How to display tool instead of html WWFSMD page at start-up?
by Neil.Burdett@csiro.au
Hi,
When Galaxy is started the centre column displays the "Hello world! It's running ..." WWFSMD? Html Page. How can this be changed so that a tool i.e. get data tool is shown up on start-up with all its text boxes etc rather than the default html file? Is this possible?
Thanks
Neil
9 years, 6 months
importing data from other public websites into galaxy
by Prasun Dutta
Hi,
I wish to import data into my local instance of galaxy from another website. Kindly let me know how to achieve that and what all is required. I want to import data from a chemoinformatic database (mainly compound structures) into galaxy and run my own analysis tools on them.
Regards,
Prasun Dutta
MSc (Bioinformatics)
School of Biological Sciences
University of Edinburgh, UK
9 years, 6 months
Auto hide tool and history panels
by Neil.Burdett@csiro.au
Hi
When starting Galaxy the tool panel and history panels appear as default. On the bottom of these panels are two arrows to minimise / hide the panels. Can someone show me how to make the panels be hidden by default rather than shown ?
Thanks
Neil
9 years, 6 months
Tool Shed test framework breaking where run_functional_tests.sh works
by Peter Cock
On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.cock(a)googlemail.com>
wrote:
>
> Hi Dave,
>
> As you hoped, these test now shows up on the tool page (as expected
> they are test failures - apparently my install script isn't quite right
yet):
>
> ...
>
> This one is more interesting, and appears to be a problem with the
> test framework (both tests pass locally via run_functional_tests.sh):
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9
> Functional test results for changeset revision 16a1a5ae98e9 of seq_rename
> 0 tests passed, 2 tests failed, 0 tests missing test components.
>
> I'll raise that on a new thread,
Here's the output from the (Test) Tool Shed where the tests fail:
Tests that failed
*Tool id:* seq_rename *Tool version:* seq_rename *Test:*test_tool_000000 (
functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...
) *Stderr:*
*Traceback:*
Traceback (most recent call last): File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name,
**page_inputs ) File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1320, in run_tool self.submit_form( **kwd ) File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1270, in submit_form raise AssertionError( errmsg ) AssertionError:
Attempting to set field 'new_column' to value '['2']' in form 'tool_form'
threw exception: cannot find value/label "2" in list control control:
<SelectControl(new_column=[1])> If the above control is a DataToolparameter
whose data type class does not include a sniff() method, make sure to
include a proper 'ftype' attribute to the tag for the control within the
<test> tag set. *Tool id:* seq_rename *Tool version:* seq_rename
*Test:*test_tool_000001 (
functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...
) *Stderr:*
*Traceback:*
Traceback (most recent call last): File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name,
**page_inputs ) File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1320, in run_tool self.submit_form( **kwd ) File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1270, in submit_form raise AssertionError( errmsg ) AssertionError:
Attempting to set field 'new_column' to value '['c2']' in form 'tool_form'
threw exception: cannot find value/label "c2" in list control control:
<SelectControl(new_column=[1])> If the above control is a DataToolparameter
whose data type class does not include a sniff() method, make sure to
include a proper 'ftype' attribute to the tag for the control within the
<test> tag set.
Both tests fail with the following assertion:
AssertionError: Attempting to set field 'new_column' to value '['c2']' in
form 'tool_form' threw exception: cannot find value/label "c2" in list
control control: <SelectControl(new_column=[1])> If the above control is a
DataToolparameter whose data type class does not include a sniff() method,
make sure to include a proper 'ftype' attribute to the tag for the control
within the <test> tag set.
Both tests pass on my development machine run via:
$ ./run_functional_tests.sh -id seq_rename
The two tests are defined as follows - identical bar the style used for the
column arguments - I was wondering if the Tool Shed testing was stricter
about numeric column names, but that does not seem to be relevant:
<tests>
<test>
<param name="input_file" value="four_human_proteins.fasta"
ftype="fasta" />
<param name="input_tabular"
value="four_human_proteins.rename.tabular" ftype="tabular" />
<param name="old_column" value="1" />
<param name="new_column" value="2" />
<output name="output_file"
file="four_human_proteins.rename.fasta" ftype="fasta" />
</test>
<test>
<param name="input_file" value="four_human_proteins.fasta"
ftype="fasta" />
<param name="input_tabular"
value="four_human_proteins.rename.tabular" ftype="tabular" />
<param name="old_column" value="c1" />
<param name="new_column" value="c2" />
<output name="output_file"
file="four_human_proteins.rename.fasta" ftype="fasta" />
</test>
</tests>
I can retest with the latest galaxy-dist once this issue is resolved:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.html
Peter
9 years, 6 months
Tool Shed Request - sanity check uploads?
by Peter Cock
Hi all,
For what is I think the second time (fortunately this was only on the
Test Tool Shed), I have managed to upload a tar-ball to the wrong
repository:
2:fae4084a0bc0
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
It could have been a glitch, but more likely is was simply inattention
on my part (most likely - multiple tab browsing has its downsides).
This leads me to offer some suggestions for how to prevent
this kind of user error in future:
(1) After the upload, show a preview of the changes for
confirmation (the drawback is this could take a long time
to process for a large upload, and lead to time outs).
(2) After upload, before committing the changes, compare
the tool contents - adding or removing some tools is normal,
replacing ALL the tools with different tools is probably an
error and should be subject to user confirmation.
(3) Offer a repository action to revert to a prior commit
(current workaround is to re-upload the old good file,
which I did as 3:81ac324efa49 in this case).
Peter
9 years, 6 months
GATK
by sridhar srinivasan
Dear Developers,
I am running GATK for first time. In galaxy i use Unified Genotyper. I am
getting error as below mentioned.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
##### ERROR The invalid arguments or inputs must be corrected before
the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to
view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation
and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option
requires a GATK Key file. Please see
http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-a...
for more information and instructions on how to obtain a key.
##### ERROR ------------------------------------------------------------------------------------------
also suggest me about the Rod file for dbSNP.
Thanks
Sridhar
9 years, 6 months
data snapshot is not the same on local instance of Galaxy
by Nikhil Mallela
Hi,
A few days ago, I have installed the stable release of of Galaxy local
instance on my Workstation & I am running it behind Apache web server proxy
.
In regard to the data snapshots, I've observed that, it is much more
organized on the Galaxy main rather than on my local instance.
For example, Take a look at these pictures:
On my local instance:
[image: Inline image 1]
On the Galaxy main: (also, this [image: Inline image 4] is missing on my
local instance)
[image: Inline image 2]
Also, when I click the view [image: Inline image 3] on my local
instance,the headers of the data is not corresponding to its respective
columns.
So, how can I fine tune these ?
Thanks in advance!
Nikhil.
--
Nikhil Vinod Mallela, PhD Student
University of Muenster,
Neil-Stensen Str. 12-14,
48149, Muenster,
Germany.
9 years, 6 months
Installing Galaxy behind an Apache proxy using mod_auth_cas for user auth
by Steve Harper
I'm trying to install Galaxy behind an Apache proxy using mod_auth_cas
for user authentication. I've got a ways in but am now stuck with
galaxy not getting the REMOTE_USER. Has anyone deployed with this module?
I have use_remote_user = true on in my universe_wsgi.ini along with a
valid maildomain.
Here's my apache config:
NameVirtualHost galaxy.utah.edu:80
NameVirtualHost galaxy.utah.edu:443
CASLoginURL https://go.utah.edu/cas/login
CASValidateURL https://go.utah.edu/cas/serviceValidate
CASValidateServer Off
CASAllowWildcardCert On
CASCertificatePath /etc/pki/tls/certs/ca-bundle.trust.crt
CASCookiePath /var/run/mod_auth_cas/
CASTimeout 3600
CASIdleTimeout 1800
CASDebug On
<VirtualHost 155.101.xx.40:80>
RedirectPermanent / https://galaxy.utah.edu/
</VirtualHost>
<VirtualHost galaxy.utah.edu:443>
SSLEngine on
SSLProtocol -ALL +SSLv3 +TLSv1
SSLCipherSuite HIGH:-aNULL:-eNULL
# Export the SSL environment variables to scripts
<Files ~ "\.(cgi|pl|shtml|phtml|php3?)$">
SSLOptions +StdEnvVars
</Files>
# Protocol adjustments for broken clients
SetEnvIf User-Agent ".*MSIE.*" \
nokeepalive ssl-unclean-shutdown \
downgrade-1.0 force-response-1.0
SSLCertificateFile /etc/pki/tls/certs/wildcard.utah.edu.crt
SSLCertificateKeyFile /etc/pki/tls/certs/wildcard.utah.edu.key
SSLCertificateChainFile /etc/pki/tls/certs/gd_bundle.crt
<Proxy http://localhost:8080>
Order deny,allow
Allow from all
</Proxy>
RewriteEngine on
<Location "/">
AuthType CAS
AuthName Galaxy
Require valid-user
# CASAuthNHeader REMOTE_SHMUSER
# Take the $REMOTE_USER environment variable and set it as a header
in the proxy request.
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
# RewriteCond %{LA-U:REMOTE_SHMUSER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e
XSendFile on
XSendFilePath /
# Compress all uncompressed content.
SetOutputFilter DEFLATE
SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary
RequestHeader set X-URL-SCHEME https
</Location>
<Location "/static">
# Allow browsers to cache everything from /static for 6 hours
ExpiresActive On
ExpiresDefault "access plus 6 hours"
</Location>
ServerName galaxy.utah.edu
RewriteRule ^/static/style/(.*)
/uufs/utah.edu/sys/pkg/galaxy/std/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*)
/uufs/utah.edu/sys/pkg/galaxy/std/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /uufs/utah.edu/sys/pkg/galaxy/std/static/$1 [L]
RewriteRule ^/favicon.ico
/uufs/utah.edu/sys/pkg/galaxy/std/static/favicon.ico [L]
RewriteRule ^/robots.txt
/uufs/utah.edu/sys/pkg/galaxy/std/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
</VirtualHost>
Any help is appreciated.
Steve Harper
Systems Administrator
Center for High Performance Computing
University of Utah
9 years, 6 months