[galaxy-dev] How to unsubscribe - was: Re: RFC: Citations for tools
Hi Shari
Have a look at the last few lines of the e-mail:
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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
jmccus...@5amsolutions.com 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 p.j.a.c...@googlemail.com
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 ja...@jamestaylor.org
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
rasche.e...@yandex.ru mailto:rasche.e...@yandex.ru wrote:
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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 citation 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:
tool
...
citation type=book
authorMilton Abramowitz and Irene A. Stegun/author
titleHandbook of Mathematical Functions with Formulas,
Graphs, and
Mathematical Tables/title
publisherDover/publisher
year1964/year
addressNew York/address
editionninth Dover printing, tenth GPO printing/edition
/citation
/tool
Cheers,
Eric
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas AM University
College Station, TX 77843
404-692-2048
e...@tamu.edu mailto:e...@tamu.edu
rasche.e...@yandex.ru mailto:rasche.e...@yandex.ru
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Re: [galaxy-dev] complex help for conditional param
Hi Jun, Thanks for the clarification - I did not read your question carefully enough, sorry. I don't think this is possible. What I would use is just: param name=type type=select label=BLAST type option value=blastnBLASTN, for DNA against DNA/option option value=blastpBLASTP, for protein against protein/option /param Regards, Peter On Tue, May 27, 2014 at 10:29 PM, Jun Fan j@qmul.ac.uk wrote: 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: conditional name=blast param name=type type=select label=BLAST type option value=blastnBLASTN/option option value=blastpBLASTP/option /param when value=blastn helpBLAST DNA against DNA/help param... /when when value=blastp helpBLAST protein against protein/help param... /when /conditional 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 help under select param like param name=type type=select label=BLAST type helpBLASTN: BLAST DNA against DNA, BLASTP: BLAST protein against protein/help option value=blastnBLASTN/option 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 ___ 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 (Dannon Baker)
Hey Eric, The connection string dialect is as follows for TCP/IP connections: dialect+driver://username:password@host:port/database So, the host=/tmp is not necessary when are specifying a hostname (resolves to the IP) and a port because that is referring to UNIX sockets. If you were using SQL Alchemy with a unix socket to connect to the postgres server, then it would look something like this. postgresql+psycopg2://user:password@/dbname?host=/var/lib/postgresql Note that there's no hostname and port. Just the socket is specified. See http://docs.sqlalchemy.org/en/rel_0_9/core/engines.html for more info. Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science Technology Branch Agriculture Agri-Food Canada iyad.kandal...@agr.gc.ca | (613) 759-1228 From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of galaxy-dev-requ...@lists.bx.psu.edu [galaxy-dev-requ...@lists.bx.psu.edu] Sent: May 27, 2014 12:00 PM To: galaxy-dev@lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 95, Issue 25 Send galaxy-dev mailing list submissions to galaxy-dev@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-ow...@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than Re: Contents of galaxy-dev digest... HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from Galaxy-dev Digest Vol ... to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Dannon Baker) 2. Changes in admin menu - Upload files (Julien Daligault) 3. Re: Changes in admin menu - Upload files (Dannon Baker) 4. Re: New tool on TestToolShed still not tested (Greg Von Kuster) 5. Re: New tool on TestToolShed still not tested (Peter Cock) 6. Re: Main ToolShed wrong report: Repository does not have a test-data directory. (Greg Von Kuster) 7. Re: Installation failure on Test Tool Shed (Greg Von Kuster) 8. Re: Old Tool Shed URL http://community.g2.bx.psu.edu/ dead (Greg Von Kuster) 9. Re: ToolShed: Uploaded archives can only include regular directories and files (Greg Von Kuster) 10. Re: Old Tool Shed URL http://community.g2.bx.psu.edu/ dead (Peter Cock) 11. Re: ToolShed: Uploaded archives can only include regular directories and files (Peter Cock) 12. Re: Old Tool Shed URL http://community.g2.bx.psu.edu/ dead (Greg Von Kuster) 13. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Paniagua, Eric) 14. Uploading files to galaxy from a folder (Kandalaft, Iyad) 15. complex help for conditional param (Jun Fan) 16. Re: complex help for conditional param (Peter Cock) 17. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Dannon Baker) 18. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Paniagua, Eric) 19. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Dannon Baker) -- Message: 1 Date: Tue, 27 May 2014 07:40:13 -0400 From: Dannon Baker dannon.ba...@gmail.com To: Paniagua, Eric epani...@cshl.edu Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host Message-ID: cagn_wzn7wkihvyidhlovl0j4cbu_xeem02n1fkggo8bcnyc...@mail.gmail.com Content-Type: text/plain; charset=utf-8 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 snip, 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 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 also hosts the corresponding PostgreSQL installation. The second also resides on genomics, but its database is hosted
[galaxy-dev] Changes in admin menu - Upload files
Hi Julien Do you mean that you want users to only upload files to data libraries and use the link to files option instead of copy files into galaxy? Can you describe your infrastructure setup so that I can provide you with a good response. From what I understand, you have SERVER A with a galaxy install and SERVER B is your compute machine? Galaxy is submitting jobs to SERVER B for analysis/processing? Or do you only have 1 server with Galaxy on it and it is also doing the processing? Do you have a storage array to house the data? Regards, Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science Technology Branch Agriculture Agri-Food Canada iyad.kandal...@agr.gc.ca | (613) 759-1228 From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of galaxy-dev-requ...@lists.bx.psu.edu [galaxy-dev-requ...@lists.bx.psu.edu] Sent: May 27, 2014 12:00 PM To: galaxy-dev@lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 95, Issue 25 Send galaxy-dev mailing list submissions to galaxy-dev@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-ow...@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than Re: Contents of galaxy-dev digest... HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from Galaxy-dev Digest Vol ... to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Dannon Baker) 2. Changes in admin menu - Upload files (Julien Daligault) 3. Re: Changes in admin menu - Upload files (Dannon Baker) 4. Re: New tool on TestToolShed still not tested (Greg Von Kuster) 5. Re: New tool on TestToolShed still not tested (Peter Cock) 6. Re: Main ToolShed wrong report: Repository does not have a test-data directory. (Greg Von Kuster) 7. Re: Installation failure on Test Tool Shed (Greg Von Kuster) 8. Re: Old Tool Shed URL http://community.g2.bx.psu.edu/ dead (Greg Von Kuster) 9. Re: ToolShed: Uploaded archives can only include regular directories and files (Greg Von Kuster) 10. Re: Old Tool Shed URL http://community.g2.bx.psu.edu/ dead (Peter Cock) 11. Re: ToolShed: Uploaded archives can only include regular directories and files (Peter Cock) 12. Re: Old Tool Shed URL http://community.g2.bx.psu.edu/ dead (Greg Von Kuster) 13. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Paniagua, Eric) 14. Uploading files to galaxy from a folder (Kandalaft, Iyad) 15. complex help for conditional param (Jun Fan) 16. Re: complex help for conditional param (Peter Cock) 17. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Dannon Baker) 18. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Paniagua, Eric) 19. Re: Problem using Galaxy with a PostgreSQL database on a remote host (Dannon Baker) -- Message: 1 Date: Tue, 27 May 2014 07:40:13 -0400 From: Dannon Baker dannon.ba...@gmail.com To: Paniagua, Eric epani...@cshl.edu Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host Message-ID: cagn_wzn7wkihvyidhlovl0j4cbu_xeem02n1fkggo8bcnyc...@mail.gmail.com Content-Type: text/plain; charset=utf-8 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 snip, 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 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 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
Re: [galaxy-dev] Old Tool Shed URL http://community.g2.bx.psu.edu/ dead
Hi all, This has been fixed. Sorry for the trouble, I am not sure when it disappeared. --nate On Tue, May 27, 2014 at 11:19 AM, Greg Von Kuster g...@bx.psu.edu wrote: 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 p.j.a.c...@googlemail.com wrote: On Tue, May 27, 2014 at 3:39 PM, Greg Von Kuster g...@bx.psu.edu 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 ___ 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/
