Hi everybody,
Our Galaxy users from my lab can upload directories of files (
user_library_import_dir in the universe_wsgi.ini). They can upload their
files by symlink, but it doesn't work with directories which are symlinks ( in
the interface, these directories are not shown).
Is there a
Hi,
recently I installed the idr_package from the Galaxy tool-shed but the
tool IDR-plot does not work for my Galaxy instance.
This is the error message:
GPL Ghostscript 8.70: Could not open temporary file
./database/tmp/gs_DtCtic
Unable to open the initial device, quitting.
mv:
I tried different combinations ...
The
DEFAULT_ENCODING = 'latin-1'
in
lib/galaxy/util/__init__.py
is what worked!
some background information:
Yes, we also use a MySQL database.
All encodings (server, R/Bioconductor, used editors, ... ) are UTF-8.
The changeset
Hi Greg,
It did not work...This is what I see:
This repository is not installed correctly (see the Repository installation
error below). Choose Reset to install from the Repository Actions menu, correct
problems if necessary and try installing the repository again.
However, there no
Hi Greg,
I have done at least twice just to double check From Repository actions - reset
to install
This is what a I see:
Monitor installing tool shed repositories
NameDescription Owner RevisionStatus
s_mart S-MART manages your RNA-Seq and ChIP-Seq data. It also
Hi,
recently I installed the idr_package from the Galaxy tool-shed but the
tool IDR-plot does not work for my Galaxy instance.
This is the error message:
GPL Ghostscript 8.70: Could not open temporary file
./database/tmp/gs_DtCtic
Unable to open the initial device, quitting.
mv:
Adding ?charset=utf8 to the connection string worked!
However, there is one really weird side effect that probably has nothing to do
with utf8. The tool creates two pdf files and one zip file as output. For the
two pdf files, the expansion of the dataset in the history bar shows 'Image in
Hi,
my guess is that some previous steps failed and the assumed tempfile was
not created. That can have many different reasons, probably some R
dependencies are missing. Try to run the generated commandline from your
terminal and catch more error messages.
Cheers,
Bjoern
Hi,
recently I
Okay all, Christian followed up off list and mentioned that his
columns had not been UTF-8 encoded.
So I think the best thing to do is use Postgres, but if you have to
use MySQL make sure columns are UTF-8 encoded with the newest Galaxy
and add ?charset=utf8 to your database connection string. I
I checked the idrPlotWrapper.sh file and it just renames the two *.sav
files to idrPlot-uri.sav and idrPlot-em.sav prior to running the R
script on them.
Running batch-consistency-plot.r manually on the two files gives this
cryptic output:
null device
1
but a idrPlot-plot.ps file
I've fixed both this error and another involving newick files. I've tested
saving and loading with the three phyloviz compatible datatypes and it
seems to be working.
If you'd like, you can update to commit 11634:2e8596a621b4 on the stable
branch and see if the fix works for your error.
Let me
Hi Sheri,
To confirm, you are using the public Main Galaxy instance at
http://usegalaxy.org?
Is the dataset red (an error)? If so, would you mind submitting this
as a bug report?
If not red, the next best option is to share the history. If you could
generate a link and email that back,
Hi - Question from a biologist on thin ice here...
I've setup a galaxy instance on cloudman AWS, and I'd like to upload some data
using FTP. When I used the public galaxy server previously I used
'usegalaxy.org' as the host in FileZilla FTP program; what do I use for the
host in the cloud
Hello all,
I am pleased to announce the *Galaxy Community Log Board
http://wiki.galaxyproject.org/Community/Logs.* The Log Board is a place
to share how you addressed a particular task in your Galaxy deployment. Log
entries describe specific solutions to particular tasks, such as the details
of
This is a stand alone instance of Galaxy built Nov 28 a small research
cluster using LSF and built on RHEL6.2.
galaxy.tools.actions.upload_common INFO 2013-12-05 14:33:01,106 tool
upload1 created job id 10
Working directory for job is:
Hi Nicola, Just thought I'd write back since I added a Wiki page in Admin/Config area for implementing access control. Thank you for sharing the snippets you posted in the email thread you linked me! http://wiki.galaxyproject.org/Admin/Config/Access%20Control Cheers,Eric Rasche 06.11.2013, 18:57,
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