[galaxy-dev] Tool test question
Dear Dev List, I am currently writing tests for a tool I am developing and am coming up short in understanding why it's failing. Using the test data, I can generate output identical to the output provided for testing every time I run the tool from my local Galaxy server. However, when I run the tool test through run_functional_tests.sh, it always fails, and apparently fails on every line. Because I consistently see the same output from the Galaxy server-based tool, I'm sure I'm missing something simple and want to look at the test-generated output. Is there a way I can set run_functional_tests to print the generated tool output file in its entirety? Thank you, Kipper Fletez-Brant ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] bed files - The uploaded binary file contains inappropriate content
Hello, We tried to upload a directory of files to our local data library and all uploads were successful except for one. The .bed file did not upload and gave an error message; The uploaded binary file contains inappropriate content. We would like to be able to share our data set with other researchers using galaxy but we need to be able to upload this bed file. -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] can not login to workflows after postgresql setup
Hi all, I tried to reconnect with the SQLite database but this time when I try to log in to use workflows it says that my password is invalid. When I try to reset it with the forgotten password option I get this message again: Mail is not configured for this Galaxy instance. Please contact an administrator. What can I do? Jaap From: Jeremy Goecks [jeremy.goe...@emory.edu] Sent: Wednesday, July 04, 2012 11:38 PM To: Heijden, J.W.F. van der (HG) Cc: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] can not login to workflows after postgresql setup I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Moving to a new database will make all your previous data inaccessible as it's no longer in the database that Galaxy is using, so this behavior is expected. You could: (a) reconnect Galaxy to your SQLite database and export (download) your workflow and then (b) change Galaxy to use your PostGres database and import (upload) your workflow. Also it seems that I am no longer able to upload files. It's only a 300kb test file but it seems to be uploading forever. The database used should not affect uploading. Are you still having problems? Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] can not login to workflows after postgresql setup
Hi, Any ideas yet on how to configure my mail in galaxy? Kind regards Jaap From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of j.w.f.van_der_heij...@lumc.nl [j.w.f.van_der_heij...@lumc.nl] Sent: Friday, July 06, 2012 11:13 AM To: jeremy.goe...@emory.edu Cc: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] can not login to workflows after postgresql setup Hi all, I tried to reconnect with the SQLite database but this time when I try to log in to use workflows it says that my password is invalid. When I try to reset it with the forgotten password option I get this message again: Mail is not configured for this Galaxy instance. Please contact an administrator. What can I do? Jaap From: Jeremy Goecks [jeremy.goe...@emory.edu] Sent: Wednesday, July 04, 2012 11:38 PM To: Heijden, J.W.F. van der (HG) Cc: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] can not login to workflows after postgresql setup I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Moving to a new database will make all your previous data inaccessible as it's no longer in the database that Galaxy is using, so this behavior is expected. You could: (a) reconnect Galaxy to your SQLite database and export (download) your workflow and then (b) change Galaxy to use your PostGres database and import (upload) your workflow. Also it seems that I am no longer able to upload files. It's only a 300kb test file but it seems to be uploading forever. The database used should not affect uploading. Are you still having problems? Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] can not login to workflows after postgresql setup
For mail configuration, see the Mail and Notification section in your universe_wsgi.ini -- all you need to do is specify an SMTP server that Galaxy can use. Regarding the invalid password, keep in mind that this would be your previously registered password (from when you were using the sqlite database originally), and not the one you used when you reregistered with a postgres database. -Dannon On Jul 6, 2012, at 8:26 AM, j.w.f.van_der_heij...@lumc.nl wrote: Hi, Any ideas yet on how to configure my mail in galaxy? Kind regards Jaap From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of j.w.f.van_der_heij...@lumc.nl [j.w.f.van_der_heij...@lumc.nl] Sent: Friday, July 06, 2012 11:13 AM To: jeremy.goe...@emory.edu Cc: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] can not login to workflows after postgresql setup Hi all, I tried to reconnect with the SQLite database but this time when I try to log in to use workflows it says that my password is invalid. When I try to reset it with the forgotten password option I get this message again: Mail is not configured for this Galaxy instance. Please contact an administrator. What can I do? Jaap From: Jeremy Goecks [jeremy.goe...@emory.edu] Sent: Wednesday, July 04, 2012 11:38 PM To: Heijden, J.W.F. van der (HG) Cc: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] can not login to workflows after postgresql setup I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Moving to a new database will make all your previous data inaccessible as it's no longer in the database that Galaxy is using, so this behavior is expected. You could: (a) reconnect Galaxy to your SQLite database and export (download) your workflow and then (b) change Galaxy to use your PostGres database and import (upload) your workflow. Also it seems that I am no longer able to upload files. It's only a 300kb test file but it seems to be uploading forever. The database used should not affect uploading. Are you still having problems? Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] pbs_python issues
I am having an issue with pbs_python loading, but not submitting jobs to the cluster. The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py –e pbs_python' it failed to generate the pbs_python egg in the /galaxy-dist/eggs/ directory. Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from my production galaxy server and restarted my test server. It appears to start, but when I attempt to run anything it uses the local runner and fails. The runner0.log shows the pbsjobrunner is loaded is below: galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner: galaxy.jobs.runners.pbs:PBSJobRunner galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue started galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue started galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue started I can't seem to get past this point since I upgraded. Can someone point me in the right direction? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Which css file does welcome.html use?
OK, this is ostensibly a simple question. However, I can't find the CSS file that welcome.html is using. In the HTML file, there's this line: link rel=stylesheet href=style/base.css type=text/css / However, I don't see a directory named style anywhere in the galaxy directory tree. When I search for base.css, from the root Galaxy installation directory, I get the following results: ./static/june_2007_style/blue/base.css ./static/light_hatched_style/blue/base.css ./static/light_hatched_style/green/base.css ./static/old_blue_style/base.css So I assume that one of these is being used? I do think it's strange though, that the HTML points to an apparently non-existent file and yet everything on my local instance looks identical to the Penn State Public site. Thanks, Dan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
