Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Ann, I'm interested. I'm running a Galaxy instance on AWS Cloud, using the standard Galaxy Cloudman. Based in Sydney, Aus and also users at SDU, Odense, Denmark. My timezone for a conf call would be UTC +10 as for some others here. Greg Edwards On Sat, Apr 28, 2012 at 4:45 AM, Ann Black-Ziegelbein < annbl...@eng.uiowa.edu> wrote: > Hi everyone - > > Here at the University of Iowa we are working on deploying Galaxy locally > for campus wide access. I am interested in forming a community of other > institutions trying to deploy Galaxy locally and mange/operate it on a > broad level. Is anyone else? If there is enough interest, possibly we > could have a community conference call every other month to have an open > discussion on how we are all deploying galaxy, customizations we are > making, problems we are encountering, bugs, and any add-on operations > management for galaxy being developed, etc. > > Would love to hear from others operating Galaxy or in process of standing > up a local deployment. > > Thanks! > > Ann Black-Ziegelbein > __**_ > 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/ > -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.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/
Re: [galaxy-dev] Best way to allow users to configure a display application url for a toolshed tool
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;
>
> target_frame="galaxy_main">http://${galaxy_url.qp}:8500/init_local?file=${encoded_filename.qp}&type=mzml
>
> 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/
___
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[galaxy-dev] Best way to allow users to configure a display application url for a toolshed tool
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;
http://${galaxy_url.qp}:8500/init_local?file=${encoded_filename.qp}&type=mzml
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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[galaxy-dev] About pileups
Hi all, I am implementing a script in Galaxy that runs samtools' pileup command. Although it is running, I always get an empty file. I'm curious: what is the datatype of the output of a pileup/mpileup command? I think I might be having a problem with the output since the output data type might be incorrect. Thanks in advance for the help! 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] Full path through API display.py
Done!. On Wed, May 2, 2012 at 4:35 PM, Dannon Baker wrote: > Yep, that's the right place to put it. And you'll never hear me suggest > someone *not* send in a pull request, so go for it :) > > -Dannon > > On May 2, 2012, at 3:08 PM, Carlos Borroto wrote: > >> Thanks Dannon. >> >> I was actually in a hurry so I poke around and found what I think is >> the right place to tie this in. >> >> In function "get_api_value" in "lib/galaxy/model/__init__.py" line 1159: >> rval = dict( id = hda.id, >> model_class = self.__class__.__name__, >> name = hda.name, >> deleted = hda.deleted, >> visible = hda.visible, >> state = hda.state, >> + file_name = hda.file_name, >> file_size = int( hda.get_size() ), >> data_type = hda.ext, >> genome_build = hda.dbkey, >> misc_info = hda.info, >> misc_blurb = hda.blurb ) >> >> Would it be helpful if I submit a pull request for this? Cause I was >> wondering if for changes so simple as this one, a pull request from a >> third party introduces more overhead than help. >> >> >> On Tue, May 1, 2012 at 3:05 PM, Dannon Baker wrote: >>> Sure, good idea. I'll tie it in. >>> >>> -Dannon >>> >>> On May 1, 2012, at 3:03 PM, Carlos Borroto wrote: >>> Hi, Recently "Full Path" display was added as an option. I was wondering if this information could also be available when accessing a dataset information through the API. Thanks, 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/ >>> > ___ 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] Difficulties using tagset with min attribute
Hi all - I've been trying to get the ... tag working with a min attribute for some time now, though without any success. It works in other tools distributed with Galaxy, but when I attempt to use it in one of our custom tools, it dies with a "AttributeError: 'ExpressionContext' object has no attribute 'keys'" exception. Can anybody offer any insight? The full traceback is: ⇝ AttributeError: 'ExpressionContext' object has no attribute 'keys' URL: http://localhost:8080/tool_runner?tool_id=scde-list-compare Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.controllers.tool_runner:68 in index view >> template, vars = tool.handle_input( trans, params.__dict__ ) Module galaxy.tools:1320 in handle_input view >> state = self.new_state( trans ) Module galaxy.tools:1248 in new_state view >> self.fill_in_new_state( trans, inputs, state.inputs ) Module galaxy.tools:1257 in fill_in_new_state view >> state[ input.name ] = input.get_initial_value( trans, context ) Module galaxy.tools.parameters.grouping:100 in get_initial_value view >> rval_dict[ input.name ] = input.get_initial_value( trans, context ) Module galaxy.tools.parameters.basic:1016 in get_initial_value view >> return SelectToolParameter.get_initial_value( self, trans, context ) Module galaxy.tools.parameters.basic:785 in get_initial_value view >> if self.need_late_validation( trans, context ): Module galaxy.tools.parameters.basic:1022 in need_late_validation view >> if super( ColumnListParameter, self ).need_late_validation( trans, context ): Module galaxy.tools.parameters.basic:766 in need_late_validation view >> for layer in context.itervalues(): Module UserDict:116 in itervalues view >> for _, v in self.iteritems(): Module UserDict:109 in iteritems view >> for k in self: Module UserDict:96 in __iter__ view >> for k in self.keys(): AttributeError: 'ExpressionContext' object has no attribute 'keys' ___ 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 cluster integration
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 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/
Re: [galaxy-dev] galaxy cluster integration
On Wed, May 2, 2012 at 9:58 PM, Anne Pajon 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 ___ 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 cluster integration
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. Anne. On 2 May 2012, at 21:51, Peter Cock wrote: > On Wed, May 2, 2012 at 9:40 PM, Anne Pajon wrote: >> Hi Peter, >> >> Thanks for your answer. >> >> No the galaxy machine is not a submitting node of the cluster. > > That's probably the problem then :) > >> So I suppose I do have those two options: >> >> (1) making the galaxy server a submitting node to the cluster >> or >> (2) install and run galaxy on a cluster node >> >> What would be best? Any suggestions? If (1), any ideas on >> what needs to be installed? > > We went with (1), partly for historical admin reasons of > machine ownership - but also this avoided having a single > critical point with one machine running both Galaxy and > being our cluster head node (since the cluster isn't just > used for Galaxy jobs). > > Regarding (2), I don't think you want Galaxy running on a > cluster compute node - Galaxy isn't that computationally > demanding but I wouldn't want the same machine to also > be running general cluster jobs. Consider a rogue job > submitted to the cluster which consumes too much RAM > and brings the node down - that can be annoying, but it > would be painful if this also killed your Galaxy server. > > It might make sense to put Galaxy on your cluster head > node - which might make sharing the data drive simpler > too, depending on how your cluster is setup. > > 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/
Re: [galaxy-dev] galaxy cluster integration
On Wed, May 2, 2012 at 9:40 PM, Anne Pajon wrote: > Hi Peter, > > Thanks for your answer. > > No the galaxy machine is not a submitting node of the cluster. That's probably the problem then :) > So I suppose I do have those two options: > > (1) making the galaxy server a submitting node to the cluster > or > (2) install and run galaxy on a cluster node > > What would be best? Any suggestions? If (1), any ideas on > what needs to be installed? We went with (1), partly for historical admin reasons of machine ownership - but also this avoided having a single critical point with one machine running both Galaxy and being our cluster head node (since the cluster isn't just used for Galaxy jobs). Regarding (2), I don't think you want Galaxy running on a cluster compute node - Galaxy isn't that computationally demanding but I wouldn't want the same machine to also be running general cluster jobs. Consider a rogue job submitted to the cluster which consumes too much RAM and brings the node down - that can be annoying, but it would be painful if this also killed your Galaxy server. It might make sense to put Galaxy on your cluster head node - which might make sharing the data drive simpler too, depending on how your cluster is setup. 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] Can someone help me spec out a new computer for using Galaxy? Need to spend money this week!
The Dell T710s can be configured pretty well and have 12cpu and if you go with the cheaper hardrives you will be able to get a lot for your money there. Andrew Genome Informatics Facility Office of Biotechnology 3110 Molecular Biology Building Iowa State University Ames, Iowa 50011 (515)-294-1320 On Wed, May 2, 2012 at 3:19 PM, Ryan Golhar wrote: > My two cents--- > > $5K won't buy everything you need, but it will get you started. I think at > least a 4-core machine with 16GB of RAM should be sufficient for most jobs. > If you know you need more, get more RAM. > > Galaxy is a hog on disk space, so try to maximize disk space. I would set > up 2 small disks (or partitions), say 20G, as RAID1 for the OS, and the > remaining disks, at least 1-2TB, for Galaxy data as RAID0. > > I think that configuration will quickly eat your $5K, but will give you > something to work with. If you still have money to spare, increase CPUs, > RAM, and disks where you can. > > Oh - One power supply, 1 NIC card, etc, no redundancy...save some money... > > On Wed, May 2, 2012 at 4:01 PM, Stephen Turner wrote: >> >> The tl;dr short story - I've come across about $5,000 I can use to >> build a machine, and this money has to be spent by Friday. I'd like >> some help spec'ing out a machine that can be used as a small-scale >> production Galaxy server for internal use by a handful of folks. >> >> Would anyone be willing to talk with me tomorrow morning, Thursday May >> 3, and tell me about your experience setting up a Galaxy installation >> on a scale like this? With about $5k to spend, what kind of hardware >> should I prioritize? I'd also like to get a sense of how much admin >> time is required to keep things running smoothly, updated, backed up, >> etc. >> >> I've had a difficult time getting ITS to help me get Galaxy running on >> the university's cluster. This will hopefully be a proof of principal >> that people here want this - hopefully I can get enough people here >> using this small-scale installation that the university ITS realizes >> the demand and has more motivation to get things working on the >> cluster. >> >> Many thanks, >> >> Stephen >> >> - >> Stephen D. Turner, Ph.D. >> Bioinformatics Core Director >> University of Virginia School of Medicine >> bioinformatics.virginia.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] galaxy cluster integration
Hi Peter, Thanks for your answer. No the galaxy machine is not a submitting node of the cluster. So I suppose I do have those two options: (1) making the galaxy server a submitting node to the cluster or (2) install and run galaxy on a cluster node What would be best? Any suggestions? If (1), any ideas on what needs to be installed? Thanks. Anne. On 2 May 2012, at 21:26, Peter Cock wrote: > On Wed, May 2, 2012 at 7:18 PM, Anne Pajon wrote: >> Hi, >> >> I am struggling at integrating galaxy with our cluster. I am currently >> running galaxy on a separate server machine from our LSF cluster. >> The DRMAA library has been installed on the cluster and I've >> re-installed galaxy into a shared file system visible and accessible >> from both the server and the cluster. > > That's good - the shared file system is highly recommended. > >> ... >> >> Am I right to think that there is no way to make the system >> works because I cannot currently configure galaxy to ssh into >> the cluster head node for submitting jobs to the scheduler? >> >> ... > > Is the Galaxy machine considered a submit node of the cluster? > i.e. Can you submit/query/kill cluster jobs at the command line > from the Galaxy server? > > 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/
Re: [galaxy-dev] Full path through API display.py
Yep, that's the right place to put it. And you'll never hear me suggest someone *not* send in a pull request, so go for it :) -Dannon On May 2, 2012, at 3:08 PM, Carlos Borroto wrote: > Thanks Dannon. > > I was actually in a hurry so I poke around and found what I think is > the right place to tie this in. > > In function "get_api_value" in "lib/galaxy/model/__init__.py" line 1159: >rval = dict( id = hda.id, > model_class = self.__class__.__name__, > name = hda.name, > deleted = hda.deleted, > visible = hda.visible, > state = hda.state, > + file_name = hda.file_name, > file_size = int( hda.get_size() ), > data_type = hda.ext, > genome_build = hda.dbkey, > misc_info = hda.info, > misc_blurb = hda.blurb ) > > Would it be helpful if I submit a pull request for this? Cause I was > wondering if for changes so simple as this one, a pull request from a > third party introduces more overhead than help. > > > On Tue, May 1, 2012 at 3:05 PM, Dannon Baker wrote: >> Sure, good idea. I'll tie it in. >> >> -Dannon >> >> On May 1, 2012, at 3:03 PM, Carlos Borroto wrote: >> >>> Hi, >>> >>> Recently "Full Path" display was added as an option. I was wondering >>> if this information could also be available when accessing a dataset >>> information through the API. >>> >>> Thanks, >>> 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/ >> ___ 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 cluster integration
On Wed, May 2, 2012 at 7:18 PM, Anne Pajon wrote: > Hi, > > I am struggling at integrating galaxy with our cluster. I am currently > running galaxy on a separate server machine from our LSF cluster. > The DRMAA library has been installed on the cluster and I've > re-installed galaxy into a shared file system visible and accessible > from both the server and the cluster. That's good - the shared file system is highly recommended. > ... > > Am I right to think that there is no way to make the system > works because I cannot currently configure galaxy to ssh into > the cluster head node for submitting jobs to the scheduler? > > ... Is the Galaxy machine considered a submit node of the cluster? i.e. Can you submit/query/kill cluster jobs at the command line from the Galaxy server? 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] Can someone help me spec out a new computer for using Galaxy? Need to spend money this week!
My two cents--- $5K won't buy everything you need, but it will get you started. I think at least a 4-core machine with 16GB of RAM should be sufficient for most jobs. If you know you need more, get more RAM. Galaxy is a hog on disk space, so try to maximize disk space. I would set up 2 small disks (or partitions), say 20G, as RAID1 for the OS, and the remaining disks, at least 1-2TB, for Galaxy data as RAID0. I think that configuration will quickly eat your $5K, but will give you something to work with. If you still have money to spare, increase CPUs, RAM, and disks where you can. Oh - One power supply, 1 NIC card, etc, no redundancy...save some money... On Wed, May 2, 2012 at 4:01 PM, Stephen Turner wrote: > The tl;dr short story - I've come across about $5,000 I can use to > build a machine, and this money has to be spent by Friday. I'd like > some help spec'ing out a machine that can be used as a small-scale > production Galaxy server for internal use by a handful of folks. > > Would anyone be willing to talk with me tomorrow morning, Thursday May > 3, and tell me about your experience setting up a Galaxy installation > on a scale like this? With about $5k to spend, what kind of hardware > should I prioritize? I'd also like to get a sense of how much admin > time is required to keep things running smoothly, updated, backed up, > etc. > > I've had a difficult time getting ITS to help me get Galaxy running on > the university's cluster. This will hopefully be a proof of principal > that people here want this - hopefully I can get enough people here > using this small-scale installation that the university ITS realizes > the demand and has more motivation to get things working on the > cluster. > > Many thanks, > > Stephen > > - > Stephen D. Turner, Ph.D. > Bioinformatics Core Director > University of Virginia School of Medicine > bioinformatics.virginia.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] Can someone help me spec out a new computer for using Galaxy? Need to spend money this week!
The tl;dr short story - I've come across about $5,000 I can use to build a machine, and this money has to be spent by Friday. I'd like some help spec'ing out a machine that can be used as a small-scale production Galaxy server for internal use by a handful of folks. Would anyone be willing to talk with me tomorrow morning, Thursday May 3, and tell me about your experience setting up a Galaxy installation on a scale like this? With about $5k to spend, what kind of hardware should I prioritize? I'd also like to get a sense of how much admin time is required to keep things running smoothly, updated, backed up, etc. I've had a difficult time getting ITS to help me get Galaxy running on the university's cluster. This will hopefully be a proof of principal that people here want this - hopefully I can get enough people here using this small-scale installation that the university ITS realizes the demand and has more motivation to get things working on the cluster. Many thanks, Stephen - Stephen D. Turner, Ph.D. Bioinformatics Core Director University of Virginia School of Medicine bioinformatics.virginia.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] Full path through API display.py
Thanks Dannon. I was actually in a hurry so I poke around and found what I think is the right place to tie this in. In function "get_api_value" in "lib/galaxy/model/__init__.py" line 1159: rval = dict( id = hda.id, model_class = self.__class__.__name__, name = hda.name, deleted = hda.deleted, visible = hda.visible, state = hda.state, + file_name = hda.file_name, file_size = int( hda.get_size() ), data_type = hda.ext, genome_build = hda.dbkey, misc_info = hda.info, misc_blurb = hda.blurb ) Would it be helpful if I submit a pull request for this? Cause I was wondering if for changes so simple as this one, a pull request from a third party introduces more overhead than help. On Tue, May 1, 2012 at 3:05 PM, Dannon Baker wrote: > Sure, good idea. I'll tie it in. > > -Dannon > > On May 1, 2012, at 3:03 PM, Carlos Borroto wrote: > >> Hi, >> >> Recently "Full Path" display was added as an option. I was wondering >> if this information could also be available when accessing a dataset >> information through the API. >> >> Thanks, >> 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/ > ___ 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 cluster integration
Hi, I am struggling at integrating galaxy with our cluster. I am currently running galaxy on a separate server machine from our LSF cluster. The DRMAA library has been installed on the cluster and I've re-installed galaxy into a shared file system visible and accessible from both the server and the cluster. I've read the wiki page: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster and tried to follow the "unified method" without much success so far. After spending some time digging/reading the mailing list, I would like to be sure that I understand the problem well enough before changing our plans. Am I right to think that there is no way to make the system works because I cannot currently configure galaxy to ssh into the cluster head node for submitting jobs to the scheduler? Is the only way forward to have a dedicated cluster node where I could run galaxy on it? Thanks in advance for your help. Kind regards, Anne. -- 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] Interested in speaking with other institutions deploying Galaxy locally?
Hello everyone! Here is a link to a brief survey about how you are using, or plan to use Galaxy locally. If you could take a moment to complete the survey, it will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public off of a new wiki site that Galaxy's Dave Clements is arranging for the group - thanks Dave! Web Survey: https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ Once the teleconference infrastructure details are in place and finalized, I will send out a web poll to see if we can find a time that works for the majority. Thanks, Ann Black-Ziegelbein On 4/27/2012 2:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein mailto:annbl...@eng.uiowa.edu>> wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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] Toolshed initial upload errors
And the saga continues. For those who came in late - I've installed a local toolshed, which allows me to create repositories, but every time I attempt to upload files, it errors out with "TypeError: array item must be char". Working off the latest Galaxy bleeding edge copy has failed to fix this. Things I've looked at: - Initial os was CentOS (4?), Mercurial 2.1.2, Python 2.6.4, with sqlite. Also tried with Ubuntu 10.04, Python 2.7. - The Mercurial and Python I used was is local to the account I was working in, so maybe the toolshed was getting confused with another version. Nope - there's no hg on the system. Galaxy seems to be calling the right Python (libraries) - This happens with plain text and binary files. I haven't attempted to upload an archive yet - Figured there could still be something peculiar to my environment, so installed Galaxy on a fresh server I had elsewhere (the Ubuntu one listed above). Nope - exactly the same error. - As there are some reported issues of Windows file names with Unicode under Mercurial, and I'm uploading from a Windows machine, I used a Mac to create a repo and add a file. Nope, same behaviour. - Further investigations reveal that the files appear to be in the repo (database/community_files). The error occurs in the middle of Mercurial, in manifest.py where it attempts to coerce a Unicode string into a character array. The Cistrome galaxy fork (https://bitbucket.org/cistrome/cistrome-harvard/src/e7e2fdd74496/lib/galaxy/webapps/community/controllers/upload.py) mentions occasional similar errors. - Wondered if it was specific to my db setup. Used Postgres instead, same behaviour. - The only changes I make to community_wsgi.ini are setting the host and port, setting the database details, and setting the admin user Frankly, I'm fresh out of inspiration. There must be something I'm consistently doing (or not doing). Any suggestions - or wild-ass guesses - where to look next? Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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] Toolshed - 502 Bad Gateway error
Hi Graham, Thanks for the heads up. It's been fixed. --nate On May 2, 2012, at 9:39 AM, graham etherington (TSL) wrote: > Hi, > The Galaxy Toolshed is giving a 502 Bad Gateway error. Is there a problem > with it at the moment? > If so, is it just a matter of restarting it or is there a likelihood of it > being down for a while? > Cheers, > Graham > > Dr. Graham Etherington > Bioinformatics Support Officer, > The Sainsbury Laboratory, > Norwich Research Park, > Norwich NR4 7UH. > UK > Tel: +44 (0)1603 450601 > > > > > ___ > 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] Toolshed - 502 Bad Gateway error
Hi, The Galaxy Toolshed is giving a 502 Bad Gateway error. Is there a problem with it at the moment? If so, is it just a matter of restarting it or is there a likelihood of it being down for a while? Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 ___ 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] Debugging upload via nginx
Hi there I've got nginx 1.0.5 in front of my Galaxy instance, and I'm trying to get uploads to work as per 'Receiving files using nginx' instructions on the Galaxy wiki. I've added the relevant config to my nginx setup (pastebin http://paste.ubuntu.com/961983/) and universe_wsgi.ini (pastebin http://paste.ubuntu.com/961985/) but it isn't working. How do I debug this? What should I be looking for in the log files? What seems to be happening is that the files are being uploaded - entries are created in database/tmp/upload_store with the contents of the relevant files - but Galaxy is not being informed that the upload is complete. 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] Interested in speaking with other, institutions deploying Galaxy locally?
We have a small collaboration between institutions in the greater Cape Town region (UCT, UWC, Stellenbosch) on this topic (the so-called Pipelines group). If anyone in South Africa is interested in talking about these topics, please get in touch because we could share expertise. Peter SANBI - UWC On 02/05/2012 09:49, Sarah Maman wrote: > Hello, > > This is a great idea. I'm interested. > > Thanks ! > Sarah Maman > > > -- > > Message: 1 > Date: Fri, 27 Apr 2012 13:45:16 -0500 > From: Ann Black-Ziegelbein > To: galaxy-dev@lists.bx.psu.edu > Subject: [galaxy-dev] Interested in speaking with other institutions > deploying Galaxy locally? > Message-ID: <4f9ae93c.20...@eng.uiowa.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi everyone - > > Here at the University of Iowa we are working on deploying Galaxy > locally for campus wide access. I am interested in forming a > community of other institutions trying to deploy Galaxy locally and > mange/operate it on a broad level. Is anyone else? If there is > enough interest, possibly we could have a community conference call > every other month to have an open discussion on how we are all > deploying galaxy, customizations we are making, problems we are > encountering, bugs, and any add-on operations management for galaxy > being developed, etc. > > Would love to hear from others operating Galaxy or in process of > standing up a local deployment. > > Thanks! > > Ann Black-Ziegelbein > > > ___ > 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] Interested in speaking with other, institutions deploying Galaxy locally?
Hello, This is a great idea. I'm interested. Thanks ! Sarah Maman -- Message: 1 Date: Fri, 27 Apr 2012 13:45:16 -0500 From: Ann Black-Ziegelbein To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? Message-ID: <4f9ae93c.20...@eng.uiowa.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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/
