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
8 years, 11 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
8 years, 11 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
8 years, 11 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
8 years, 11 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
8 years, 11 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
8 years, 11 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.
8 years, 11 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
8 years, 11 months
