Re: [galaxy-dev] I can't see or access pictures in FastQC
Hi Ross, thanks for the reply! I ran FastQC from the command line, and it did give the proper output. Furthermore, FastQC generating the proper output when I run it from Galaxy. However, Galaxy is having trouble accessing the files. If I go into the filesystem, I can find all of the files in .../database/files/[###]/dataset_[###]_files/ I ran FastQC on the Penn State public instance, and it gives HTML output with pictures in-line and all of the linked files accessible. When I mouseover the link, it looks the same as it does on my local instances, in that the address is in the following format: [Galaxy web address]/datasets/[16 character hash]/display/[filename] Knowing what's going on under the hood would be extremely helpful towards my troubleshooting. So far I can't find anything interesting in paster.log, nor in the Apache log files. Thanks! Dan -Original Message- From: Ross [mailto:ross.laza...@gmail.com] Sent: Wednesday, June 06, 2012 6:07 PM To: Dorset, Daniel C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] I can't see or access pictures in FastQC Hi, Daniel. The wrapper doesn't introduce any new dependencies other than a working FastQC install in the right place so can you please let us know what happens when you run FastQC from the command line as the user running your Galaxy processes - it should start an interactive FastQC session where you can try running a real fastq input and check that you get the HTML outputs. Once it's all working from the command line, try the tool again and let us know how that turns out please? On Thu, Jun 7, 2012 at 6:58 AM, Dorset, Daniel C daniel.dor...@vanderbilt.edu wrote: I'm running two separate instances of Galaxy on two different servers. On both servers, whenever I run FastQC, I can see the result HTML file, but none of the pictures show up. Furthermore, if I try to access the links at the bottom of the page, they don't lead to any real files. If I look in my database/files/subfolder, I see a dataset_### file that contains the HTML info, which I am able to see in Galaxy. There is another folder named dataset_###_files, and all of the pictures and the FastQC results zip file are contained in there. I can access them with full read permissions, and the sizes appear correct. Has anyone else experienced this problem? ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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] LookupError: No section 'main' (prefixed by 'server') found in config
Hi Nate, I try it with a script for galaxy service, but it did not work. I successfully did it with one daemon file for each process... regards. 2011/8/26 Nate Coraor n...@bx.psu.edu Hi Iry, By default, PasteScript is looking for a section named [server:main]. With this config, you can start the servers with: % sh run.sh --server-name=web0 % sh run.sh --server-name=web1 % sh run.sh --server-name=web2 --nate Iry Witham wrote: I have performed a new install of Galaxy for development and deployment purposes. However, when I run the run.sh script I get the following error: Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 274, in command relative_to=base, global_conf=vars) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 308, in loadserver relative_to=relative_to, **kw) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 210, in loadserver return loadobj(SERVER, uri, name=name, **kw) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 224, in loadobj global_conf=global_conf) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 248, in loadcontext global_conf=global_conf) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 363, in get_context object_type, name=name) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 528, in find_config_section self.filename)) LookupError: No section 'main' (prefixed by 'server') found in config /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini I have modified the universe_wsgi.ini to reflect the way our production server is configured. The following is the server section of that file: # # Galaxy is configured by default to be useable in a single-user development # environment. To tune the application for a multi-user production # environment, see the documentation at: # # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer # # Throughout this sample configuration file, except where stated otherwise, # uncommented values override the default if left unset, whereas commented # values are set to the default value. # examples of many of these options are explained in more detail in the wiki: # # Config hackers are encouraged to check there before asking for help. # HTTP Server -- # Configuration of the internal HTTP server. [server:web0] use = egg:Paste#http port = 8080 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # Configuration of web server 2 [server:web1] use = egg:Paste#http port = 8081 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # Configuration of web server 3 [server:web2] use = egg:Paste#http port = 8082 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # The internal HTTP server to use. Currently only Paste is provided. This # option is required. #use = egg:Paste#http # The port on which to listen. #port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. #host = 0.0.0.0 # Use a threadpool for the web server instead of creating a thread for each # request. #use_threadpool = True # Number of threads in the web server thread pool. #threadpool_workers = 5 # Filters -- # Filters sit between Galaxy and the HTTP server. # These filters are disabled by default. They can be enabled with # 'filter-with' in the [app:main] section
Re: [galaxy-dev] TopHat fusion
There's a Tophat2 wrapper in galaxy-central right now that you're welcome to try, but it's still under development and may be buggy and is still subject to (potentially) major changes. I'd guess that Tophat2 support will make it to beta near the end of this month and be available on the public server shortly thereafter. J. On Jun 7, 2012, at 10:31 AM, suzan katie wrote: Hi Jeremy, Good to hear this and I would really appreciate if you could give me any time line of when Galaxy is planing to implement TopHat 2? On Wed, Jun 6, 2012 at 3:14 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: The plan is to support Tophat2, which includes support for doing fusion search, in the future. Best, J. On Jun 4, 2012, at 2:56 PM, suzan katie wrote: Hello, Is there any plan of installing TopHat fusion in Galaxy in near future. Thanks Katie ___ 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] Incomplete datasets when dowloaded from history
Hello Jean-François, For larger files, or if complete downloads seem to be a problem, using curl at a command or Terminal prompt is a great option. The syntax is: % curl -O 'copied-link-from-dataset-disc-icon' http://user.list.galaxyproject.org/Download-multiple-files-from-history-td4303996.html (wget is not currently supported, so please disregard those instructions in the post) I used the 'mailing list' version of the Galaxy custom google searches to find this thread. http://galaxy.psu.edu/search/mailinglists/ Links to all of the Galaxy custom searches are in the wiki in the side bar and other places, but also at the top of the Support page for quick access: http://wiki.g2.bx.psu.edu/Support Hopefully this helps, Jen Galaxy team On 6/6/12 6:53 AM, Jean-Francois Payotte wrote: Hi folks, Some of our local Galaxy instance users seem to be experiencing some strange behaviour lately. I searched the mailing-list archive but I didn't found anything related, so I'd be interested to know if somebody already had the same issue. The problem is that sometimes, when people are trying to download their datasets from their history, although the file seems to download successfully, it appears that the downloaded file is incomplete (for example a 3000 lines text file will show only maybe 2000 lines at the first download, 1600 lines at the second download, and so on... and eventually, the file will download completely. This issue happened with more than one user and with different tools. Does anybody ever had this kind of issue? Or does somebody would have an idea of where to look to solve this problem? Best regards, Jean-François ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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] Sharing data in Cistrome
Hi, I am trying to share my files/history in Galaxy/Cistrome with my colleague, but the 'Share with user' link gives the following error. Could you please help me, am i doing something wrong or is there a bug in the system? Best regards, Päivi Server Error URL: http://cistrome.org/ap/history/share?use_panels=Falseid=7b2014ae6b4b7c3f Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:90 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.history:960 in share send_to_err=send_to_err ) Module galaxy.web.framework:733 in fill_template return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako return template.render( **data ) Module mako.template:296 in render return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template callable_(context, *args, **kwargs) Module _base_mako:42 in render_body __M_writer(unicode(next.body())) Module _history_share_mako:74 in render_body __M_writer(unicode(history.name)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128) -- Päivi Pihlajamaa, M.Sc. Biomedicum Helsinki Institute of Biomedicine University of Helsinki phone +358-9-19125294 email paivi.pihlaja...@helsinki.fi ___ 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] Group by c1: max[c2] --skipped 11489 invalid lines starting with line 3. Value '' in column 0 is not numeric
input file example in galaxy:WASH7P 0.305384KLHL17 6.4404GLTPD1 22.8633PUSL122.9327CPSF3L 0.446421SAMD11 0.0267019 output:AAAS then the error message complaint is on the tile column.After updating R to latest version the grouping function is no longer working. I have been searching very hard on the internet regarding to this issue. However, I have no luck to get any solution. This issue tracker is my last option by far. I have no idea what happened. thank ___ 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] Incomplete datasets when dowloaded from history
Hi Jennifer, Thank you for your answer. Although using curl command might be a good solution to overcome the incomplete downloads issue, this solution might not be enough user-oriented (as I don't think our users are familiar with using the command line). Anyway, we have developed a tool which allows the user to select one file from his history and to copy it to another user-given location on our server. So using this tool allows us to download the files correctly. Also, this issue happened while trying to download a file of size about 250Mb.. Is this considered a large file? And finally an other question comes to mind: What about people downloading their result files not knowing that the download was incomplete? If the user doesn't check if the number of lines in the downloaded file correspond to what is shown in Galaxy history, he won't be able to know that the download fails. And this is why I was wondering if there was some way to prevent incomplete downloads (using the download button). Or if there was some way to be warned automatically when the download fails. Once again, thanks for your help and for that incredible tool that is Galaxy. Best regards, Jean-François From: Jennifer Jackson j...@bx.psu.edu To: Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 07/06/2012 10:49 AM Subject:Re: [galaxy-dev] Incomplete datasets when dowloaded from history Hello Jean-François, For larger files, or if complete downloads seem to be a problem, using curl at a command or Terminal prompt is a great option. The syntax is: % curl -O 'copied-link-from-dataset-disc-icon' http://user.list.galaxyproject.org/Download-multiple-files-from-history-td4303996.html (wget is not currently supported, so please disregard those instructions in the post) I used the 'mailing list' version of the Galaxy custom google searches to find this thread. http://galaxy.psu.edu/search/mailinglists/ Links to all of the Galaxy custom searches are in the wiki in the side bar and other places, but also at the top of the Support page for quick access: http://wiki.g2.bx.psu.edu/Support Hopefully this helps, Jen Galaxy team On 6/6/12 6:53 AM, Jean-Francois Payotte wrote: Hi folks, Some of our local Galaxy instance users seem to be experiencing some strange behaviour lately. I searched the mailing-list archive but I didn't found anything related, so I'd be interested to know if somebody already had the same issue. The problem is that sometimes, when people are trying to download their datasets from their history, although the file seems to download successfully, it appears that the downloaded file is incomplete (for example a 3000 lines text file will show only maybe 2000 lines at the first download, 1600 lines at the second download, and so on... and eventually, the file will download completely. This issue happened with more than one user and with different tools. Does anybody ever had this kind of issue? Or does somebody would have an idea of where to look to solve this problem? Best regards, Jean-François ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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] Sharing data in Cistrome
Hi, Did you have special characters (é, à,...) in the email of the person you try to share with? If so, try whitout this special characters (è - e or à - a), it should works.. Bests, Alban Le 07/06/2012 16:26, Päivi Pihlajamaa a écrit : Hi, I am trying to share my files/history in Galaxy/Cistrome with my colleague, but the 'Share with user' link gives the following error. Could you please help me, am i doing something wrong or is there a bug in the system? Best regards, Päivi Server Error URL: http://cistrome.org/ap/history/share?use_panels=Falseid=7b2014ae6b4b7c3f Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:90 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.history:960 in share send_to_err=send_to_err ) Module galaxy.web.framework:733 in fill_template return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako return template.render( **data ) Module mako.template:296 in render return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template callable_(context, *args, **kwargs) Module _base_mako:42 in render_body __M_writer(unicode(next.body())) Module _history_share_mako:74 in render_body __M_writer(unicode(history.name)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128) -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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] Load Balancer config doesn't work
On Jun 1, 2012, at 4:36 AM, julie dubois wrote: Hi, After several post in an Apache Forum, I've solve any problem of my apache configuration to enable load balancer configuration. It seems work but when I launch my galaxy application, I arrive in this web page : Service temporarily Unavailable And my log apache shows this : [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8083 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8082 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8081 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8080 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) It means that galaxy doesn't listen the port 8080, 8081 ... I think it's my run.sh which cannot read my universe_wsgi.ini correctly. Because if it could read correctly, in my terminal I could see this type of line : Handling web0 with log file web0.log... Entering daemon mode... Now, Idon't see that! after the command GALAXY_RUN_ALL=1 sh run.sh --daemon, I just see : Entering Daemon mode. So in my view, it's not an Apache problem but a shell script galaxy problem. Somedy has already met this problem ? Have you a solution ? Hi Julie, If you have a look in run.sh you can see how the script is attempting to parse your config file. It's possible that the inline sed script is not working correctly in your environment. This: % sed -n 's/^\[server:\(.*\)\]/\1/ p' universe_wsgi.ini | xargs echo Should return a list of the servers you have defined in your universe_wsgi.ini, so if you have: [server:web0] [server:web1] The output of the above command should be: web0 web1 You can also start each server individually with: % python ./scripts/paster.py serve universe_wsgi.ini --server-name=web0 --pid-file=web0.pid --log-file=web0.log --daemon ... --nate Thank you. Julie ___ 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] How to upload local files in Galaxy
Hi Everyone, I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list. The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally. I did some reading, and hoped that library_import_dir in universe_wsgi.ini would do the trick, but it didn't. Therefore, I will really appreciate any suggestions. Thanks a lot in advance! -Mehmet ___ 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] How to upload local files in Galaxy
Mehmet: It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive. I found that confusing at first too. Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote: Hi Everyone, I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list. The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally. I did some reading, and hoped that library_import_dir in universe_wsgi.ini would do the trick, but it didn't. Therefore, I will really appreciate any suggestions. Thanks a lot in advance! -Mehmet ___ 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/ -- Brad Langhorst langho...@neb.commailto:langho...@neb.com 978-380-7564 ___ 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] AttributeError: 'module' object has no attribute 'FakeSocket'
On May 22, 2012, at 11:18 AM, Peter Cock wrote: On Tue, May 22, 2012 at 4:14 PM, Sarah Diehl di...@immunbio.mpg.de wrote: Thanks Peter! It's very likely that I have the exact same problem, because I also have CentOS and needed to compile Python. In that case make sure you've done this: sudo yum install openssl openssl-dev and then repeat the Python 2.6 configure, make, make test, make install. Peter P.S. We also wanted this: sudo yum install bzip2 bzip2-devel At the end of the configure output you get told what Python modules are disabled due to missing libraries - check this list for any other potential problems later on. Hi Peter, Thanks for pointing this out, this information is useful and I've added it to Step 0 at http://getgalaxy.org/ --nate ___ 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] I can't see or access pictures in FastQC
I appreciate you taking the time to help! I'm almost positive it's a local configuration issue, like you said, but without knowing how Galaxy generates or parses its internal links (in the form of [Galaxy web address]/datasets/[16 character hash]/display/[filename] ) it's tough to know how to attack the problem. I dug through some of the database tables in psql, but I couldn't find much of interest there either. hg tip result is: 7148:17d57db9a7c0 -- that's the May 9th release Thanks again for your help! 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/
Re: [galaxy-dev] I can't see or access pictures in FastQC
Hi, Daniel, The configuration suggested at http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy is what you followed to set your proxy up? That obfuscated link hash element is generated from internal database ids to help secure against malicious users viewing specific datasets - not something your web server configuration normally needs to know about or do anything about. The Galaxy paste process takes care of generating and interpreting them. If you want to dig deeper, the external scripting api has code for accessing datasets by generating the right hashes - see code and minimal docs at scripts/api On Fri, Jun 8, 2012 at 7:59 AM, Dorset, Daniel C daniel.dor...@vanderbilt.edu wrote: I appreciate you taking the time to help! I'm almost positive it's a local configuration issue, like you said, but without knowing how Galaxy generates or parses its internal links (in the form of [Galaxy web address]/datasets/[16 character hash]/display/[filename] ) it's tough to know how to attack the problem. I dug through some of the database tables in psql, but I couldn't find much of interest there either. hg tip result is: 7148:17d57db9a7c0 -- that's the May 9th release Thanks again for your help! Dan -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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] Galaxy Test Not Producing Output
Hi List, I'm trying to write a test for Galaxy and it fails on the result of the test differing from the expected output. As the output of diff (below) lists nothing but local_file data, I'm assuming that the issue is that no output is being generated by the test. The test config is a series of passed values, with the exception of one parameter, which is actually an entry pulled from a loc file directing my tool to the location of the file on disk (i.e. it's a identifier value). I'm not really sure what's happening, but I'd appreciate any help or pointers. Thanks, Kipper --- local_file +++ history_data @@ -1,100 +1,100 @@ -chr10 4522044 4522438 -chr10 5650896 5651310 -chr10 5772258 5772663 -chr10 9135867 9136467 -chr10 9946900 9947273 -chr10 10793689 10794313 -chr10 15790023 15790478 -chr10 16048435 16049028 -chr10 17620155 17620367 -chr10 21718404 21719020 -chr10 22967169 22967533 -chr10 22999383 22999802 -chr10 24511845 24512748 -chr10 24773636 24774006 -chr10 25975943 25976389 -chr10 26620032 26620396 -chr10 26907992 26908408 -chr10 28309833 28310034 -chr10 30908407 30909220 -chr10 31184776 31185151 -chr10 31191717 31192170 -chr10 31651098 31651551 -chr10 32422502 32422880 -chr10 33316453 33316817 -chr10 34353700 34354168 -chr10 34570612 34571026 -chr10 34853178 34853542 -chr10 34857471 34857818 -chr10 34994111 34994269 -chr10 38557788 38558691 -chr10 43296854 43297454 -chr10 44159102 44159480 -chr10 45208753 45209123 -chr10 45246414 45246794 -chr10 46861707 46862080 -chr10 47021051 47021457 -chr10 47716908 47717259 ___ 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] populating history with input files automatically from remote site?
Hello Nik, I have put together a project that builds heavily on mi-deployment that does some of what you want to do (and probably a bunch of things you don't), but you could hopefully pull out just the parts you need. The idea behind the project is to build really cheap cloud galaxy instances by not using EBS or S3. From one simple command-line execution you can launch an instance, configure Galaxy, and transfer data into it (including optionally placing the data in a configured history). The command for doing this would be: ./run.sh --action=configure --action=transfer file1 file2 file3 The entire system is configure from one yaml file (including tools, genomes, and galaxy data (users, passwords, workflows, histories), etc...). See settings.yaml-sample for the myriad of options. This project is the driver, configure everything you need here and run the launch/configure/transfer script: https://bitbucket.org/jmchilton/galaxy-vm-launcher This project is a fork of galaxy-dist with changesets needed to implement this functionality: https://bitbucket.org/jmchilton/cloud-galaxy-dist So to prepopulate a history the way you described, you will want to define a user and create a history for that user by modifying the galaxy section of settings.yaml: galaxy: ## In order to create data libraries. First user should be admin@localhost ## and an API key must be specified, be sure to change API keys and passwords users: - username: admin@localhost password: adminpass api_key: 1234556789 - username: us...@example.com password: pass1 api_key: 987654321 ## Histories to create for this user histories: - TransferExampleHistory Then at the top-level of the yaml file you will need to specify the transferred data should be loaded into this history specified above: transfer_history_name: TransferExampleHistory transfer_history_api_key: 987654321 I think you will want to look at the seed_database function in lib/galaxy.py of galaxy-vm-launcher and the scripts/api/handle_uploads.py script in cloud-galaxy-dist. https://bitbucket.org/jmchilton/galaxy-vm-launcher/src/8ac4834dc08c/lib/galaxy.py https://bitbucket.org/jmchilton/cloud-galaxy-dist/src/af9199b15195/scripts/api/handle_uploads.py Hope this is helpful, -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 On Tue, Jun 5, 2012 at 4:43 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, I have a galaxy instance running in the Amazon Cloud that I have customized and I want to be able to transfer files (via scp) to the instance (or its attached storage) and then have those files show up automatically in the history. Is this possible? Alternatively, is there some way to automatically populate the history of a registered user, so that when that user logs in, the files are automatically in a saved history? A third possibility would be to transfer the files and restart galaxy and then have the files show up automatically? Just to be clear, I do not want to use the Upload Files tool at all. Is there any way to implement any of these options? Any help would be highly appreciated. Thanks! - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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] Tool Shed Workflow
I have read through the documentation a couple times, but I still have a few questions about the recent tool shed enhancements. At MSI we have a testing environment and a production environment and I want to make sure the tool versions and configurations don't get out of sync, I would also like to test everything in our testing environment before it reaches production. Is there a recommended way to accomplish this rather than just manually repeating the same set of UI interactions twice? Can I just import tools through the testing UI and run the ./scripts/migrate_tools/ scripts on our testing repository and then move the resulting migrated_tools_conf.xml and integrated_tool_panel.xml files into production? I have follow up questions, but I will wait for a response on this point. Also as you are removing tools from Galaxy and placing them into our tool shed, what is the recommended course of actions for deployers that have made local minor tweaks to those tool configs and scripts and adapt them to our local environments? Along the same lines, what is the recommended course of action if we need to make minor tweaks to tools pulled into through the UI to adapt them to our institution. Thanks for your time, -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 ___ 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/
