd like to see. I'll try
> and implement it if I can find time this summer. I didn't see a trello
> card for anything like this yet, but please feel free to direct me there
> if I missed it.
>
>
> I'd like to see citations as a part of every tool.
>
> This would happen in the form of a  block in the XML, which
> would contain sub-elements with text. These sub-elements could be based
> off of BibTeX, since they have existing specs for citing things:
> https://en.wikipedia.org/wiki/BibTeX
>
> These citations would then be accessible in the HTML generated tool
> pages, or via a View/Download button somewhere on the tool page. By
> storing as an XML tree, we could render these citations as BibTeX
> entries for the LaTeX users, and I believe there are ways to convert
> BibTeX to EndNote XML and so on.
>
> This could be extended for use in workflows so that when you run
> workflows, somehow a list of citations for all tools used could be
> generated.
>
> Anyone have thoughts or opinions on this?
>
>
>
>
> Using the example bibtex entry from the wikipedia page:
>
> @Book{abramowitz+stegun,
>  author= "Milton {Abramowitz} and Irene A. {Stegun}",
>  title = "Handbook of Mathematical Functions with
>   Formulas, Graphs, and Mathematical Tables",
>  publisher = "Dover",
>  year  =  1964,
>  address   = "New York",
>  edition   = "ninth Dover printing, tenth GPO printing"
> }
>
> I imagine it'd look like the following in a real-life tool:
>
> 
>   ...
>   
> Milton Abramowitz and Irene A. Stegun"
> Handbook of Mathematical Functions with Formulas, Graphs, and
> Mathematical Tables
> Dover
> 1964
> New York
> ninth Dover printing, tenth GPO printing
>   
> 
>
>
> Cheers,
> Eric
> - --
> Eric Rasche
> Programmer II
> Center for Phage Technology
> Texas A&M University
> College Station, TX 77843
> 404-692-2048
> e...@tamu.edu
> rasche.e...@yandex.ru
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> 7Vu5UFeL8gcigRmQv5NA
> =ceAo
> -END PGP SIGNATURE-
> ___
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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[galaxy-dev] RFC: Citations for tools

[Eric Rasche]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I'd want to open up discussion on a feature I'd like to see. I'll try
and implement it if I can find time this summer. I didn't see a trello
card for anything like this yet, but please feel free to direct me there
if I missed it.


I'd like to see citations as a part of every tool.

This would happen in the form of a  block in the XML, which
would contain sub-elements with text. These sub-elements could be based
off of BibTeX, since they have existing specs for citing things:
https://en.wikipedia.org/wiki/BibTeX

These citations would then be accessible in the HTML generated tool
pages, or via a View/Download button somewhere on the tool page. By
storing as an XML tree, we could render these citations as BibTeX
entries for the LaTeX users, and I believe there are ways to convert
BibTeX to EndNote XML and so on.

This could be extended for use in workflows so that when you run
workflows, somehow a list of citations for all tools used could be
generated.

Anyone have thoughts or opinions on this?




Using the example bibtex entry from the wikipedia page:

@Book{abramowitz+stegun,
 author= "Milton {Abramowitz} and Irene A. {Stegun}",
 title = "Handbook of Mathematical Functions with
  Formulas, Graphs, and Mathematical Tables",
 publisher = "Dover",
 year  =  1964,
 address   = "New York",
 edition   = "ninth Dover printing, tenth GPO printing"
}

I imagine it'd look like the following in a real-life tool:


  ...
  
Milton Abramowitz and Irene A. Stegun"
Handbook of Mathematical Functions with Formulas, Graphs, and
Mathematical Tables
Dover
1964
New York
ninth Dover printing, tenth GPO printing
  



Cheers,
Eric
- -- 
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu
rasche.e...@yandex.ru
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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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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

[Paniagua, Eric]

Correction.  The job has entered the "waiting to run" phase, and doesn't appear 
to be leaving it.  There is nothing of note in the server log.

From: Paniagua, Eric
Sent: Tuesday, May 27, 2014 12:41 PM
To: Dannon Baker
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

I have created a fresh dump with

$ pg_dump -U galaxyprod galaxyprod

This time the import proceeded cleanly.

Further, using PostgreSQL 9.1, I no longer get the error regarding a read only 
database cursor and getting the next history item number.  I am currently 
running a test job to confirm that things are working as expected.  However, 
just the fact that this job is running is a very good sign.

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Tuesday, May 27, 2014 11:58 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

Since the database has lost consistency, I'd really try a fresh pg_dump / 
import if that's possible.  If there's an error this time around, note it and 
send it on over and we can figure out where to go from there.


On Tue, May 27, 2014 at 11:48 AM, Paniagua, Eric 
mailto:epani...@cshl.edu>> wrote:
The "dataset" table is populated.  I looked at the SQL dump file I used to copy 
the database, and it has create table and copy into statements for 
history_dataset_association, but it looks like there may have been an error 
while executing them.  Trying to figure out how to get  my data in...

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Tuesday, May 27, 2014 11:43 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric 
mailto:epani...@cshl.edu>>>
 wrote:
Thanks for pointing that out!  I missed it.  I am now connecting to the remote 
database.  I ran "sh manage_db.sh upgrade" and it upgraded from schema 114 to 
118 without error messages.  I then ran "sh 
./scripts/migrate_tools/0010_tools.sh install_dependencies" and received the 
following error:

line 35, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 
'gatk_picard_indexes'

I fixed this by adding the appropriate entries to tool_data_table_conf.xml.  I 
then reran the migrate_tools command successfully.  However, now my 
"history_dataset_association" table in the database was blown away at some 
point.  The table is now completely empty.  Have you ever seen this before?

I have not seen the tool migration issue before, but it seems harmless.  The 
fact that your history_dataset_association table is empty is concerning if 
there was ever anything in it.  Can you verify that there are datasets in the 
same database that *should* be associated to a history?  It sounds like this 
galaxy instance has been used with different databases, and my hope is that the 
wires are crossed up here and there actually should not be any.


___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

[Paniagua, Eric]

I have created a fresh dump with

$ pg_dump -U galaxyprod galaxyprod

This time the import proceeded cleanly.

Further, using PostgreSQL 9.1, I no longer get the error regarding a read only 
database cursor and getting the next history item number.  I am currently 
running a test job to confirm that things are working as expected.  However, 
just the fact that this job is running is a very good sign.

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Tuesday, May 27, 2014 11:58 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

Since the database has lost consistency, I'd really try a fresh pg_dump / 
import if that's possible.  If there's an error this time around, note it and 
send it on over and we can figure out where to go from there.


On Tue, May 27, 2014 at 11:48 AM, Paniagua, Eric 
mailto:epani...@cshl.edu>> wrote:
The "dataset" table is populated.  I looked at the SQL dump file I used to copy 
the database, and it has create table and copy into statements for 
history_dataset_association, but it looks like there may have been an error 
while executing them.  Trying to figure out how to get  my data in...

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Tuesday, May 27, 2014 11:43 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric 
mailto:epani...@cshl.edu>>>
 wrote:
Thanks for pointing that out!  I missed it.  I am now connecting to the remote 
database.  I ran "sh manage_db.sh upgrade" and it upgraded from schema 114 to 
118 without error messages.  I then ran "sh 
./scripts/migrate_tools/0010_tools.sh install_dependencies" and received the 
following error:

line 35, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 
'gatk_picard_indexes'

I fixed this by adding the appropriate entries to tool_data_table_conf.xml.  I 
then reran the migrate_tools command successfully.  However, now my 
"history_dataset_association" table in the database was blown away at some 
point.  The table is now completely empty.  Have you ever seen this before?

I have not seen the tool migration issue before, but it seems harmless.  The 
fact that your history_dataset_association table is empty is concerning if 
there was ever anything in it.  Can you verify that there are datasets in the 
same database that *should* be associated to a history?  It sounds like this 
galaxy instance has been used with different databases, and my hope is that the 
wires are crossed up here and there actually should not be any.


___
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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[galaxy-dev] Cluster Admins - Call for experiences/issues encountered

[Eric Rasche]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

This is specifically to galaxy administrators and developers who have
worked with galaxy and cluster deployment.

If you have successfully deployed a galaxy instance backed by one (or
more) clusters, I'm looking to hear about your experience;

- - the configuration
- - any pitfalls encountered
- - any extra tools that needed to be installed
- - any ugly hacks you had to implement

The current cluster documentation is somewhat lacking, and I'm willing
to compile everyone's experiences deploying to clusters if you're
willing to send them in. I'll update the cluster page on the wiki as I
receive replies and can allocate time.



By way of example, here's the summary of what I would reply to this
email with my experiences deploying to an HTCondor cluster

- - HTcondor ran fine, accepted jobs and worked for all users
- - Connecting galaxy to it would result in some jobs running/some jobs
failing. It was determined that those jobs which ran, were only on
localhost.
- - This was a result of the fact that galaxy's home directory/data was
not exported
- - Galaxy was made an LDAP user and a folder created in the correct
location on all computers
- - This still failed, as galaxy does not transfer files by default (as
far as I can tell), even though that's available in HTCondor
- - Finally galaxy's home directory was NFS exported and things seemed to
work.




Cheers,
Eric

- -- 
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu
rasche.e...@yandex.ru
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Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

[Dannon Baker]

Since the database has lost consistency, I'd really try a fresh pg_dump /
import if that's possible.  If there's an error this time around, note it
and send it on over and we can figure out where to go from there.


On Tue, May 27, 2014 at 11:48 AM, Paniagua, Eric  wrote:

> The "dataset" table is populated.  I looked at the SQL dump file I used to
> copy the database, and it has create table and copy into statements for
> history_dataset_association, but it looks like there may have been an error
> while executing them.  Trying to figure out how to get  my data in...
> 
> From: Dannon Baker [dannon.ba...@gmail.com]
> Sent: Tuesday, May 27, 2014 11:43 AM
> To: Paniagua, Eric
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database
> on a remote host
>
> On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric  > wrote:
> Thanks for pointing that out!  I missed it.  I am now connecting to the
> remote database.  I ran "sh manage_db.sh upgrade" and it upgraded from
> schema 114 to 118 without error messages.  I then ran "sh
> ./scripts/migrate_tools/0010_tools.sh install_dependencies" and received
> the following error:
>
> line 35, in __getitem__ return self.data_tables.__getitem__( key )
> KeyError: 'gatk_picard_indexes'
>
> I fixed this by adding the appropriate entries to
> tool_data_table_conf.xml.  I then reran the migrate_tools command
> successfully.  However, now my "history_dataset_association" table in the
> database was blown away at some point.  The table is now completely empty.
>  Have you ever seen this before?
>
> I have not seen the tool migration issue before, but it seems harmless.
>  The fact that your history_dataset_association table is empty is
> concerning if there was ever anything in it.  Can you verify that there are
> datasets in the same database that *should* be associated to a history?  It
> sounds like this galaxy instance has been used with different databases,
> and my hope is that the wires are crossed up here and there actually should
> not be any.
>
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Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

[Paniagua, Eric]

The "dataset" table is populated.  I looked at the SQL dump file I used to copy 
the database, and it has create table and copy into statements for 
history_dataset_association, but it looks like there may have been an error 
while executing them.  Trying to figure out how to get  my data in...

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Tuesday, May 27, 2014 11:43 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric 
mailto:epani...@cshl.edu>> wrote:
Thanks for pointing that out!  I missed it.  I am now connecting to the remote 
database.  I ran "sh manage_db.sh upgrade" and it upgraded from schema 114 to 
118 without error messages.  I then ran "sh 
./scripts/migrate_tools/0010_tools.sh install_dependencies" and received the 
following error:

line 35, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 
'gatk_picard_indexes'

I fixed this by adding the appropriate entries to tool_data_table_conf.xml.  I 
then reran the migrate_tools command successfully.  However, now my 
"history_dataset_association" table in the database was blown away at some 
point.  The table is now completely empty.  Have you ever seen this before?

I have not seen the tool migration issue before, but it seems harmless.  The 
fact that your history_dataset_association table is empty is concerning if 
there was ever anything in it.  Can you verify that there are datasets in the 
same database that *should* be associated to a history?  It sounds like this 
galaxy instance has been used with different databases, and my hope is that the 
wires are crossed up here and there actually should not be any.

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Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

[Dannon Baker]

On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric  wrote:

> Thanks for pointing that out!  I missed it.  I am now connecting to the
> remote database.  I ran "sh manage_db.sh upgrade" and it upgraded from
> schema 114 to 118 without error messages.  I then ran "sh
> ./scripts/migrate_tools/0010_tools.sh install_dependencies" and received
> the following error:
>


> line 35, in __getitem__ return self.data_tables.__getitem__( key )
> KeyError: 'gatk_picard_indexes'
>
> I fixed this by adding the appropriate entries to
> tool_data_table_conf.xml.  I then reran the migrate_tools command
> successfully.  However, now my "history_dataset_association" table in the
> database was blown away at some point.  The table is now completely empty.
>  Have you ever seen this before?
>

I have not seen the tool migration issue before, but it seems harmless.
 The fact that your history_dataset_association table is empty is
concerning if there was ever anything in it.  Can you verify that there are
datasets in the same database that *should* be associated to a history?  It
sounds like this galaxy instance has been used with different databases,
and my hope is that the wires are crossed up here and there actually should
not be any.
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Re: [galaxy-dev] complex help for conditional param

[Peter Cock]

On Tue, May 27, 2014 at 4:32 PM, Jun Fan  wrote:
> Hi all,
>
>
>
>In the conditional param, when sub-element allows you to write
> specific parameters for a particular value selected. I am wondering how to
> write the help context according to the value selection. For example, if
> there is a conditional param called blast_type, when “blastn” is selected,
> the help context will be “blast dna against dna” and when “blastp” is
> selected, the help context will be “blast protein against protein”.
> Basically this selection-based help text provides a general description of
> the selection, which could help to set up the corresponding parameters.
>
>   By the way, is there any document about formatting text in the help
> element?
>
> Best regards!
>
> Jun

You can do this kind of thing with one-line Cheetah syntax within the output
XML tag, but it quickly gets very complicated. e.g.

https://github.com/peterjc/pico_galaxy/commit/3991893c6ee2cc69c33aaa391bbed412c85fa9db

Peter

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[galaxy-dev] complex help for conditional param

[Jun Fan]

Hi all,

   In the conditional param, when sub-element allows you to write specific 
parameters for a particular value selected. I am wondering how to write the 
help context according to the value selection. For example, if there is a 
conditional param called blast_type, when "blastn" is selected, the help 
context will be "blast dna against dna" and when "blastp" is selected, the help 
context will be "blast protein against protein". Basically this selection-based 
help text provides a general description of the selection, which could help to 
set up the corresponding parameters.
  By the way, is there any document about formatting text in the help 
element?

Best regards!
Jun
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[galaxy-dev] Uploading files to galaxy from a folder

[Kandalaft, Iyad]

Hi Everyone

I'm throwing this out there for some feedback and recommendations.


Objective: Facilitate transferring large files (> 2GB) from an HPC cluster (and 
its associated fast tier storage) to galaxy for my clients.  I enabled the FTP 
upload option in galaxy but it involves users learning to copy files over FTP.

So, I created a galaxy folder in each users' home directory on the HPC Cluster 
that symbolically links to the FTP upload folder for galaxy.  Hence, users can 
use either FTP to upload files (drag and drop in windows) or simply copy files 
into this folder from an ssh session on the cluster.  The problem with that 
strategy was that galaxy had to be the owner of the file (similar to the 
ProFTPd configuration that sets the UID and GID of uploads files to galaxy's 
UID/GID).  Otherwise, galaxy threw errors when it tried deleting the original 
file from the FTP upload folder.  I could have added the galaxy user to the 
same group as all user but this meant that users would have to ensure the 
correct permissions are set on files so that galaxy can read and delete the 
file thereafter.  The alternative involved modifying the upload.py tool to 
chown/chmod files that were being uploaded.  Upload.py now sudo executes an 
external script that sets ownership to the galaxy user and corrects the 
permissions if required (see attachment for code modification).  The galaxy 
user has sudo rights on this script and the script restricts chown/chmod to the 
ftp folder path for security reasons.

I was planning to clean up the code and make it production ready by adding an 
option in universe_wsgi.ini for this "feature", but I thought I would check 
with the galaxy devs first. Am I taking the wrong approach?  Is there a better 
alternative?

As an alternative, I thought about locating the handler code for dataset.type 
== file and possibly making it support the SETGID sticky bits on folders.  In 
that case, the FTP upload folder would have the sticky bit set for UID and can 
assume the role of the user to upload that file.

Your input is much appreciated.

Iyad Kandalaft

Bioinformatics Application Developer
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
KW Neatby Bldg | éd. KW Neatby
960 Carling Ave| 960, avenue Carling
Ottawa, ON | Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel: 
iyad.kandal...@agr.gc.ca
Telephone | Téléphone 613- 759-1228
Facsimile | Télécopieur 613-759-1701
Government of Canada | Gouvernement du Canada

diff -r 29ce93a13ac7 tools/data_source/upload.py
--- a/tools/data_source/upload.py   Mon Feb 10 13:22:47 2014 -0500
+++ b/tools/data_source/upload.py   Tue May 27 10:54:42 2014 -0400
@@ -4,7 +4,7 @@
 # WARNING: Changes in this tool (particularly as related to parsing) may need
 # to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
 
-import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs, 
binascii
+import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs, 
binascii, subprocess
 from galaxy import eggs
 # need to import model before sniff to resolve a circular import dependency
 import galaxy.model
@@ -352,6 +352,19 @@
  stdout = 'uploaded %s file' % dataset.file_type )
 json_file.write( to_json_string( info ) + "\n" )
 
+def _chown( dataset ):
+if ( dataset.type != 'file' ):
+return
+
+try:
+cmd = [ '/usr/bin/sudo', '-E', 
'/home/galaxy/server-conf/chown_script.pl', dataset.path ]
+sys.stdout.write( 'Changing ownership of %s with: %s' % ( 
dataset.path, ' '.join( cmd ) ) )
+p = subprocess.Popen( cmd, shell=False, stdout=subprocess.PIPE, 
stderr=subprocess.PIPE )
+sys.stdout.write( p.stdout.read() )
+sys.stderr.write( p.stderr.read() )
+except Exception, e:
+sys.stderr.write( 'Changing ownership of uploaded file %s failed: %s' 
% ( dataset.path, str( e ) ) )
+
 def __main__():
 
 if len( sys.argv ) < 4:
@@ -372,6 +385,9 @@
 except:
 print >>sys.stderr, 'Output path for dataset %s not found on 
command line' % dataset.dataset_id
 sys.exit( 1 )
+
+_chown( dataset )   
+
 if dataset.type == 'composite':
 files_path = output_paths[int( dataset.dataset_id )][1]
 add_composite_file( dataset, registry, json_file, output_path, 
files_path )
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Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

[Paniagua, Eric]

Hey Dannon,

Thanks for pointing that out!  I missed it.  I am now connecting to the remote 
database.  I ran "sh manage_db.sh upgrade" and it upgraded from schema 114 to 
118 without error messages.  I then ran "sh 
./scripts/migrate_tools/0010_tools.sh install_dependencies" and received the 
following error:

Traceback (most recent call last): File 
"./scripts/migrate_tools/migrate_tools.py", line 21, in app = 
MigrateToolsApplication( sys.argv[ 1 ] ) File 
"/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/migrate/common.py",
 line 59, in __init__ install_dependencies=install_dependencies ) File 
"/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/install_manager.py",
 line 122, in __init__ is_repository_dependency=is_repository_dependency ) File 
"/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/install_manager.py",
 line 506, in install_repository 
is_repository_dependency=is_repository_dependency ) File 
"/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/install_manager.py",
 line 345, in handle_repository_contents guid = self.get_guid( 
repository_clone_url, relative_install_dir, tool_config ) File 
"/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/install_manager.py",
 line 253, in get_guid tool = self.toolbox.load_tool( full_path )!
  File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 
671, in load_tool return ToolClass( config_file, root, self.app, guid=guid, 
repository_id=repository_id, **kwds ) File 
"/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1045, in 
__init__ self.parse( root, guid=guid ) File 
"/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1260, in 
parse self.parse_inputs( root ) File 
"/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1351, in 
parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File 
"/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1655, in 
parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File 
"/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1723, in 
parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, 
context ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", 
line 1679, in pa!
 rse_input_elem group.inputs = self.parse_input_elem( elem, enc!
 types, c
ontext ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", 
line 1751, in parse_input_elem param = self.parse_param_elem( elem, enctypes, 
context ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", 
line 1764, in parse_param_elem param = ToolParameter.build( self, input_elem ) 
File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/parameters/basic.py", 
line 215, in build return parameter_types[param_type]( tool, param ) File 
"/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/parameters/basic.py", line 
1566, in __init__ ToolParameter.__init__( self, tool, elem ) File 
"/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/parameters/basic.py", line 
54, in __init__ self.validators.append( validation.Validator.from_element( 
self, elem ) ) File 
"/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/parameters/validation.py", 
line 23, in from_element return validator_types[type].from_element( param, elem 
) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/t!
 ools/parameters/validation.py", line 283, in from_element tool_data_table = 
param.tool.app.tool_data_tables[ table_name ] File 
"/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/data/__init__.py", line 35, 
in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 
'gatk_picard_indexes'

I fixed this by adding the appropriate entries to tool_data_table_conf.xml.  I 
then reran the migrate_tools command successfully.  However, now my 
"history_dataset_association" table in the database was blown away at some 
point.  The table is now completely empty.  Have you ever seen this before?

Thanks,
Eric

From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Tuesday, May 27, 2014 7:40 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a 
remote host

Hey Eric,

It looks like you have connection info for both tcp/ip connections and unix 
sockets in the connection strings.  If you're logging in using "psql -h 
wigserv5.cshl.edu ", then you only want the 
tcp/ip connection info.  Drop the ?host=tmp off the third option you listed and 
I think you'll be up and running, so:

postgresql://glxeric:xx...@wigserv5.cshl.edu:5432/glxeric

-Dannon


On Sat, May 24, 2014 at 1:49 AM, Paniagua, Eric 
mailto:epani...@cshl.edu>> wrote:
Dear Galaxy Developers,

I've been banging my head against this one for a few days now.

I have two Galaxy instances.  One resides on a server called "genomics", which

Re: [galaxy-dev] Old Tool Shed URL http://community.g2.bx.psu.edu/ dead

[Greg Von Kuster]

Peter, sorry, this one is "out of my hands".  I'm hoping Nate can answer this 
when he gets a chance.

Greg Von Kuster

On May 27, 2014, at 11:16 AM, Peter Cock  wrote:

> On Tue, May 27, 2014 at 3:39 PM, Greg Von Kuster  wrote:
>> Hi peter,
>> 
>> It seems that we have stopped redirecting the old Tool Shed URL
>> http://community.g2.bx.psu.edu/ to the new Tool Shed URL
>> http://toolshed.g2.bx.psu.edu/ .  I'm not sure when this happened.
>> 
>> Sorry for the inconvenience.
>> 
>> Greg Von Kuster
> 
> Can the old domain be restored to fix pre-existing 3rd party links?
> There could be some in published papers, certainly there are on
> the mailing list archives.
> 
> Peter


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Re: [galaxy-dev] ToolShed: Uploaded archives can only include regular directories and files

[Peter Cock]

On Tue, May 27, 2014 at 4:15 PM, Greg Von Kuster  wrote:
> Hello Peter,
>
> This issue should be resolved in 13630:33b1ff4b9985, which is now running on 
> the test Tool Shed.  Thanks for reporting this!
>
> Greg Von Kuster

Thanks - clearer error messages are a good thing :)

Peter
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Re: [galaxy-dev] Old Tool Shed URL http://community.g2.bx.psu.edu/ dead

[Peter Cock]

On Tue, May 27, 2014 at 3:39 PM, Greg Von Kuster  wrote:
> Hi peter,
>
> It seems that we have stopped redirecting the old Tool Shed URL
> http://community.g2.bx.psu.edu/ to the new Tool Shed URL
> http://toolshed.g2.bx.psu.edu/ .  I'm not sure when this happened.
>
> Sorry for the inconvenience.
>
> Greg Von Kuster

Can the old domain be restored to fix pre-existing 3rd party links?
There could be some in published papers, certainly there are on
the mailing list archives.

Peter
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Re: [galaxy-dev] ToolShed: Uploaded archives can only include regular directories and files

[Greg Von Kuster]

Hello Peter,

This issue should be resolved in 13630:33b1ff4b9985, which is now running on 
the test Tool Shed.  Thanks for reporting this!

Greg Von Kuster

On May 19, 2014, at 1:41 PM, Peter Cock  wrote:

> Hi Greg, Dave,
> 
> I just tried to upload an updated tar-ball to the Test ToolShed and
> got a red error message:
> 
> 
> Uploaded archives can only include regular directories and files (no
> symbolic links, devices, etc). Offender:
> 
> 
> Note no offending files were listed. When I double checked I had prepared
> my tar-ball from the wrong source directory and it did contain symlinks, but
> the Tool Shed error message failed to list these.
> 
> Regards,
> 
> Peter
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Re: [galaxy-dev] Old Tool Shed URL http://community.g2.bx.psu.edu/ dead

[Greg Von Kuster]

Hi peter,

It seems that we have stopped redirecting the old Tool Shed URL 
http://community.g2.bx.psu.edu/ to the new Tool Shed URL 
http://toolshed.g2.bx.psu.edu/ .  I'm not sure when this happened.

Sorry for the inconvenience.

Greg Von Kuster


On May 21, 2014, at 9:37 AM, Peter Cock  wrote:

> Hi Greg,
> 
> That Trello card link doesn't work for me, but the old domain is
> currently not redirecting to the ToolShed.
> 
> Regards,
> 
> Peter
> 
> 
> On Wed, Mar 6, 2013 at 12:32 PM, Greg Von Kuster  wrote:
>> Hi Peter,
>> 
>> I've added this to the same Trello card.  These URL redirects lie outside of 
>> my control, so I'll bug the right person to get them set up.
>> 
>> https://trello.com/card/toolshed-galaxyproject-org-url-redirects/506338ce32ae458f6d15e4b3/697
>> 
>> Thanks!
>> 
>> 
>> On Mar 6, 2013, at 6:52 AM, Peter Cock wrote:
>> 
>>> Hello all,
>>> 
>>> Either I made a typo in some old README files, or the old
>>> URL for the Tool Shed http://community.g2.bx.psu.edu/ has
>>> stopped working. Could this redirect to the current Tool Shed
>>> address http://toolshed.g2.bx.psu.edu/ please?
>>> 
>>> Thanks,
>>> 
>>> Peter
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>> 
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Re: [galaxy-dev] Installation failure on Test Tool Shed

[Greg Von Kuster]

Hi Peter,

I've created the following Trello card for this - we'll take a look and get 
this resolved as soon as possible.

https://trello.com/c/G5hZEajv/210-tool-dependency-installation-may-not-be-properly-handling-broken-package-urls

Thanks for reporting this!

Greg Von Kuster


On May 21, 2014, at 7:00 AM, Peter Cock  wrote:

> On Mon, May 12, 2014 at 11:40 AM, Peter Cock  
> wrote:
>> On Wed, May 7, 2014 at 3:01 PM, Peter Cock  wrote:
>>> Hi Dave,
>>> 
>>> Can you tell me any more about this failed tool dependency error:
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
>>> 
>>> Installation errors
>>> Tool dependencies
>>> TypeNameVersion
>>> MIRA package 4.0
>>> Error
>>> File 
>>> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py",
>>> line 345, in install_and_build_package_via_fabric tool_dependency =
>>> fabric_util.install_and_build_package( app, tool_shed_repository,
>>> tool_dependency, actions_dict ) File
>>> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py",
>>> line 93, in install_and_build_package initial_download=False ) File
>>> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
>>> line 418, in execute_step initial_download=initial_download ) File
>>> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
>>> line 1312, in execute_step return_output=False ) File
>>> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
>>> line 247, in handle_command output = self.handle_complex_command(
>>> command ) File 
>>> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
>>> line 287, in handle_complex_command cwd=state.env[ 'lcwd' ] ) File
>>> "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread,
>>> errwrite) File "/usr/lib/python2.7/subprocess.py", line 1308, in
>>> _execute_child raise child_exception [Errno 2] No such file or
>>> directory: 
>>> '/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpxFCguW/tmp-toolshed-mtdt0b857/MIRA'
>>> 
>>> I presume this was a Python stack trace but the whitespace
>>> has been lost when rendered as HTML. However, I don't quite
>>> see what is going wrong here...
>> 
>> Still failing. This is presumably something in my tool_dependencies.xml
>> which is breaking... that defines 
>> 
>> I've recently been changing the download URL - is it possible that
>> the ToolShed didn't catch a failed download?
>> 
>> Thanks,
>> 
>> Peter
> 
> I'm pretty sure the above failure is down to a broken URL - due to
> a change on the project files for MIRA, see:
> http://www.freelists.org/post/mira_talk/Stable-download-URLs-on-sourceforge
> 
> If I am right, then the ToolShed is not handling the failed download nicely?
> 
> I've just updated this to download MIRA v4.0.2, so fingers crossed...
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
> 
> Peter
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Re: [galaxy-dev] Main ToolShed wrong report: Repository does not have a test-data directory.

[Greg Von Kuster]

Hi Peter,

I've looked into this as well and again believe it is caused by a problem in 
the buildbot configuration for the main Tool Shed's Install and Test framework. 
 I've created the following Trello card for this, and we'll get it resolved 
when Dave B returns next week.

https://trello.com/c/9mLrFhTJ/209-install-and-test-framework-does-not-locate-test-data-directory-for-repositories-on-main-tool-shed

Greg Von Kuster

On May 26, 2014, at 6:54 AM, Peter Cock  wrote:

> Hi guys,
> 
> I just noticed two of my tools on the main ToolShed were listed under
> "Latest revision: missing tool tests" unexpectedly.
> 
> http://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
> 
> Test runs
> 2014-05-25 15:12:04
>Automated test environment
>Tools missing tests or test data
>Tool id: sample_seqs
>Tool version: 0.0.1
>Tool guid: 
> toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.0.1
>Missing components:
>Repository does not have a test-data directory.
> 2014-05-13 01:43:51
>Automated test environment
>Tests that passed successfully
>Successful installations
> 2014-05-11 01:38:18
>Automated test environment
>Tests that passed successfully
>Successful installations
> 2014-05-09 01:43:58
>Automated test environment
>Tests that passed successfully
>Successful installations
> 2014-05-07 01:55:08
>Automated test environment
>Tests that passed successfully
>Successful installations
> 
> And, http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
> 
> Test runs
> 2014-05-25 15:10:53
>Automated test environment
>Tools missing tests or test data
>Tool id: get_orfs_or_cdss
>Tool version: 0.0.5
>Tool guid: 
> toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.5
>Missing components:
>Repository does not have a test-data directory.
> 2014-05-13 05:11:12
>Automated test environment
>Tests that passed successfully
>Successful installations
> 2014-05-11 05:06:15
>Automated test environment
>Tests that passed successfully
>Successful installations
> 2014-05-09 05:17:53
>Automated test environment
>Tests that passed successfully
>Successful installations
> 2014-05-07 05:52:29
>Automated test environment
>Tests that passed successfully
>Successful installations
> 
> In both cases the most recent test run (2014-05-25) has failed in some
> way, and the ToolShed *wrongly* reports the repository does not have
> a test-data directory.
> 
> Regards,
> 
> Peter
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Re: [galaxy-dev] New tool on TestToolShed still not tested

[Peter Cock]

Thanks - I'll leave this until next week then.

Peter

On Tue, May 27, 2014 at 3:05 PM, Greg Von Kuster  wrote:
> Hello peter,
>
> I've looked inot this and discovered what I suspect is a problem with
> the buildbot configuration for the Tool Shed's install and test framework.
> The framework is executed in 2 stages where stage 1 installs and tests
> repositories that contain tool dependency packages, and stage 2 installs
> and test repositories that contain tools the require them.  For the past
> few test runs, only stage 1 executes, so no repositories that contain
> tools are tested (this affects all stage 2 repositories, not just yours).
> The buildbot environment is Dave B's realm (I've not been involved in
> setting it up), so he'll have to take a look to see what may be the problem.
> Unfortunately, Dave is out of the lab this week, so we'll have to wait until
> next week to get this resolved.
>
> Sorry for the inconvenience on this, and the unfortunate timing with Dave 
> being out.
>
> I've added the following Trello card for this issue:
>
> https://trello.com/c/YElEsCWl/208-install-and-test-framework-stage-2-does-not-run
>
> Greg Von Kuster
>
>
> On May 26, 2014, at 6:46 AM, Peter Cock  wrote:
>
>> Hi guys,
>>
>> I updated this new tool on Wednesday last week, but it still
>> has no functional test results:
>>
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
>>
>> Has it been excluded for some reason? If so, could some
>> indicator be shown (at least to the tool authors)?
>>
>> I looked over some of my other tools and the test dates
>> are quite variable. I thought you had gone from nightly
>> tests to every second night - but is the scheme now more
>> complex, or have there been technical difficulties?
>>
>> Thanks,
>>
>> Peter
>> ___
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>>
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>>  http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] New tool on TestToolShed still not tested

[Greg Von Kuster]

Hello peter,

I've looked inot this and discovered what I suspect is a problem with the 
buildbot configuration for the Tool Shed's install and test framework.  The 
framework is executed in 2 stages where stage 1 installs and tests repositories 
that contain tool dependency packages, and stage 2 installs and test 
repositories that contain tools the require them.  For the past few test runs, 
only stage 1 executes, so no repositories that contain tools are tested (this 
affects all stage 2 repositories, not just yours).  The buildbot environment is 
Dave B's realm (I've not been involved in setting it up), so he'll have to take 
a look to see what may be the problem.  Unfortunately, Dave is out of the lab 
this week, so we'll have to wait until next week to get this resolved.

Sorry for the inconvenience on this, and the unfortunate timing with Dave being 
out.  

I've added the following Trello card for this issue:

https://trello.com/c/YElEsCWl/208-install-and-test-framework-stage-2-does-not-run

Greg Von Kuster


On May 26, 2014, at 6:46 AM, Peter Cock  wrote:

> Hi guys,
> 
> I updated this new tool on Wednesday last week, but it still
> has no functional test results:
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
> 
> Has it been excluded for some reason? If so, could some
> indicator be shown (at least to the tool authors)?
> 
> I looked over some of my other tools and the test dates
> are quite variable. I thought you had gone from nightly
> tests to every second night - but is the scheme now more
> complex, or have there been technical difficulties?
> 
> Thanks,
> 
> Peter
> ___
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Re: [galaxy-dev] Changes in admin menu - Upload files

[Dannon Baker]

Cross-post from biostar, answered there:
https://biostar.usegalaxy.org/p/7747/#7760


On Mon, May 26, 2014 at 6:47 AM, Julien Daligault <
daliga...@ijm.univ-paris-diderot.fr> wrote:

> Hi,
>
> I manage a galaxy instance on a local server and I want that users use
> only the "filesystem paths" to create a link to their data by the Admin
> Menu. Where can I find the source file to modify the web page in order to
> appear directly this option in first in the drop-down menu ?
> It will avoid to load directly big data on our computing machine.
> Thanks
>
> Julien
>
> --
> Julien Daligault
> Plateforme Génomique-Transcriptomique (583B)
> INSTITUT JACQUES MONOD
> CNRS-Université Paris Diderot
> Bât. Buffon - 15 rue Hélène Brion
> 75205 Paris Cedex 13 - France
> tel : +33 1 57 27 81 31
> daliga...@ijm.univ-paris-diderot.fr
>
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[galaxy-dev] Changes in admin menu - Upload files

[Julien Daligault]

Hi,

I manage a galaxy instance on a local server and I want that users use 
only the "filesystem paths" to create a link to their data by the Admin 
Menu. Where can I find the source file to modify the web page in order 
to appear directly this option in first in the drop-down menu ?

It will avoid to load directly big data on our computing machine.
Thanks

Julien

--
Julien Daligault
Plateforme Génomique-Transcriptomique (583B)
INSTITUT JACQUES MONOD
CNRS-Université Paris Diderot
Bât. Buffon - 15 rue Hélène Brion
75205 Paris Cedex 13 - France
tel : +33 1 57 27 81 31
daliga...@ijm.univ-paris-diderot.fr

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Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

[Dannon Baker]

Hey Eric,

It looks like you have connection info for both tcp/ip connections and unix
sockets in the connection strings.  If you're logging in using "psql -h
wigserv5.cshl.edu ", then you only want the tcp/ip connection info.
 Drop the ?host=tmp off the third option you listed and I think you'll be
up and running, so:

postgresql://glxeric:xx...@wigserv5.cshl.edu:5432/glxeric

-Dannon


On Sat, May 24, 2014 at 1:49 AM, Paniagua, Eric  wrote:

> Dear Galaxy Developers,
>
> I've been banging my head against this one for a few days now.
>
> I have two Galaxy instances.  One resides on a server called "genomics",
> which also hosts the corresponding PostgreSQL installation.  The second
> also resides on "genomics", but its database is hosted on "wigserv5".
>
> Based on the tests I just ran and code I just read, sqlalchemy (not
> Galaxy) is ignoring the hostname/port part of the database_connection
> string.  For reference, the connection strings I've tried are:
>
> postgresql://glxeric:X@/glxeric?host=/tmp
> postgresql://glxeric:xx...@wigserv5.cshl.edu/glxeric?host=/tmp
> postgresql://glxeric:xx...@wigserv5.cshl.edu:5432/glxeric?host=/tmp
> postgresql://glxeric:X@adgdgdfdflkhjfdhfkl/glxeric?host=/tmp
>
> All of these appear to result in Galaxy connecting to the PostgreSQL
> installation on genomics, as determined by Galaxy schema version
> discrepancies and other constraints.  With each connection string, Galaxy
> starts up normally.  I force database activity by browsing saved histories.
>  It works every time.  By all appearances, the second Galaxy instance is
> using the PostgreSQL database hosted on "genomics", not on "wigserv5".
>
> All databases and roles exist, and the databases are populated.
>
> When I comment out the "database_connection" line in universe_wsgi.ini, I
> get errors arising from the later configuration of PostgreSQL-specific
> Galaxy options, as expected.
>
> I can connect to the database server on "wigserv5" using "psql -h
> wigserv5.cshl.edu -d glxeric -U glxeric" from the server "genomics".
>
> Have you ever observed this behavior from Galaxy or sqlalchemy?
>
> Thanks,
> Eric
>
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