Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance
Hello Dave, Can you clarify how your users are accessing the following URL http://galaxy.jax.org/user/create I originally assumed they were using the Galaxy UI to register by clicking the Register link on the User popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link? If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here: http://galaxy.jax.org/user/create?cntrller=user Greg ~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote: Greg. We do not use the template_cache_path in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71 We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the galaxy process. 3 Web applications and 1 job runner. We get the error on both servers, but I'm doing all of this troubleshooting on our development server. This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help). I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help. We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade. Thanks, Dave On 5/24/11 11:29 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Dave, If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates. Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause. You mention your development server in your response. Are you running only 1 Galaxy instance, or more than 1? Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand? What version of Galaxy are your running? Thanks Dave, Greg Von Kuster On May 24, 2011, at 6:06 PM, Dave Walton wrote: Greg, We've tried just reloading the browser and that didn't do anything. As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you. The only cache related variable in my universe_wsgi files is static_cache_time = 360. Thanks, Dave On 5/24/11 4:27 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Dave, The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ). However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored. Greg Von Kuster On May 24, 2011, at 4:02 PM, Dave Walton wrote: We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] GET /user/create HTTP/1.0 500 - http://galaxy/user/login; Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2 Error - type 'exceptions.TypeError': create() takes at least 3 arguments (2 given) Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade. Did something change, in configuration of the create user page? Any thoughts what might be causing this? Thanks, Dave ___ Please keep all replies on the list by using
Re: [galaxy-dev] Is dynamic associated information per dataset possible?
Duddy, John wrote: We'd like to be able to associate fixed things (project, Sample, sequencer used) with user's FASTQ files, and we'd also like to allow users to associate dynamic, site-specific stuff with the sequencing run. Currently, users track their runs using a CSV sample sheet, and often they add columns to that sample sheet for their own information. Is it possible to associate that information with the FASTQ file when it is placed in Galaxy? I know about metadata, but the supported fields look like they are fixed in the code. I was hoping for a solution where the users do not need to modify the Galaxy code to pull this off. Hi John, You could accomplish this with library templates: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates --nate John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.commailto:jdu...@illumina.com ___ 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] Is dynamic associated information per dataset possible?
Nate, is it just me or all the .png links on that wikipage are broken/missing ? :-S On 2011-05-26 10:38, Nate Coraor wrote: Duddy, John wrote: We'd like to be able to associate fixed things (project, Sample, sequencer used) with user's FASTQ files, and we'd also like to allow users to associate dynamic, site-specific stuff with the sequencing run. Currently, users track their runs using a CSV sample sheet, and often they add columns to that sample sheet for their own information. Is it possible to associate that information with the FASTQ file when it is placed in Galaxy? I know about metadata, but the supported fields look like they are fixed in the code. I was hoping for a solution where the users do not need to modify the Galaxy code to pull this off. Hi John, You could accomplish this with library templates: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates --nate John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.commailto:jdu...@illumina.com ___ 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] problem with build_chrom_db.py
I've been configuring my local instance of galaxy to use trackster according to the instructions on https://bitbucket.org/galaxy/galaxy-central/wiki/Visualization when I run the script: python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ I get files that begin with: META http-equiv=Content-Script-Type content=text/javascript chr1247249719 chr1_random 166326 ... this causes an error in the browser: Could not load chroms for this dbkey: if i delete the first line META http-equiv=Content-Script-Type content=text/javascript from the .len file, then trackster works fine. I'm thinking there is a new line the input to build_chrom_db.py that is not getting stripped by this script thanks, Curt Palm *** Curtis J. Palm cp...@stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994cell: 408 858-7849 *** ___ 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] Is dynamic associated information per dataset possible?
On Thu, May 26, 2011 at 10:34 AM, Roman Valls brainst...@nopcode.org wrote: Nate, is it just me or all the .png links on that wikipage are broken/missing ? :-S I've noticed this on other pages, I think some stuff got moved a while back. They just need the folder name prefixed... Peter ___ 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] Is dynamic associated information per dataset possible?
Roman Valls wrote: Nate, is it just me or all the .png links on that wikipage are broken/missing ? :-S Hi Roman, We've had occasional problems with the images in the wiki, and I think sometimes they'll show up, sometimes they won't. We're in the process of migrating the wiki to our own Moin install, so this should be fixed then. --nate On 2011-05-26 10:38, Nate Coraor wrote: Duddy, John wrote: We'd like to be able to associate fixed things (project, Sample, sequencer used) with user's FASTQ files, and we'd also like to allow users to associate dynamic, site-specific stuff with the sequencing run. Currently, users track their runs using a CSV sample sheet, and often they add columns to that sample sheet for their own information. Is it possible to associate that information with the FASTQ file when it is placed in Galaxy? I know about metadata, but the supported fields look like they are fixed in the code. I was hoping for a solution where the users do not need to modify the Galaxy code to pull this off. Hi John, You could accomplish this with library templates: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates --nate John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.commailto:jdu...@illumina.com ___ 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/ ___ 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] Error getting to http://galaxy/user/create on local instance
I just checked, Using the User-Register menu works, however we require our users to log in so when they go to galaxy.jax.orghttp://galaxy.jax.org they are redirected to a login page if they are not already logged in. That page has the text This installation of Galaxy has been configured such that only users who are logged in may use it. If you don't already have an account, you may create onehttp://galaxy.jax.org/user/create. , and you may create one links to http://galaxy.jax.org/user/create. clicking on the link results in the error. -glen On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote: Hello Dave, Can you clarify how your users are accessing the following URL http://galaxy.jax.org/user/create I originally assumed they were using the Galaxy UI to register by clicking the Register link on the User popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link? If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here: http://galaxy.jax.org/user/create?cntrller=user Greg ~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote: Greg. We do not use the template_cache_path in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71 We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the galaxy process. 3 Web applications and 1 job runner. We get the error on both servers, but I'm doing all of this troubleshooting on our development server. This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help). I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help. We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade. Thanks, Dave On 5/24/11 11:29 PM, Greg Von Kuster g...@bx.psu.edumailto:g...@bx.psu.edu wrote: Hi Dave, If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates. Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause. You mention your development server in your response. Are you running only 1 Galaxy instance, or more than 1? Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand? What version of Galaxy are your running? Thanks Dave, Greg Von Kuster On May 24, 2011, at 6:06 PM, Dave Walton wrote: Greg, We've tried just reloading the browser and that didn't do anything. As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you. The only cache related variable in my universe_wsgi files is static_cache_time = 360. Thanks, Dave On 5/24/11 4:27 PM, Greg Von Kuster g...@bx.psu.edumailto:g...@bx.psu.edu wrote: Hello Dave, The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ). However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored. Greg Von Kuster On May 24, 2011, at 4:02 PM, Dave Walton wrote: We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] GET /user/create HTTP/1.0 500 - http://galaxy/user/login; Mozilla/5.0 (Macintosh; U; Intel Mac OS X
Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance
Hi Glen, I've never seen this before, but perhaps your user controller is using an old version ( I'm just grasping here, because this is pretty obscure behavior ). Try deleting the following file - make sure it is the .pyc file. ~/lib/galaxy/web/controllers/user.pyc The user controller contains the code that generates the you may create one link, but the current versions of this controller is using the new method signature as well, so the only thing I can think of is that your compiled version ( user.pyc ) is old. Let us know if this doesn't resolve the issue. Thanks! On May 26, 2011, at 7:39 AM, Glen Beane wrote: I just checked, Using the User-Register menu works, however we require our users to log in so when they go to galaxy.jax.org they are redirected to a login page if they are not already logged in. That page has the text This installation of Galaxy has been configured such that only users who are logged in may use it. If you don't already have an account, you may create one. , and you may create one links to http://galaxy.jax.org/user/create. clicking on the link results in the error. -glen On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote: Hello Dave, Can you clarify how your users are accessing the following URL http://galaxy.jax.org/user/create I originally assumed they were using the Galaxy UI to register by clicking the Register link on the User popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link? If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here: http://galaxy.jax.org/user/create?cntrller=user Greg ~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote: Greg. We do not use the template_cache_path in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71 We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the galaxy process. 3 Web applications and 1 job runner. We get the error on both servers, but I'm doing all of this troubleshooting on our development server. This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help). I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help. We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade. Thanks, Dave On 5/24/11 11:29 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Dave, If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates. Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause. You mention your development server in your response. Are you running only 1 Galaxy instance, or more than 1? Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand? What version of Galaxy are your running? Thanks Dave, Greg Von Kuster On May 24, 2011, at 6:06 PM, Dave Walton wrote: Greg, We've tried just reloading the browser and that didn't do anything. As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you. The only cache related variable in my universe_wsgi files is static_cache_time = 360. Thanks, Dave On 5/24/11 4:27 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Dave, The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ). However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user
Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance
Just removed user.pyc and restarted the server. Did not resolve the problem. Dave On 5/26/11 8:09 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Glen, I've never seen this before, but perhaps your user controller is using an old version ( I'm just grasping here, because this is pretty obscure behavior ). Try deleting the following file - make sure it is the .pyc file. ~/lib/galaxy/web/controllers/user.pyc The user controller contains the code that generates the you may create one http://galaxy.jax.org/user/create link, but the current versions of this controller is using the new method signature as well, so the only thing I can think of is that your compiled version ( user.pyc ) is old. Let us know if this doesn't resolve the issue. Thanks! On May 26, 2011, at 7:39 AM, Glen Beane wrote: I just checked, Using the User-Register menu works, however we require our users to log in so when they go to galaxy.jax.org http://galaxy.jax.org/ they are redirected to a login page if they are not already logged in. That page has the text This installation of Galaxy has been configured such that only users who are logged in may use it. If you don't already have an account, you may create one http://galaxy.jax.org/user/create . , and you may create one links to http://galaxy.jax.org/user/create. clicking on the link results in the error. -glen On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote: Hello Dave, Can you clarify how your users are accessing the following URL http://galaxy.jax.org/user/create I originally assumed they were using the Galaxy UI to register by clicking the Register link on the User popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link? If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here: http://galaxy.jax.org/user/create?cntrller=user Greg ~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote: Greg. We do not use the template_cache_path in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71 We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the galaxy process. 3 Web applications and 1 job runner. We get the error on both servers, but I'm doing all of this troubleshooting on our development server. This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help). I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help. We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade. Thanks, Dave On 5/24/11 11:29 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Dave, If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates. Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause. You mention your development server in your response. Are you running only 1 Galaxy instance, or more than 1? Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand? What version of Galaxy are your running? Thanks Dave, Greg Von Kuster On May 24, 2011, at 6:06 PM, Dave Walton wrote: Greg, We've tried just reloading the browser and that didn't do anything. As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you. The only cache related variable in my universe_wsgi files is static_cache_time = 360. Thanks, Dave On 5/24/11 4:27 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Dave, The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ). However, sometimes this isn't enough to clear the cache, so you can fix
[galaxy-dev] stdout and stderr
Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job failed) in browser.How can i resolve such type of problem. Regards shashi shekhar ___ 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] stdout and stderr
You need a wrapper to capture the stderr It would be nice if there were an option to base a tools status on the unix return value (for well behaved programs) On May 26, 2011, at 8:36 AM, shashi shekhar meshash...@gmail.com wrote: Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job failed) in browser.How can i resolve such type of problem. Regards shashi shekhar ___ 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] stdout and stderr
On Thu, May 26, 2011 at 1:36 PM, shashi shekhar meshash...@gmail.com wrote: Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job failed) in browser.How can i resolve such type of problem. Regards shashi shekhar See issue 325, https://bitbucket.org/galaxy/galaxy-central/issue/325/ Until that is fixed, you'll probably need a wrapper script, there is an example of this in tools/ncbi_blast_plus/hide_stderr.py Peter ___ 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] stdout and stderr
Alternatively you can redirect your STDOUT and/or STDERR into a LOG txt file as additional output to the tool. I do many times the same since it allows the realtime tracking in the log file of the process where it is and when it's expected to be finished. Indeed a wrapper can be used but if you just have a plain cmdline with options in your tool xml you can use 1dev/null and 2dev/null (or 2- and 1- in short). For the XML to keep it valid you need to encode the and into: 2gt;amp;- Or port both into a logfile which you specify as output. 2$logfile (2gt;$logfile) Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens shashi shekhar Verzonden: donderdag 26 mei 2011 14:36 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] stdout and stderr Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job failed) in browser.How can i resolve such type of problem. Regards shashi shekhar ___ 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] The powers of Cheetah, how?
On Thu, May 26, 2011 at 1:22 PM, Kempenaar, M (med) m.kempen...@med.umcg.nl wrote: Hi list, I've been working on a single Galaxy tool for a while now, and I'm running into all sorts of difficulties that can probably all be fixed using Cheetah. However I've been trying several ways of utilizing the (enormous) powers of Cheetah but so far I'm not successful. I'll try to ask my questions as clear as possible, please let me know if anything is unclear. In my tool I use the following input parameter: --- param name=report_options type=select multiple=True display=checkboxes option value=overviewphyla distribution/option option value=phyladendphyla dendograms/option option value=heatmapheatmap/option option value=dendogramdendogram/option option value=pcaprincipal component analysis/option option value=mdsmulti dimensional scaling/option /param --- Each of these options corresponds to a function in my R script, thus I want to do an if-else if-else to execute these functions that the user selected (note that multiple=True). Now the problem is, I also use R Sweave (sweaving R output (text/graphics) into LaTeX) to generate a nice looking PDF report, and since that's not a 'real' programming/ scripting language, I can't for instance split the string (as I used to do in R) and check for the boxes a user selected, so my questions are: I planned on using Cheetah to include sections of Sweave LaTeX code for each box checked by the user, perfectly doable with an #if-#elif you'd think, however since the $report_options contains a comma-separated single string, I would need to split (or use regular expressions) to be able to do such an #if-#elif like: #if heatmap in $report_options.split(,) results in: NotFound: cannot find 'split' while searching for 'split' Try changing this: #if heatmap in $report_options.split(,) to: #if heatmap in str($report_options).split(,) Although $report_options acts a bit like a Python string, it isn't one, and lacks lots of useful string methods. We can turn it into a string using the Python str function. Q: Followup from previous question, where within the sections of my tool XML file can I actually use Cheetah? This of course has to do with the order in which a tool is executed. I believe only within the command.../command tag. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] stdout and stderr
PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT and STDOUT to a logfile. You won't get a red box though when errors occur! Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: donderdag 26 mei 2011 15:19 Aan: 'shashi shekhar' CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] stdout and stderr Alternatively you can redirect your STDOUT and/or STDERR into a LOG txt file as additional output to the tool. I do many times the same since it allows the realtime tracking in the log file of the process where it is and when it's expected to be finished. Indeed a wrapper can be used but if you just have a plain cmdline with options in your tool xml you can use 1dev/null and 2dev/null (or 2- and 1- in short). For the XML to keep it valid you need to encode the and into: 2gt;amp;- Or port both into a logfile which you specify as output. 2$logfile (2gt;$logfile) Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens shashi shekhar Verzonden: donderdag 26 mei 2011 14:36 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] stdout and stderr Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job failed) in browser.How can i resolve such type of problem. Regards shashi shekhar ___ 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] stdout and stderr
On Thu, May 26, 2011 at 2:42 PM, Bossers, Alex alex.boss...@wur.nl wrote: PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT and STDOUT to a logfile. You won’t get a red box though when errors occur! Right - if you need to detect an error state via the return code, currently you have to do this with a wrapper script. If you don't ever expect any errors, then you can treat stderr as an output, or just redirect to to /dev/nul - but I don't like that idea - silent failures are bad. I regard fixing issue 325 as one of the top priorities in Galaxy, but in the short term I'd settle for treating any output on stderr OR a non-zero return code as a failure. i.e. Something like this patch, even if more work is needed for PBS jobs: https://bitbucket.org/galaxy/galaxy-central/issue/325/#comment-331776 Peter ___ 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] cluster files directory configuration
On May 25, 2011, at 8:18 AM, Nate Coraor wrote: Shantanu Pavgi wrote: On May 19, 2011, at 4:05 PM, Shantanu Pavgi wrote: I have configured custom cluster_files_directory in universe_wsgi.ini file. The cluster jobs are running fine, however job scripts, stdout and stderr are being written in default database/pbs location. Am I missing something in the configuration here? Any help on what might be wrong here? Is this option getting overridden by some other config? SGE or DRMAA? I think this was broken in the dist version of Galaxy prior to the one just released on Friday - try the latest and let us know if there's still an issue. Well, we are using SGE with drmaa interface (job runner configured with drmaa url). I will check out the latest version sometime soon. Thanks for the update. -- Shantanu. ___ 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] Paper on workflow patterns
As discussed in the Workflows and APIs breakaway session, here is the paper on Workflow patterns: van der Aalst, ter Hofsted, Kiepuszewski and Barros, Distributed and Parallel Databases, Volume 14, Number 1, 5-51: Workflow Patterns PDF available at: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.90.1538rep=rep1type=pdf ___ 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] Display column headers in data_column parameter
On Thu, May 26, 2011 at 3:45 PM, Johannes Eichner johannes.eich...@uni-tuebingen.de wrote: Hi Peter, I defined an additional metadata element for the column names analogously to the column_types element in the module galaxy_basedir/lib/galaxy/tools/datatypes/tabular.py: MetadataElement( name=column_names, default=[], desc=Column names, param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] ) Then I read the column names in the function set.meta and saved them in the new metadata element: dataset.metadata.column_names = column_names Do you look for a tab separated # header line at the start of the file for these names? Finally, I changed a line of code in the function get.column.list in galaxy_basedir/lib/galaxy/tools/parameters/basic.py, such that Galaxy displays the column names in the data_column parameter: original line: column_list.append( str( i + 1 ) ) changed line: column_list.append( str( i + 1 ) + : + dataset.metadata.column_names[i]) ) Kind regards, Johannes From a Python style point of view, I'd use string formatting here: column_list.append(%i: %s % (i+1, dataset.metadata.column_names[i])) Do you have a branch on bitbucket for this, or a patch? I'd like to try it. You could attach a patch to issue 554: https://bitbucket.org/galaxy/galaxy-central/issue/554 Thanks, Peter ___ 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] Is dynamic associated information per dataset possible?
That's good news. Is this available via the API as well? I didn't see examples of this anywhere in the code, but I thought it might be available by passing additional values in the dictionary. -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Thursday, May 26, 2011 1:38 AM To: Duddy, John Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Is dynamic associated information per dataset possible? Duddy, John wrote: We'd like to be able to associate fixed things (project, Sample, sequencer used) with user's FASTQ files, and we'd also like to allow users to associate dynamic, site-specific stuff with the sequencing run. Currently, users track their runs using a CSV sample sheet, and often they add columns to that sample sheet for their own information. Is it possible to associate that information with the FASTQ file when it is placed in Galaxy? I know about metadata, but the supported fields look like they are fixed in the code. I was hoping for a solution where the users do not need to modify the Galaxy code to pull this off. Hi John, You could accomplish this with library templates: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates --nate John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.commailto:jdu...@illumina.com ___ 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] stdout and stderr
Peter, can't agree more. Its more a workaround to get warnings not turning up red. Porting it to the log file would mean you have to check the logfile! Alex Van: Peter Cock [p.j.a.c...@googlemail.com] Verzonden: donderdag 26 mei 2011 16:04 Aan: Bossers, Alex CC: shashi shekhar; galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] stdout and stderr On Thu, May 26, 2011 at 2:42 PM, Bossers, Alex alex.boss...@wur.nl wrote: PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT and STDOUT to a logfile. You won’t get a red box though when errors occur! Right - if you need to detect an error state via the return code, currently you have to do this with a wrapper script. If you don't ever expect any errors, then you can treat stderr as an output, or just redirect to to /dev/nul - but I don't like that idea - silent failures are bad. I regard fixing issue 325 as one of the top priorities in Galaxy, but in the short term I'd settle for treating any output on stderr OR a non-zero return code as a failure. i.e. Something like this patch, even if more work is needed for PBS jobs: https://bitbucket.org/galaxy/galaxy-central/issue/325/#comment-331776 Peter ___ 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] Is dynamic associated information per dataset possible?
The sample tracking system looks interesting. It looks like this is designed to have the sequencers modeled in Galaxy, have Galaxy pull the data from the sequencers, and might assume 1-1 pairing between sequencing run and samples. I'd like to be able to support pushing files from a central location and variably multiplexed runs, all via the API (or extensions to the API). Is there any up-to-date documentation on this feature? John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.com -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, May 26, 2011 2:18 AM To: Duddy, John Cc: galaxy-dev Subject: Re: [galaxy-dev] Is dynamic associated information per dataset possible? In addition to Data Library templates, which are useful after the sequencer data has arrived in a Galaxy Data Library, Galaxy's sample tracking system includes sample run templates which are very similar to the Data Library templates, but are associated with a sample as it progresses through it's sequence run lifecycle in the facility. Sample run details templates are defined by the facility administrator. They can be created in the Admin view via the Manage form definitions menu link. ___ 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] The powers of Cheetah, how?
Hi Peter, Thanks very much for you answer, this was exactly the problem, I thought I was dealing with a Python string and the Cheetah error was not as clear as the Python error that you'd get when calling a function from an unsupported object. I also joined in with one of the Breakout sessions at the Galaxy conference in which Dan also explained my error (https://bitbucket.org/galaxy/galaxy-central/wiki/2011_Galaxy_Community_Conference/Complex_Tools_and_Datasources:_Parameters,_Datatypes_and_Metadata) I've been toying with Cheetah a bit more now, and it's getting better real fast once you get the grips with it! Thanks again, also for your nice presentation (worked very well!) - Marcel Van: Peter Cock [p.j.a.c...@googlemail.com] Verzonden: donderdag 26 mei 2011 15:25 Aan: Kempenaar, M (med) CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] The powers of Cheetah, how? On Thu, May 26, 2011 at 1:22 PM, Kempenaar, M (med) m.kempen...@med.umcg.nl wrote: Hi list, I've been working on a single Galaxy tool for a while now, and I'm running into all sorts of difficulties that can probably all be fixed using Cheetah. However I've been trying several ways of utilizing the (enormous) powers of Cheetah but so far I'm not successful. I'll try to ask my questions as clear as possible, please let me know if anything is unclear. In my tool I use the following input parameter: --- param name=report_options type=select multiple=True display=checkboxes option value=overviewphyla distribution/option option value=phyladendphyla dendograms/option option value=heatmapheatmap/option option value=dendogramdendogram/option option value=pcaprincipal component analysis/option option value=mdsmulti dimensional scaling/option /param --- Each of these options corresponds to a function in my R script, thus I want to do an if-else if-else to execute these functions that the user selected (note that multiple=True). Now the problem is, I also use R Sweave (sweaving R output (text/graphics) into LaTeX) to generate a nice looking PDF report, and since that's not a 'real' programming/ scripting language, I can't for instance split the string (as I used to do in R) and check for the boxes a user selected, so my questions are: I planned on using Cheetah to include sections of Sweave LaTeX code for each box checked by the user, perfectly doable with an #if-#elif you'd think, however since the $report_options contains a comma-separated single string, I would need to split (or use regular expressions) to be able to do such an #if-#elif like: #if heatmap in $report_options.split(,) results in: NotFound: cannot find 'split' while searching for 'split' Try changing this: #if heatmap in $report_options.split(,) to: #if heatmap in str($report_options).split(,) Although $report_options acts a bit like a Python string, it isn't one, and lacks lots of useful string methods. We can turn it into a string using the Python str function. Q: Followup from previous question, where within the sections of my tool XML file can I actually use Cheetah? This of course has to do with the order in which a tool is executed. I believe only within the command.../command tag. Peter De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ 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] Accessing Data Library Template fields in tools?
I have my data in a data library and have a form template defined so I can
enter the sample information.
So, I import a data file into a history and want to run a tool on it. Can I
pass the values of those form templates to my tool? Sort of line
${input.form_field_id} ?
Thanks!
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.commailto:jdu...@illumina.com
___
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] stdout and stderr
On 27/05/11 00:04, Peter Cock wrote: I regard fixing issue 325 as one of the top priorities in Galaxy Can't agree more with you Peter! This bug and other tool wrapper related bugs make it harder and more tedious to contribute tool wrappers. It's a big turn off for me. Florent ___ 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] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool
Can anyone comment on my email please? Florent On 22/05/11 14:03, Florent Angly wrote: Let me know if you have any questions about this. Thanks, Florent Original Message Subject:Request for pulling the updated FASTQ (de-)interlacer tool Date: Tue, 17 May 2011 17:47:13 +1000 From: Florent Angly florent.an...@gmail.com To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Dear Galaxy team, Please consider pulling these changes I made to the interlacer/de-interlacer tools into the main Galaxy repository: https://bitbucket.org/fangly/galaxy-central/changeset/7f7ec8f05d36 While the tools were handling mate pairs fine, I now added the ability to also keep single reads (reads that miss their mate) in a separate file. The functional tests were updated and pass. Thanks, Florent ___ 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/
