July 2013 - galaxy-dev - lists.galaxyproject.org

How to display tool instead of html WWFSMD page at start-up?
by Neil.Burdett＠csiro.au 30 Jul '13

30 Jul '13

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

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importing data from other public websites into galaxy
by Prasun Dutta 30 Jul '13

30 Jul '13

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

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Auto hide tool and history panels
by Neil.Burdett＠csiro.au 30 Jul '13

30 Jul '13

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

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Does the xml tool wrapper language have ifs or functions?
by Ben Gift 29 Jul '13

29 Jul '13

I'm finding it hard to deal with mutually exclusive options that also share many options between them for certain command line tools. Functions of if statements could solve this copy/pasting problem. Thanks

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Tool Shed test framework breaking where run_functional_tests.sh works
by Peter Cock 29 Jul '13

29 Jul '13

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/peterj… ) *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/peterj… ) *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

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Cloudman - When will the symlinks be resolved ?
by Ravpreet Setia 29 Jul '13

29 Jul '13

I am referring to the following bug: https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-t… We are waiting for this bug to resolve before we fix any other issues with our Cloudman scripts. I am wondering when you think this bug will be resolved so I can plan my time. Thanks.

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Tool Shed Request - sanity check uploads?
by Peter Cock 29 Jul '13

29 Jul '13

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

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GATK
by sridhar srinivasan 29 Jul '13

29 Jul '13

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-and… for more information and instructions on how to obtain a key. ##### ERROR ------------------------------------------------------------------------------------------ also suggest me about the Rod file for dbSNP. Thanks Sridhar

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data snapshot is not the same on local instance of Galaxy
by Nikhil Mallela 29 Jul '13

29 Jul '13

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.

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Installing Galaxy behind an Apache proxy using mod_auth_cas for user auth
by Steve Harper 26 Jul '13

26 Jul '13

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

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