Active Directory
by Alexander Kurze
Hi there,
I have a server set up of galaxy. I would like to have a system setup where
people can login via their active directory name and then use their mounted
share drive to download processed data from the galaxy server.
I saw that it is possible via apache to login through the AD, but will the
AD also mount the share drives? If yes, is there a wrapper that allows to
download Galaxy Histories onto the shared drive?
Alex
8 years, 7 months
Active Directory
by Alexander Kurze
Hi there,
I have a server set up of galaxy. I would like to have a system setup where
people can login via their active directory name and then use their mounted
share drive to download processed data from the galaxy server.
I saw that it is possible via apache to login through the AD, but will the
AD also mount the share drives? If yes, is there a wrapper that allows to
download Galaxy Histories onto the shared drive?
Alex
--
Alexander Kurze
70 Sunningwell Road
Oxford, OX1 4SX
Tel: +44 1865-243-609
Mobile: +44 7962-425-865
8 years, 7 months
Add a tool to galaxy
by sun liang
hello all,
We have a transcript classification tool named CNCI, that published on NAR August 6 2013, and the title of this article is "Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts". The source code is writen by python, and can be download at : http://www.bioinfo.org/software/cnci/ .
We would like to add CNCI to galaxy cloudman, and help more researchers in transcriptome analysis community .
If have any question please contact me!
Looking forward to hearing from you soon.
Yours sincerely,
8 years, 7 months
Dynamic tool loading
by Mikel Egaña Aranguren
Hi;
I have developed a tool generator that performs a SPARQL query (defined by
the user) and creates new Galaxy tools depending on result.
I have the basic system (i.e. it generates the tool XML files and edits the
tool_conf.xml in the "traditional" way) but I would like my tool generator
to be a regular Galaxy tool that is able to "inject" the new tools in the
Galaxy menu without having to restart Galaxy. Is there an easy way of doing
so?
I have come across this thread (
http://osdir.com/ml/galaxy-development-source-control/2010-07/msg00094.html)
but it is not clear for me:
- If this change has been implemented in Galaxy.
- If it has been implemented, what should be the output of my tool
generator.
Thanks
Regards
--
Mikel Egaña Aranguren, Ph.D.
http://mikeleganaaranguren.com
8 years, 7 months
Library permission page broken
by David Hoover
After the latest update, the "Manage library permissions" page is broken. The "Roles not associated" boxes are pushed to the left of the frame, and the double arrow buttons are misplaced down the page. This occurs under Safari (5.1.10) and Chrome (31.0.1650.57) on a Mac running OS X 10.6.8. Firefox (25.0.1), however, seems ok.
8 years, 7 months
Error while trying to extract DNA
by Alan WiIliams
Hi,
I am new here. I have a interval file with the columns chr,start,end.
When I run it I get 10 warnings, 1st is: Unable to fetch the sequence
from '172591712' to '3209' for chrom 'chr5'. Skipped 10 invalid lines,
1st is #1, "chr5 172591712 172594921" Which doesn't make sense. Can
someone help?
Thanks,
--
Alan Williams
Life is short, art long, opportunity fleeting, experience deceptive,
judgement difficult.
8 years, 7 months
Compressed data files in Galaxy? (e.g. GZIP or BGZF)
by Peter Cock
Hello all,
What is the current status in Galaxy for supporting compressed files?
We've talked about this before, for example in addition to FASTQ,
many of us have expressed a wish to work with gzipped FASTQ.
I understand that some have customized their local Galaxy
installations to use gzipped FASTQ as a specific data type - I'm
more interested in a general file format neutral solution.
Also, I'd like to be able to used BGZF (not just GZIP) because it
is better for random access - see for example
http://blastedbio.blogspot.com/2011/11/bgzf-blocked-bigger-better-gzip.html
- and makes it much easier to break up large datafiles for sharing
over a cluster (i.e. it could be exploited in the current Galaxy code
for splitting large sequence files).
The 11 May 2012 Galaxy Development News Brief
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-May/009757.html
mentions tabix indexing - that uses bgzip, so is there something
general in place yet to allow tool wrappers to say they accept not just
given file formats, but different compressed versions of file formats?
Ideally I'd like to be able to write an XML tool description saying
a tool produced BGZF compressed tabular data, or GZIP
compressed Sanger FASTQ etc. Similarly, I'd like to specify my
tool accepts FASTA or gzipped FASTA (including BGZF FASTA).
While for older tools if they say they accept only uncompressed
FASTA, Galaxy could automatically decompress any compressed
FASTA entries in my history on demand.
Peter
8 years, 7 months
Why does check_html only read first 100 lines?
by Robert Davidson
Hi all,
I recently tried uploading an couple of xml files to my
local Galaxy installation using the standard ‘Upload File (version 1.1.3)’
tool. For some files this produced the error: The uploaded file contains
inappropriate HTML content.
Given the files had been created by the same automated
code and contained the same tags etc, I couldn't understand why one would
produce this error and the other not.
Finally tracking down the function check_html() in
galaxy-dist/lib/galaxy/datatypes/checkers.py, I discovered that my use of the
tag <metabolite> had flagged up as a likely <META > tag and
produced the warning/failed upload.
The reason this did not happen in every case is that
check_html only reads the first 100 lines of the file and depending upon how
many samples were in my dataset, my <metabolite> tag could appear before
or after this cutoff.
I've solved the problem by changing my xml tag names but
my question is:
a) why does check_html only read up to line 100?
b) would it be possible to change the regular expressions
in check_html so that e.g. <meta ...> would be found but e.g. <metaxxx
...> would not?
Thanks for reading.
Rob
Dr Robert L Davidson
NERC Metabolomics Facility
School of Biosciences
University of Birmingham
Edgbaston, UK
8 years, 7 months
