pages problems - inserting one of many datasets
by Anno Nemus
Firstly, thanks for Galaxy - it's great!
I have a lot of items in various histories and I think I can reproduce what
looks like 2 bugs in editing user pages, using either latest chrome and
firefox on ubuntu 11.10 on Main
First bug - cannot choose anything to insert to a page once the second or
subsequent pages of multiple history items are showing when trying to
insert a dataset into a page
choose: User | saved pages
Create a new page and edit content
choose: insert a link to a galaxy object | insert dataset link
A small window opens with the start of many pages of history items - the
box is too small but if you scroll down you see Insert/Cancel action buttons
Select the next page (#2)
The small window opens up to the full screen - but the insert/cancel
buttons are no longer there and you can scroll through the list of history
items but you can't seem to get back
to those buttons. Even from the second page, the browser back button takes
me back to the edit page screen and the #1 link takes me back to the first
page without any insert/cancel options.
It seems that you can't select any dataset that's not on the first page to
insert?
Search can be used to limit the options and select a history item so I've
managed to kind of get things to work bur ir sure isn't easy.
Second bug: Once you've used the search option on the list of datasets,
all the other pages of history items are gone - even if you remove the
search term - it doesn't resume the paging mode properly so you have to go
back to the main edit screen and start again.
Thanks!
10 years, 7 months
How to add tag in tool xml file
by sshashi
Hi,
How to add a new tag in tool_xml file.is there any possibility to add a
tag in tool xml file ?
Regards
shashi
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10 years, 7 months
Which css file does welcome.html use?
by Dorset, Daniel C
OK, this is ostensibly a simple question. However, I can't find the CSS file that welcome.html is using. In the HTML file, there's this line:
<link rel="stylesheet" href="style/base.css" type="text/css" />
However, I don't see a directory named "style" anywhere in the galaxy directory tree. When I search for "base.css," from the root Galaxy installation directory, I get the following results:
./static/june_2007_style/blue/base.css
./static/light_hatched_style/blue/base.css
./static/light_hatched_style/green/base.css
./static/old_blue_style/base.css
So I assume that one of these is being used? I do think it's strange though, that the HTML points to an apparently non-existent file and yet everything on my local instance looks identical to the Penn State Public site.
Thanks,
Dan
10 years, 7 months
can not login to workflows after postgresql setup
by J.W.F.van_der_Heijden＠lumc.nl
Hi all,
I have set up postgresql to work with galaxy because the standard mysqlite didn't work with my workflow.
Now that postgresql seems to be working I can not login to galaxy. When I try to login it says that it can't find my username. And also when I click "forgot password" it says: "Mail is not configured for this Galaxy instance. Please contact an administrator."
Any ideas?
Kind Regards
Jaap
10 years, 7 months
History items get REMOVED when using the API to run workflows
by Thon Deboer
Hi,
I am continueing to struggle with the API....
I have created a workflow execution engine that submits a workflow using the examples in the API (scripts/api).
When I run the WF on data in the LIBRARIES everything works fine.
But when I choose a HISTORY as my source of data, the WF executes fine, but the history I use is emptied of all the files in there!
This is very bizarre....Any ideas what is going on here?
I know not a lot of people are using the API, but it is the only way I can run paired end WF on more than a couple of samples...
Regards,
Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839
thondeboer(a)me.com
LinkedIn Profile
10 years, 7 months
Has anyone implemented PINDEL as a tool in their GALAXY
by Anthonius deBoer
Hi,
I am about to embark of embedding PINDEL into GALAXY since it is not available in the TOOLSHED.
Before I do, I thought I check if someone has already done this and could send me their XML so I don't have to start from scratch...
Thanks!
Thon
10 years, 7 months
Interested in speaking with other institutions deploying Galaxy locally?
by Ann Black-Ziegelbein
Hi everyone -
Here at the University of Iowa we are working on deploying Galaxy
locally for campus wide access. I am interested in forming a community
of other institutions trying to deploy Galaxy locally and mange/operate
it on a broad level. Is anyone else? If there is enough interest,
possibly we could have a community conference call every other month to
have an open discussion on how we are all deploying galaxy,
customizations we are making, problems we are encountering, bugs, and
any add-on operations management for galaxy being developed, etc.
Would love to hear from others operating Galaxy or in process of
standing up a local deployment.
Thanks!
Ann Black-Ziegelbein
10 years, 7 months
Looking for recommendations: How to run galaxy workflows in batch
by Dave Lin
Hi All,
I'm looking to batch process 40 large data sets with the same galaxy
workflow.
This obviously can be done in a brute-force manual manner.
However, is there a better way to schedule/invoke these jobs in batch
1) from the UI with a plugin
2) command-line
3) web-service
Thanks in advance for any pointers.
Dave
10 years, 7 months
Liftover tool installation woes
by Kwon SoonJae
Hi Everyone,
I installed a local instance of galaxy and some tools using the command
line, and for some reason liftover will work in the command line but won't
work in galaxy. Here's what I've done so far:
- Downloaded liftover standalone executable from the tool-dependencies page
in the Gwiki.
- Changed permissions on liftover executable to make it usable in the
command prompt (terminal, macosx) -> otherwise I get permission denied.
- Copied executable over to /usr/local/bin likewise to use in command
prompt and in Galaxy.
- Modified liftover.loc to include all the conversion types and directories
of chain.gz files I downloaded to use with the tool (I believe liftover can
make use of both .chain and .chain.gz files).
After that I tried to run liftover in Galaxy and it didn't work, giving me
some error that said hg19ToMm9 mapping is currently not available. It seems
to work fine using the command line though.
Since my goal is to setup galaxy locally, I really want to get this working
correctly. Can anyone guide me through what's gone wrong?
Also, there must be a better way of installing all these tools than
manually downloading every single one and using the command line, surely? I
had to type out the format of liftover.loc file manually for around 130
chain files... I'm convinced there has to be a better way.
Thanks in advance,
SJ
10 years, 7 months
Display with IGV local
by Chebbi Mohamed Amine
HI Galaxy-team !
I 'am trying to display BAM files whith the * local* IGV.
However D*isplay with IGV "local*" use the already running copy of IGV on
the server machine. So I need evry time to run manually igv by the command
above:
java -Xmx750m -jar igv.jar
Is there any way to do this automatically
I guess that I have to configure bam.xml file to call "java -Xmx750m -jar
igv.jar" command , when cliking on D*isplay with IGV local*. ?
Thanks for help
Regards
Amine
10 years, 7 months
