Multiple fastq files per forward/reverse mates (tophat and related tools)
by W. Augustine Dunn III
I want to customize the tophat and related interfaces to allow more than one
fastq file per fwd/rev set as is allowed and very helpful in the CLI
version:
$ tophat -o output -p 8 -r 125 -G annotation.gtf myBowtieIndex
run1_fwd.fastq,run2_fwd.fastq run1_rev.fastq,run2_rev.fastq
Is there a way to select multiple items from a dropdown menu or can/should i
convert that part of the interface to a text input field so I can simply
feed the command a list of files like on the command line? This last method
seems like it might be a little unsafe though. But even if its not, it
divorces the file management from the history which seems like its not a
good idea.
Has anyone done this?
Thanks,
Gus
--
In science, "fact" can only mean "confirmed to such a degree that it would
be perverse to withhold provisional assent." I suppose that apples might
start to rise tomorrow, but the possibility does not merit equal time in
physics classrooms.
*-Stephen Jay Gould*
11 years, 6 months
fyi: can't upload to toolshed
by Edward Kirton
Server ErrorAn error occurred. See the error logs for more information.
(Turn debug on to display exception reports here)
11 years, 6 months
Sending Data to Galaxy
by Amirhossein Kiani
Hey Galaxy developers!
I was wondering if anyone knows how to send data to a local galaxy instance from another server (I'm interested in sending a BAM file to Galaxy). I see that UCSC and others have done it but couldn't find anything about the API doc they are using...
Looking at the request headers from UCSC, I see that this request:
tool_id:bx_browser
URL:http://main.genome-browser.bx.psu.edu/cgi-bin/hgTables
hguid:883956
db:hg18
org:Human
hgta_table:seq
hgta_track:gold
hgta_regionType:genome
hgta_outputType:primaryTable
position:chr10:90997300-90997350
hgta_doTopSubmit:get output
hgsid:62857
hgta_doGalaxyQuery:Send query to Galaxy
has been sent to:
http://main.g2.bx.psu.edu/tool_runner
Is this all needed? If so how is the URL to the data file passed to Galaxy?
Many thanks!
Amir
11 years, 6 months
more cleanup scripts messages
by Assaf Gordon
Hi Greg (again),
This patch adds messages for the "purge histories" step:
1. A message is printed when processing a new history (so that the user can tell to which history the following dataset/hda messages belong).
2. in "info_only" mode, a message is printed about each deleted history
3. in "info_only" mode, a message is printed for each HDA that is checked
4. The message for HDA is changed to include the associated dataset id.
Comments are welcomed,
-gordon
11 years, 6 months
Saved Histories - default view on deleted histories (bug)
by Michal Stuglik
hi all,
in galaxy-central:
1. default view in "Saved Histories" section is set on deleted items (
Jeremy, I did double check this morning on fresh instance :))
2. in advanced search option: one of the filter switch is deleted and
does the same job as active switch
3. Sugestion:
Saved Histories->Advanced Search
sharing: private | shared | accessible | published | all
deleted: active | deleted | all
maybe it is better to change it to:
sharing: private | shared | accessible | published | all
status: active | deleted | all
I think "deleted" is not clear..
all the best,
michal
11 years, 6 months
toolExample.pl script bug report
by Casey Bergman
Dear Galaxy Team -
We stumbled across a potential bug in the toolExample.pl script on the Galaxy Add Tool Tutorial today:
http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial
In our hands, this script only works on fasta files that contain >1 sequence, and reports gc content only for the first n-1 sequences.
If you could confirm this and modify if possible, this might help other users.
All the best,
Casey Bergman, Ph.D.
Faculty of Life Sciences
University of Manchester
Michael Smith Building
Oxford Road, M13 9PT
Manchester, UK
Tel: +44-(0)161-275-1713
Lab: +44-(0)161-275-5980
Fax: +44-(0)161-275-5082
skype: caseymbergman
Email: casey.bergman(a)manchester.ac.uk
Web: http://bergmanlab.smith.man.ac.uk/
11 years, 6 months
Possible to re-use toolconfig xml files outside Galaxy?
by Samuel Lampa
Hi,
I have been looking into re-using the galaxy toolconfig xml files
outside galaxy, for auto-generating wizards for command line tools, in
an own little (eclipse based) software (For a short background, see [1]).
I have come to realize though that the xml-files are not really
independent, but (almost?) always is accompanied by a correpsonding .py
file, which does more or less tricks, which seemingly makes it very hard
to use the xml-files outside a galaxy/python environment at all.
My questions:
1. Are the xml-files *always* accompanied by the .py file, or is that
optional?
2. Would my idea be possible/reasonable at all?
3. Are there other more general tool config formats that I could use,
since I'm not using galaxy atm?
4. Any other suggestions or ideas?
Best Regards
// Samuel
[1]: The tool is built as a complement to some galaxy initiatives at the
UPPMAX HPC Center in Uppsala. Specifically we need a light-weight way to
configure batch scripts for the software installed at UPPMAX, of which
bioinformatics tools are just a part. The galaxy toolconfig xml-format
looked useful though, and seemed to enable us to have at least most of
our bioinformatics tools (the category with most installed tools at
UPPMAX) already configured.
--
System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
--------------------------------------
E-mail: samuel.lampa(a)scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se
11 years, 6 months
removing "Select All" / "Unselect All" buttons from a set of check boxes
by Hans-Rudolf Hotz
Hi
Is there a way to remove the "Select All" and "Unselect All" buttons
from a set of check boxes? - crated with:
<param name="samples" type="select"
display="checkboxes" multiple="true"
dynamic_options="ds_samplesFromServer()"/>
I have a very long list, and I don't want to encourage people to tick
all boxes.
Thank you very much for your help, Hans
11 years, 6 months
empty status for non-empty datasets
by Shantanu Pavgi
Hi,
In our local galaxy install (currently revision 50e249442c5a) we are seeing few output datasets as 'empty' in the galaxy web interface. The actual file size on the filesystem is ~ 4GB. These 'empty' files can be downloaded by clicking on download/view icons, however they can't be imported in other workflows. I looked into the database and figured out that file_size column value for corresponding dataset id is zero. I am guessing that's why it is being shown as empty in the web interface. Any suggestions on how to resolve this will be helpful.
--
Thanks,
Shantanu.
11 years, 6 months
Re: [galaxy-dev] LAJ Error
by Ellul Jason
Hi All,
I have been able to workaround the problem I was having by modifying the LAJ_code.py to include 'and data != None' on each of the elif statements.
i.e.
if name == "maf_input":
params["alignfile1"] = "display?id=%s" % data.id
elif name == "seq_file1" and data != None and data.state == data.states.OK and data.has_data():
params["file1seq1"] = "display?id=%s" % data.id
elif name == "seq_file2" and data != None and data.state == data.states.OK and data.has_data():
params["file1seq2"] = "display?id=%s" % data.id
elif name == "exonfile" and data != None and data.state == data.states.OK and data.has_data():
params["exonfile"] = "display?id=%s" % data.id
elif name == "repeatfile" and data != None and data.state == data.states.OK and data.has_data():
params["repeatfile"] = "display?id=%s" % data.id
elif name == "annotationfile" and data != None and data.state == data.states.OK and data.has_data():
params["annotationfile"] = "display?id=%s" % data.id
elif name == "underlayfile" and data != None and data.state == data.states.OK and data.has_data():
params["underlayfile"] = "display?id=%s" % data.id
elif name == "highlightfile" and data != None and data.state == data.states.OK and data.has_data():
params["highlightfile"] = "display?id=%s" % data.id
For some reason, even though repeatfile is optional the script always thinks that a file has been selected, even when one has not. Hence data is equal to None and it throws a 'nonetype has no attribute state' error when it checks data.state==data.states.OK.
Could a developer please look into why it would think a file for the option repeatfile had been selected when one hasn't.
Cheers,
--
Jason Ellul
Bioinformatician
Cancer Research Division
Peter MacCallum Cancer Centre
TEL: +61 3 9656 1512
FAX: +61 3 9656 1411
EMAIL: jason.ellul(a)petermac.org
Address: St Andrew's Place East Melbourne Victoria 3002 Australia
Postal Address: Locked Bag No. 1 A'Beckett St., Victoria, 8006, Australia
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11 years, 6 months
