Re: [galaxy-dev] How to customize Galaxy web interface?
Hi Pascal I didn't see anyone else reply to this, but for our local Galaxy install I use the front page in static/welcome.html as a place to put information on usage policies and recent changes. There are also some options in universe_wsgi.ini: - logo_url sets the URL that’s linked from the Galaxy logo in the masthead (I set it to the URL for the local installation) - brand sets text that's appended to the Galaxy title in the masthead There is also a static_style_dir parameter which sets where the CSS files are found, by default these are in /static/june_2007_style/blue - I didn't change this but I have edited some of the styles in base.css and panel_layout.css to change the colours for the local Galaxy. Hope this is some help, best wishes Peter On 30/04/12 11:07, Pascal Maugeri wrote: Hi, I m running my own Galaxy instance and I would like to do some simple customization of the web interface such as adding my logos in the header frame, changing background colors, etc. I am having a look to static/ folders but I can't see clearly where the header frame is defined. Could you please tell me if there is any tutorial for doing so? Any starting point? Or which folder/file(s) corresponds to the web interface in the distribution? Best Regards, Pascal ___ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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 customize Galaxy web interface?
Thanks Peter for your response! Since I posted my question I also discovered that the header panel (aka masthead) is controled by the script database/compiled_templates/webapps/galaxy/base_panels.mako.py Best Regards, Pascal On Thu, May 3, 2012 at 10:16 AM, Peter Briggs peter.bri...@manchester.ac.uk wrote: Hi Pascal I didn't see anyone else reply to this, but for our local Galaxy install I use the front page in static/welcome.html as a place to put information on usage policies and recent changes. There are also some options in universe_wsgi.ini: - logo_url sets the URL that’s linked from the Galaxy logo in the masthead (I set it to the URL for the local installation) - brand sets text that's appended to the Galaxy title in the masthead There is also a static_style_dir parameter which sets where the CSS files are found, by default these are in /static/june_2007_style/blue - I didn't change this but I have edited some of the styles in base.css and panel_layout.css to change the colours for the local Galaxy. Hope this is some help, best wishes Peter On 30/04/12 11:07, Pascal Maugeri wrote: Hi, I m running my own Galaxy instance and I would like to do some simple customization of the web interface such as adding my logos in the header frame, changing background colors, etc. I am having a look to static/ folders but I can't see clearly where the header frame is defined. Could you please tell me if there is any tutorial for doing so? Any starting point? Or which folder/file(s) corresponds to the web interface in the distribution? Best Regards, Pascal __**_ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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] update problem
Hi Guys, After the most recent 'hg pull -u' followed by 'hg merge', I get the following error in paster.log when I try to restart Galaxy: galaxy.tools.imp_exp DEBUG 2012-05-03 11:17:10,375 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2012-05-03 11:17:10,376 Loaded history import tool: __IMPORT_HISTORY__ Traceback (most recent call last): File /usr/local/bin/moma/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /usr/local/bin/moma/galaxy/galaxy-dist/lib/galaxy/app.py, line 129, in __init__ self.job_manager = manager.JobManager( self ) File /usr/local/bin/moma/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py, line 30, in __init__ if self.app.config.server_name in self.app.config.job_handlers: AttributeError: 'Configuration' object has no attribute 'server_name' What am I doing wrong? Is there another way to update, when I don't want to loose my own changes - actually additions as in new tools ans tool xml-files? When I run 'hg merge' I get vim showing me a bunch of changed files. I don't actually know what to do with them, so I just exit vim by :q! until I've been through all the files. Any ideas? Kind regards - Frank -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363 ___ 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 Admin - Browsing any user's histories?
Hi all, Is it possible for a Galaxy Admin to browse any user's history? Sadly the Admin page on the wiki is still rather lean: http://wiki.g2.bx.psu.edu/Admin/Interface For instance, I've monitored a large Galaxy job on our cluster, and now that it has finished I'd like to see the results (in this case, the error messages) - without having to first ask the user to share their history with me. Is that possible via the normal Galaxy Admin pages? Alternatively, is this something I could do via the impersonation option? i.e. enable allow_user_impersonation in universe_wsgi.ini 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] Best way to allow users to configure a display application url for a toolshed tool
Hi Ira,
You'll need to include an entry for the display application in a
datatype_conf.xml file in the tool shed repository- this will result in the
display application being properly installed with the repository and made
functional in the local Galaxy instance. For details about this, see the
following section of the tool shed wiki.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Tool_Shed.Including_datatype_converters_and_display_applications
Let me know if you have any questions on this.
Thanks!
On May 2, 2012, at 11:19 PM, Daniel Blankenberg wrote:
Hi Ira,
You'll want to set this up as a dynamic display application, where the link
id, name, url, port, etc are defined in an external tab-delimited file. Most
of the displays included in the dist are set up this way, one example would
be the display_applications/ucsc/bam.xml.
For an example where the external display application needs to access
Galaxy's datasets directly on a shared filesystem have a look at
display_applications/genetrack.xml.
Thanks for using Galaxy,
Dan
On May 2, 2012, at 10:58 PM, Ira Cooke wrote:
Dear All,
Our toolshed tools include a custom display application. Although the
display application is open source (
https://bitbucket.org/Andrew_Brock/proteomics-visualise ) we do not yet have
a public server for it. Actually, at present it isn't possible to have the
application work properly if it is running on a completely separate server
because it needs access to galaxy's database/files directory (I'll leave
that for another question). For now I just need to be able to provide a way
for administrators of a local galaxy to configure the url to this display
application.
At the moment we have it hard coded .. like this;
url
target_frame=galaxy_mainhttp://${galaxy_url.qp}:8500/init_local?file=${encoded_filename.qp}amp;type=mzml/url
Using the galaxy_url (because we are on the same server) .. and hard coding
the port.
What would be the best way to allow local admins to configure this?
Thanks
Ira
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Re: [galaxy-dev] Galaxy Admin - Browsing any user's histories?
On 05/03/2012 12:10 PM, Peter Cock wrote: Hi all, Is it possible for a Galaxy Admin to browse any user's history? Sadly the Admin page on the wiki is still rather lean: http://wiki.g2.bx.psu.edu/Admin/Interface For instance, I've monitored a large Galaxy job on our cluster, and now that it has finished I'd like to see the results (in this case, the error messages) - without having to first ask the user to share their history with me. Is that possible via the normal Galaxy Admin pages? for cases like this, we use the additional galaxy report server. It is very handy to track down what went wrong (ie how did the executed command look like) and who was the 'culprit' (see: 'reports_wsgi.ini' ) Alternatively, is this something I could do via the impersonation option? i.e. enable allow_user_impersonation in universe_wsgi.ini allow_user_impersonation is great and will probably help in your situation as well. Unfortunately, it does not (yet) work with external authentication, to follow up, see: https://bitbucket.org/galaxy/galaxy-central/issue/705/ Regards, Hans 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/ ___ 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] Best way to allow users to configure a display application url for a toolshed tool
Hi Dan and Greg,
Thanks for your answers on this. So far I have managed to make things work
following Dan's suggestion ... except that I can't seem to get my configuration
data file to install into tool-data. I'm not sure why this might be since all
my XXX.loc.sample files install into tool-data fine. I tried adding a file to
my tool repository under tool-data/protk_site_config.txt.sample ... and had
hoped it would result in a file being installed (when the tools are installed)
into tool-data/protk_site_config.txt .. but unfortunately this doesn't happen.
If I hack things and copy the file in place manually then Dan's instructions
work (after modifying my display applications).
Anyway, I'll investigate this a bit more tomorrow. Hopefully you can shed some
light on why my .loc.sample files are copied fine, but my other file is not.
Does galaxy only install tool-data files with the .loc.sample naming
convention? Or is there some other internal filter/check that could be stopping
my config file being installed.
Thanks
Ira
On 03/05/2012, at 8:35 PM, Greg Von Kuster wrote:
Hi Ira,
You'll need to include an entry for the display application in a
datatype_conf.xml file in the tool shed repository- this will result in the
display application being properly installed with the repository and made
functional in the local Galaxy instance. For details about this, see the
following section of the tool shed wiki.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Tool_Shed.Including_datatype_converters_and_display_applications
Let me know if you have any questions on this.
Thanks!
On May 2, 2012, at 11:19 PM, Daniel Blankenberg wrote:
Hi Ira,
You'll want to set this up as a dynamic display application, where the link
id, name, url, port, etc are defined in an external tab-delimited file. Most
of the displays included in the dist are set up this way, one example would
be the display_applications/ucsc/bam.xml.
For an example where the external display application needs to access
Galaxy's datasets directly on a shared filesystem have a look at
display_applications/genetrack.xml.
Thanks for using Galaxy,
Dan
On May 2, 2012, at 10:58 PM, Ira Cooke wrote:
Dear All,
Our toolshed tools include a custom display application. Although the
display application is open source (
https://bitbucket.org/Andrew_Brock/proteomics-visualise ) we do not yet
have a public server for it. Actually, at present it isn't possible to
have the application work properly if it is running on a completely
separate server because it needs access to galaxy's database/files
directory (I'll leave that for another question). For now I just need to
be able to provide a way for administrators of a local galaxy to configure
the url to this display application.
At the moment we have it hard coded .. like this;
url
target_frame=galaxy_mainhttp://${galaxy_url.qp}:8500/init_local?file=${encoded_filename.qp}amp;type=mzml/url
Using the galaxy_url (because we are on the same server) .. and hard coding
the port.
What would be the best way to allow local admins to configure this?
Thanks
Ira
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and other Galaxy lists, please use the interface at:
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___
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and other Galaxy lists, please use the interface at:
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___
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Re: [galaxy-dev] galaxy cluster integration
Hi, Just to keep you updated of my progress. I've just been talking with our cluster administrator, and they are going to install LSF client on the machine which currently host our Galaxy server making it a submitting node to the cluster. I am now waiting to test how it is going to work when all ready. I'll let you know. Cheers, Anne. On 2 May 2012, at 22:16, Anne Pajon wrote: Yes we do have an LSF cluster. Thanks indeed for all the information, Peter. I'll contact our cluster administrator tomorrow and keep you posted on my progress. Kind regards, Anne. On 2 May 2012, at 22:07, Peter Cock wrote: On Wed, May 2, 2012 at 9:58 PM, Anne Pajon anne.pa...@cancer.org.uk wrote: Hi Peter, Thanks for the clarification, it is really helpful. Would you mind sharing what needs to be done in term of configuration and instalation to transform the galaxy server into a submitting job to the cluster? Thanks. You said you have an LSF cluster - so I have no idea, sorry :( We're using SGE here. I'm presuming similar concepts apply - in our case a key step was getting qsub/qstat/qdel to work from the Galaxy server as well as the cluster head node - which required our cluster administrator to setup our Galaxy server as an SGE submit node. Regards, Peter -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)7958 511 353 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ 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/ -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)1223 404 334 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ 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] Galaxy Admin - Browsing any user's histories?
On Thu, May 3, 2012 at 11:40 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: On 05/03/2012 12:10 PM, Peter Cock wrote: Hi all, Is it possible for a Galaxy Admin to browse any user's history? Sadly the Admin page on the wiki is still rather lean: http://wiki.g2.bx.psu.edu/Admin/Interface For instance, I've monitored a large Galaxy job on our cluster, and now that it has finished I'd like to see the results (in this case, the error messages) - without having to first ask the user to share their history with me. Is that possible via the normal Galaxy Admin pages? for cases like this, we use the additional galaxy report server. It is very handy to track down what went wrong (ie how did the executed command look like) and who was the 'culprit' (see: 'reports_wsgi.ini' ) That does cover my immediate needs for job post mortems. Thanks. Alternatively, is this something I could do via the impersonation option? i.e. enable allow_user_impersonation in universe_wsgi.ini allow_user_impersonation is great and will probably help in your situation as well. Unfortunately, it does not (yet) work with external authentication, to follow up, see: https://bitbucket.org/galaxy/galaxy-central/issue/705/ We're not currently using that - although it would be interesting to explore in combination with running cluster jobs as the user, something we may want to do in future. Thank you, 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/
[galaxy-dev] Can't upload Cuffmerge files to Galaxy Cloudman
Hello, I can not upload Cuffmerge files to Galaxy Cloudman. I can load other .gtf files just fine, but not the merged transcripts.gtf file from Cuffmerge. This is the first time this has happened. After I upload my merged transcripts.gtf file (via ftp) I can not move the file to the history pane. Upon asking Galaxy Cloudman to move the file from the ftp queue to the history pane, I get the error: No data was entered in the upload form, please go back and choose data to upload Even if I try to zip the file to fool Galaxy Cloudman the file still won't load. This may be unrelated, but I have never been able to download Cuffdiff out put files from Galaxy Cloudman directly, I always have to export my history to a file and then rename the files after download. Any help would be great! Cheers, Mo Heydarian ___ 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't upload Cuffmerge files to Galaxy Cloudman
Also, this issue with uploading Cuffmerge files to Galaxy Cloudman is specific to Cuffmerge files I have generated within the last ~24 hours (on Galaxy Main). I can upload these same files to main Galaxy server with no problem. It is specific to Galaxy Cloudman. Thanks for any help! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Thu, May 3, 2012 at 8:19 AM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hello, I can not upload Cuffmerge files to Galaxy Cloudman. I can load other .gtf files just fine, but not the merged transcripts.gtf file from Cuffmerge. This is the first time this has happened. After I upload my merged transcripts.gtf file (via ftp) I can not move the file to the history pane. Upon asking Galaxy Cloudman to move the file from the ftp queue to the history pane, I get the error: No data was entered in the upload form, please go back and choose data to upload Even if I try to zip the file to fool Galaxy Cloudman the file still won't load. This may be unrelated, but I have never been able to download Cuffdiff out put files from Galaxy Cloudman directly, I always have to export my history to a file and then rename the files after download. Any help would be great! Cheers, Mo Heydarian ___ 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] Galaxy not killing split cluster jobs
On Tue, May 1, 2012 at 3:46 PM, Dannon Baker dannonba...@me.com wrote: I'll take care of it. Thanks for reminding me about the TODO! On a related point, I've noticed sometimes one child job from a split task can fail, yet the rest of the child jobs continue to run on the cluster wasting CPU time. As soon as one child job dies (assuming there are no plans for attempting a retry), I would like the parent task to kill all the other children, and fail itself. I suppose you could merge the output of any children which did finish... but it would be simpler not to bother. Regards, 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] Galaxy not killing split cluster jobs
On a related point, I've noticed sometimes one child job from a split task can fail, yet the rest of the child jobs continue to run on the cluster wasting CPU time. As soon as one child job dies (assuming there are no plans for attempting a retry), I would like the parent task to kill all the other children, and fail itself. I suppose you could merge the output of any children which did finish... but it would be simpler not to bother. Right now, yes, this would make sense- I'll see about adding it. Ultimately we want to build in a mechanism for retrying child tasks that fail due to cluster errors, etc, so it isn't necessary to rerun the entire job. -Dannon ___ 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] Galaxy not killing split cluster jobs
On Thu, May 3, 2012 at 3:54 PM, Dannon Baker dannonba...@me.com wrote: On a related point, I've noticed sometimes one child job from a split task can fail, yet the rest of the child jobs continue to run on the cluster wasting CPU time. As soon as one child job dies (assuming there are no plans for attempting a retry), I would like the parent task to kill all the other children, and fail itself. I suppose you could merge the output of any children which did finish... but it would be simpler not to bother. Right now, yes, this would make sense- I'll see about adding it. Great. Ultimately we want to build in a mechanism for retrying child tasks that fail due to cluster errors, etc, so it isn't necessary to rerun the entire job. That could be helpful - but also rather fiddly for detecting when it is appropriate to retry a job or now. For the split-tasks, right now I'm finding some child-jobs fail when the OS kills them due to running out of RAM - in which case a neat idea would be to further sub-divide the jobs and resubmit. This is probably over-engineering though... KISS principle. 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/
[galaxy-dev] Sub-task splitting
Hello all, Currently the Galaxy experimental task splitting code allows splitting into N chunks, e.g. 8 parts, with: parallelism method=multi split_mode=number_of_parts split_size=8 ... / Or, into chunks of at most size N (units dependent on the file type, e.g. lines in a tabular file or number of sequences in FASTA/FASTQ), e.g. at most 1000 sequences: parallelism method=multi split_mode=to_size split_size=1000 ... / As an aside I found it confusing that the meaning of the split_size attribute depend on the split_mode (number of jobs, or size of jobs). I would prefer to be able to set both sizes - in this case tell Galaxy to try to use at least 8 parts, each of at most 1000 sequences. Thus in a BLAST task, initially the split would be (up to) eight ways: 8 queries = 8 jobs each with 1 query 80 queries = 8 jobs each with 10 queries 800 queries = 8 jobs each with 100 queries 8000 queries = 8 jobs each with 1000 queries Then, once the max chunk size comes into play, you'd just get more jobs: 9000 queries = 9 jobs each with 1000 queries 1 queries = 10 jobs each with 1000 queries 2 queries = 20 jobs each with 1000 queries etc The appeal of this is it takes advantage of parallelism for small jobs (under 100 queries) and large jobs (1000s of queries), while able to impose a maximum size on each cluster job. The problem is this requires changing the XML tags, and getting rid of the current two modes in favour of this combined one. Perhaps this: parallelism method=multi min_jobs=8 max_size=1000 ... / The jobs threshold isn't strictly a minimum - if you have N 8 query sequences, you'd just have N jobs of 1 query each. Does this sound sufficiently general? The split code is still rather experimental so I don't expect breaking the API to be a big issue (not many people are using it). 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/
[galaxy-dev] Keep header and output BAM options for NGS: SAM Tools/Filter SAM tool
Hi, I regularly use NGS: SAM Tools/Filter SAM tool. Filtering after mapping with BWA is a required step. I feel my current approach to reintroduce the header after filtering is very wasteful. Wouldn't be great if this tool had an option to keep the header? This sounds simple enough. In fact looking at the logic in the python script: for line in infile: line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ) and not line.startswith( '@' ) : fields = line.split( '\t' ) flags = int( fields[flag_col] ) valid_line = True for index, opt_bool in used_indices: if bool(flags 0x0001 index) != opt_bool: valid_line = False break if valid_line: print line It seems like it could be done by adding at most a couple of lines. Also, most of the time after filtering what you really want is a sorted BAM file. Most tools dealing with SAM/BAM files in Galaxy already have the option to output a sorted BAM file. I think it would be nice if Filter SAM followed the same path. Are these enhances in the radar? Would you take a pull request implementing them? Best, Carlos ___ 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] Sub-task splitting
+1. This is especially useful for us, with hardware-accelerated algorithms having limits on input size. On 12-05-03 9:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hello all, Currently the Galaxy experimental task splitting code allows splitting into N chunks, e.g. 8 parts, with: parallelism method=multi split_mode=number_of_parts split_size=8 ... / Or, into chunks of at most size N (units dependent on the file type, e.g. lines in a tabular file or number of sequences in FASTA/FASTQ), e.g. at most 1000 sequences: parallelism method=multi split_mode=to_size split_size=1000 ... / As an aside I found it confusing that the meaning of the split_size attribute depend on the split_mode (number of jobs, or size of jobs). I would prefer to be able to set both sizes - in this case tell Galaxy to try to use at least 8 parts, each of at most 1000 sequences. Thus in a BLAST task, initially the split would be (up to) eight ways: 8 queries = 8 jobs each with 1 query 80 queries = 8 jobs each with 10 queries 800 queries = 8 jobs each with 100 queries 8000 queries = 8 jobs each with 1000 queries Then, once the max chunk size comes into play, you'd just get more jobs: 9000 queries = 9 jobs each with 1000 queries 1 queries = 10 jobs each with 1000 queries 2 queries = 20 jobs each with 1000 queries etc The appeal of this is it takes advantage of parallelism for small jobs (under 100 queries) and large jobs (1000s of queries), while able to impose a maximum size on each cluster job. The problem is this requires changing the XML tags, and getting rid of the current two modes in favour of this combined one. Perhaps this: parallelism method=multi min_jobs=8 max_size=1000 ... / The jobs threshold isn't strictly a minimum - if you have N 8 query sequences, you'd just have N jobs of 1 query each. Does this sound sufficiently general? The split code is still rather experimental so I don't expect breaking the API to be a big issue (not many people are using it). 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/ ___ 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] Best way to allow users to configure a display application url for a toolshed tool
Hi Ira,
Sample fiel handling for installed tool shed repositories was restricted to
.loc.sample files as you discovered. I've enhanced this feature to copy all
appropriate .sample files contained in the installed repository to the
tool-data directory of the Galaxy instance to which the repository was
installed. This enhancement is available in change set 7145:ea9f3c25a415 in
our central repository. Thanks for reporting this problem!
Greg Von Kuster
On May 3, 2012, at 6:49 AM, Ira Cooke wrote:
Hi Dan and Greg,
Thanks for your answers on this. So far I have managed to make things work
following Dan's suggestion ... except that I can't seem to get my
configuration data file to install into tool-data. I'm not sure why this
might be since all my XXX.loc.sample files install into tool-data fine. I
tried adding a file to my tool repository under
tool-data/protk_site_config.txt.sample ... and had hoped it would result in a
file being installed (when the tools are installed) into
tool-data/protk_site_config.txt .. but unfortunately this doesn't happen. If
I hack things and copy the file in place manually then Dan's instructions
work (after modifying my display applications).
Anyway, I'll investigate this a bit more tomorrow. Hopefully you can shed
some light on why my .loc.sample files are copied fine, but my other file is
not. Does galaxy only install tool-data files with the .loc.sample naming
convention? Or is there some other internal filter/check that could be
stopping my config file being installed.
Thanks
Ira
On 03/05/2012, at 8:35 PM, Greg Von Kuster wrote:
Hi Ira,
You'll need to include an entry for the display application in a
datatype_conf.xml file in the tool shed repository- this will result in the
display application being properly installed with the repository and made
functional in the local Galaxy instance. For details about this, see the
following section of the tool shed wiki.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Tool_Shed.Including_datatype_converters_and_display_applications
Let me know if you have any questions on this.
Thanks!
On May 2, 2012, at 11:19 PM, Daniel Blankenberg wrote:
Hi Ira,
You'll want to set this up as a dynamic display application, where the link
id, name, url, port, etc are defined in an external tab-delimited file.
Most of the displays included in the dist are set up this way, one example
would be the display_applications/ucsc/bam.xml.
For an example where the external display application needs to access
Galaxy's datasets directly on a shared filesystem have a look at
display_applications/genetrack.xml.
Thanks for using Galaxy,
Dan
On May 2, 2012, at 10:58 PM, Ira Cooke wrote:
Dear All,
Our toolshed tools include a custom display application. Although the
display application is open source (
https://bitbucket.org/Andrew_Brock/proteomics-visualise ) we do not yet
have a public server for it. Actually, at present it isn't possible to
have the application work properly if it is running on a completely
separate server because it needs access to galaxy's database/files
directory (I'll leave that for another question). For now I just need to
be able to provide a way for administrators of a local galaxy to configure
the url to this display application.
At the moment we have it hard coded .. like this;
url
target_frame=galaxy_mainhttp://${galaxy_url.qp}:8500/init_local?file=${encoded_filename.qp}amp;type=mzml/url
Using the galaxy_url (because we are on the same server) .. and hard
coding the port.
What would be the best way to allow local admins to configure this?
Thanks
Ira
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] Problems saving a cloned workflow
Hello, I cloned a workflow on my local Galaxy installation, renamed it, made some edits and pressed save. It has been saving now for about 3 hours. It only has 12 steps. Any suggestions? Thanks in advance, Liisa ___ 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] ImportError: No module named NSISSoft.NSISBase
Dear all, I have a local installation of Galaxy. I need to create a new galaxy tool. My python program runs outside Galaxy. When I call it through Galaxy it does not find my custom libraries. * * *ImportError: No module named NSISSoft.NSISBase* * * *I understand it is a PYTHONPATH problem. How can I fix it?* * * *Kleo Achilleos* *MSc student at UCY, Cyprus* ___ 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] Problems saving a cloned workflow
Liisa, Are there any errors in your paster.log or javascript console? What revision are you running? -Dannon On May 3, 2012, at 2:28 PM, Liisa Koski wrote: Hello, I cloned a workflow on my local Galaxy installation, renamed it, made some edits and pressed save. It has been saving now for about 3 hours. It only has 12 steps. Any suggestions? Thanks in advance, Liisa ___ 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] Running Galaxy on PBS/Torque cluster
I have had Galaxy running on a local BAS, and after success with that we're ready to create an instance on our local cluster computing service. The local cluster uses PBS/Torque. I'm familiar with the basics of configuration, but our particular scheduler rewards those who specify accurate walltimes. I would like to be able to define specific walltimes for each tool. I'm mapping out a strategy for how best to specify accurate walltimes. For instance, if someone is running tophat, it will take longer if they're mapping against a complex reference genome like human, as opposed to nematode. I'd like to use different walltimes to account for that. Is there anyone who has tackled this and would be willing to share their approach with me? 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/
[galaxy-dev] Empty file generation
This is my code for running samtools pileup:
open INP, $ARGV[0]
or die Cannot open file! $!;
open INP2, $ARGV[1]
or die Cannot open file! $!;
open OUT, $ARGV[2]
or die Cannot open file! $!;
open SCRIPT,samtools pileup -cv -f $ARGV[0] $ARGV[1] 2/dev/null | ;
while(SCRIPT) {
print OUT $_;
}
close INP;
close INP2;
close OUT;
close SCRIPT;
In the console, it works perfectly. But when run in Galaxy, it gives me an
empty file. I don't think it has something to do with the files that I am
using as input, for I just uploaded the ones that I used in the console
test-run. Any idea why this might be happening?
Cheers,
CL
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[galaxy-dev] Are uploads already indexed and/or sorted?
Hi all, Do the uploaded files in Galaxy get indexed or sorted already? Cheers, CL ___ 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] Best way to allow users to configure a display application url for a toolshed tool
Hi Greg,
Thanks ... that's great. It's all working now.
Ira
On 04/05/2012, at 3:41 AM, Greg Von Kuster wrote:
Hi Ira,
Sample fiel handling for installed tool shed repositories was restricted to
.loc.sample files as you discovered. I've enhanced this feature to copy all
appropriate .sample files contained in the installed repository to the
tool-data directory of the Galaxy instance to which the repository was
installed. This enhancement is available in change set 7145:ea9f3c25a415 in
our central repository. Thanks for reporting this problem!
Greg Von Kuster
On May 3, 2012, at 6:49 AM, Ira Cooke wrote:
Hi Dan and Greg,
Thanks for your answers on this. So far I have managed to make things work
following Dan's suggestion ... except that I can't seem to get my
configuration data file to install into tool-data. I'm not sure why this
might be since all my XXX.loc.sample files install into tool-data fine. I
tried adding a file to my tool repository under
tool-data/protk_site_config.txt.sample ... and had hoped it would result in
a file being installed (when the tools are installed) into
tool-data/protk_site_config.txt .. but unfortunately this doesn't happen.
If I hack things and copy the file in place manually then Dan's instructions
work (after modifying my display applications).
Anyway, I'll investigate this a bit more tomorrow. Hopefully you can shed
some light on why my .loc.sample files are copied fine, but my other file is
not. Does galaxy only install tool-data files with the .loc.sample naming
convention? Or is there some other internal filter/check that could be
stopping my config file being installed.
Thanks
Ira
On 03/05/2012, at 8:35 PM, Greg Von Kuster wrote:
Hi Ira,
You'll need to include an entry for the display application in a
datatype_conf.xml file in the tool shed repository- this will result in the
display application being properly installed with the repository and made
functional in the local Galaxy instance. For details about this, see the
following section of the tool shed wiki.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Tool_Shed.Including_datatype_converters_and_display_applications
Let me know if you have any questions on this.
Thanks!
On May 2, 2012, at 11:19 PM, Daniel Blankenberg wrote:
Hi Ira,
You'll want to set this up as a dynamic display application, where the
link id, name, url, port, etc are defined in an external tab-delimited
file. Most of the displays included in the dist are set up this way, one
example would be the display_applications/ucsc/bam.xml.
For an example where the external display application needs to access
Galaxy's datasets directly on a shared filesystem have a look at
display_applications/genetrack.xml.
Thanks for using Galaxy,
Dan
On May 2, 2012, at 10:58 PM, Ira Cooke wrote:
Dear All,
Our toolshed tools include a custom display application. Although the
display application is open source (
https://bitbucket.org/Andrew_Brock/proteomics-visualise ) we do not yet
have a public server for it. Actually, at present it isn't possible to
have the application work properly if it is running on a completely
separate server because it needs access to galaxy's database/files
directory (I'll leave that for another question). For now I just need to
be able to provide a way for administrators of a local galaxy to
configure the url to this display application.
At the moment we have it hard coded .. like this;
url
target_frame=galaxy_mainhttp://${galaxy_url.qp}:8500/init_local?file=${encoded_filename.qp}amp;type=mzml/url
Using the galaxy_url (because we are on the same server) .. and hard
coding the port.
What would be the best way to allow local admins to configure this?
Thanks
Ira
___
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/
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
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