Re: [galaxy-dev] [gsoc2017-papers] Project Publication Reference Tracking Tool -- are you interested in?

[Dave Clements]

Hi Anton,

We've already got folks from the Galaxy Project, Reactome, InterMine, and
BioPython on board.  And now several more folks are on the Gitter channel
as well.  I think we may end up with too many people involved.  *(But
that's the kind of problem I want to have!  :-)*

Also, the project isn't about biology per se. It's about finding papers
that reference software projects often in indirect ways.  The software can
be from any domain.

And I would argue that identifying where to search and what to search for
is up to the people using the software (for example, me), rather than the
person developing the software (Chris).

Questions?  I suggest continuing this conversation on gitter
.

Cheers,

Dave C


On Mon, May 15, 2017 at 6:00 AM, Anton Nekrutenko  wrote:

> Krzysztof:
>
> This can be very interesting potentially. However, to be useful such a
> tool needs to take into account how real-world researchers (biologists)
> perform literature searches. Do you have someone who can guide in
> understanding this "very non-linear" process?
>
>
> a.
>
> Anton Nekrutenko
> Professor of Biochemistry
> and Molecular Biology
> Penn State University
> http://nekrut.bx.psu.edu
> (814) 826-9628
>
>
> On Mon, May 15, 2017 at 1:14 AM, Krzysztof Kutt 
> wrote:
> >
> > Hi!
> >
> > We do not know each other yet, so I will briefly introduce myself.
> >
> > I'm Chris, a Polish PhD candidate in Computer Science field at AGH
> University of Science and Technology in Krakow. In my work I deal with the
> broad concept of artificial intelligence. In particular the semantic web
> technologies (RDF, SPARQL, Linked Data) and the ability to support a group
> of knowledge engineers who create knowledge inside (semantic) wiki systems
> - in my PhD I propose some methods and prototypical tools for quality
> management, change management and motivation. I have also finished the
> Master's degree in Psychology and as a result I also deal with Affective
> Computing field.
> >
> > I know, I'm quite far away from bioinformatics :) so, what I am doing
> here?
> > As a part of Google Summer of Code program I will prepare a tool to keep
> track of publications that reference a specific project (project's papers,
> tools, etc). I think that at the end it will be a quite good tool that any
> researcher can use for dealing with the task, regardless of the research
> field.
> >
> > Specifically, it will be a set of Python scripts + GUI that will do four
> tasks:
> > 1) performs database search for new projects (search terms),
> > 2) handles alerts for updating the results later,
> > 3) gives the user the possibility to manually annotate results (e.g. as
> irrelevant),
> > 4) generates citation reports (e.g. list of papers that cite our project
> during last year).
> >
> > If you are interested in such a tool, do not hesitate to:
> > * read the more detailed description placed in the project's github
> wiki: https://github.com/kkutt/references-tracking/wiki/Tool-Description
> > * discuss it on the Gitter channel: https://gitter.im/references-
> tracking/Lobby or simply write me an e-mail
> > We already have interest from members of the Galaxy, Reactome,
> InterMine, and BioPython communities.
> > I am waiting for your comments :)
> >
> > If you are not interested in a project, maybe your colleagues are? :)
> >
> > Best regards,
> > Chris Kutt
> >
> > ___
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>


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Re: [galaxy-dev] location of history id

[John Chilton]

(Once more with the list cc'ed - sorry for the duplicate message.)

The IDs are encoded before they are shared out via the API so that raw
integers aren't exposed. The ID the API returns is generally the value
in the id column for that table.

Eric Rasche kindly contributed a script to the development version of
Galaxy that converts IDs

python scripts/secret_decoder_ring.py decode 

You can probably add the script to older versions of Galaxy and it
will work: 
https://github.com/galaxyproject/galaxy/blob/dev/scripts/secret_decoder_ring.py.

I hope this helps and thanks for hacking on Galaxy!

-John

On Wed, May 3, 2017 at 11:05 PM, Aarthi Mohan  wrote:
> Hello all,
>
>
>
> I have a local instance of galaxy version 15.03.1 (this is needed by IRIDA
> tool).
>
>
>
> I have retrieved datasets associated with a history using Bioblend.
>
> I want to confirm, if the history id used in get_histories(hid) or
> show_history(hid) is stored in the database? I have tried searching the
> entire database by mysqldump, and couldn’t find such values in it.
>
> Where else is this id stored and will this be deleted periodically?
>
>
>
> Appreciate your help!
>
>
>
> Thanks,
>
> Aarthi
>
>
> 
>
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Re: [galaxy-dev] Galaxy Start Up Error - Double Requirements, Tempita

[John Chilton]

I've never seen anything like this - have you modified Galaxy's
requirements.txt file or are you using the one that ships with Galaxy?

On Fri, May 12, 2017 at 11:20 AM, Yip, Miu ki  wrote:
> Hi all,
>
> When attempting to start up Galaxy, via the run.sh script, we’re getting the 
> following error:
>
> galaxyd@genomics:/galaxy$ sh run.sh
> Activating virtualenv at .venv
> Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages
> Double requirement given: Tempita==0.5.3.dev0 (from -r requirements.txt (line 
> 155)) (already in Tempita==0.5.3dev (from -r requirements.txt (line 57)), 
> name='Tempita')
>
> This occurs when the start up script is run with the —no-create-venv and 
> without the flag. It looks like there are two “Tempita” items in the 
> requirements.txt, if one of them is removed, it leads to another error about 
> “ethtools”
>
> galaxyd@genomics:/galaxy$ sh run.sh --daemon --no-create-venv
> Activating virtualenv at .venv
> Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages
> ...
> Collecting crypto==1.4.1 (from -r requirements.txt (line 81))
>   Using cached crypto-1.4.1-py2.py3-none-any.whl
> Requirement already satisfied: cycler==0.10.0 in 
> ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82))
> Collecting Cython==0.25.2 (from -r requirements.txt (line 83))
>   Using cached Cython-0.25.2-cp27-cp27mu-manylinux1_x86_64.whl
> Requirement already satisfied: docopt==0.6.2 in 
> ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 86))
> Requirement already satisfied: drmaa==0.7.6 in 
> ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 88))
> Collecting ethtool==0.8 (from -r requirements.txt (line 90))
>   Could not find a version that satisfies the requirement ethtool==0.8 (from 
> -r requirements.txt (line 90)) (from versions: )
> No matching distribution found for ethtool==0.8 (from -r requirements.txt 
> (line 90))
>
> We’re not sure if both versions of “Tempita” are required and if they are, 
> how can the application be started up? Running both the run.sh and the 
> run_reports.sh scripts lead to this error about “Tempita”. Has anyone 
> encountered this error before?
>
> Thanks!
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