[galaxy-dev] Suitability of Galaxy Instance for Project
HI there, I work for Dr. Sonia Anand in the Medicine department of McMaster University in Hamilton, Ontario, Canada. The project we are working on requires the set up of queriable/searchable database(s) that can handle a large volume of clinical, diet, microbiome, methylation, genotype and expression data. We have 4 cohorts worth of data that we want to store and access from one platform (even though we will be using multiple database softwares to actually store the data) because we want all data to be able to be linked back to an id number. Ideally we are creating something user-friendly that would allow others to view what data we have collected (hence searchable) while not actually giving the data away (we want to be able to control who has access to the data - i.e. create user accounts for them with their requested data if approved). So far we are thinking of using a software called Opal to store our clinical and dietary data as well as Mica, a web-based software that will act as the platform from which interested parties could view and request data from. However, we still need multiple other software to be able to store the other types of data (methylation, microbiome, genotype and expression data). So where Galaxy comes in (I think) is with regards to our genotype data. From what I've gathered, we would want to create our own Galaxy system as a multi-user production environment. Ideally, we would have this system linked to our Mica web page so that our data is still linked in some way. So on that note, would someone be able to tell me if Galaxy is suitable for this type of project? I have already looked into the installation instructions. What I'm more interested in is the data storage aspect. Can it only store genome data or can it also store say methylation data? We want to use as few software as we need to accommodate our data storage issue. Sorry for the long email. I hope I explained everything well enough. We have a large task on our hands so any input at all is greatly appreciated! Alecia Korkowski Data Management Assistant McMaster University 1280 Main St. West, MDCL Rm. 3200Hamilton, ON L8S 4L8 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] html output with javascript
Hi Dannon,
It works after setting sanitize_all_html to True, thanks a lot.
Laure
Le 05/02/2014 16:42, Dannon Baker a écrit :
Hi Laure,
This is intentional behavior; galaxy sanitizes all html output as a
security measure by default. You can turn this off on your instance by
changing "sanitize_all_html" to False in your universe_wsgi.ini.
There's a Trello card to track implementation of allowing administrators
to individually pick which tools to trust, which you can see (and vote
for, or follow) here: https://trello.com/c/8iMhKlPX
-Dannon
On Wed, Feb 5, 2014 at 9:44 AM, Laure QUINTRIC
mailto:laure.quint...@ifremer.fr>> wrote:
Hello galaxy users,
one of my tools returns an html output in which I have links to
images and javascripts.
Images and Javascripts of the dataset_XXX.dat file are located in a
dataset_XXX_files directory. Images are well displayed in galaxy
output but javascripts aren't executed. Even an alert('foo') cannot
be retrieved.
Has somebody already experiment this ? In other related posts, it's
said to look at rgenetics fastqc wrapper but no javascript fonctions
are called in the fastqc_report.html.
Thanks,
Laure
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Re: [galaxy-dev] running tools within tool
Ketan, Are workflows not the way to go for this? We have similar tools that are usually run in sequence. We made them all separate to allow reusing them elsewhere. For these linked tools one could write a superscript/wrapper or design a workflow which can be public or privately shared. Best wishes, Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens John Chilton Verzonden: woensdag 5 februari 2014 22:54 Aan: Ketan Maheshwari CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] running tools within tool Galaxy has an API that is capable of running tools - certainly this is one path forward on something like this. I am not sure it is the best path forward though. Probably the best way to enhance Galaxy's execution capabilities is to extend the Galaxy core framework itself - this has its own downsides though. If you can offer more details about how you would like to enhance Galaxy - what it cannot do that you would like it to do - I or others may be able to provide more specific ideas. Otherwise, sorry I have not been or more help. -John On Tue, Feb 4, 2014 at 2:51 PM, Ketan Maheshwari wrote: > Hi, > > This is a question I posted to galaxy user mailing list a while back > and was redirected to dev for possible answers: > Is it possible in Galaxy to design a tool whose sole purpose is to run > other tools. This is motivated by our desire to enhance execution > capabilities of existing tools via a generic tool which acts as a wrapper. > > Thanks, > Ketan > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] running tools within tool
Galaxy has an API that is capable of running tools - certainly this is one path forward on something like this. I am not sure it is the best path forward though. Probably the best way to enhance Galaxy's execution capabilities is to extend the Galaxy core framework itself - this has its own downsides though. If you can offer more details about how you would like to enhance Galaxy - what it cannot do that you would like it to do - I or others may be able to provide more specific ideas. Otherwise, sorry I have not been or more help. -John On Tue, Feb 4, 2014 at 2:51 PM, Ketan Maheshwari wrote: > Hi, > > This is a question I posted to galaxy user mailing list a while back and was > redirected to dev for possible answers: > Is it possible in Galaxy to design a tool whose sole purpose is to run other > tools. This is motivated by our desire to enhance execution capabilities of > existing tools via a generic tool which acts as a wrapper. > > Thanks, > Ketan > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Launching External functional tests fails with: local variable 'galaxy_test_proxy_port' referenced before assignment
I asked around a while ago about this (GALAXY_TEST_EXTERNAL) and I believe the consensus was it does not work and has not worked for sometime - this is unfortunate because it was very useful. I have created a Trello card - please up vote it if you feel this should be a priority. https://trello.com/c/8K86l4Qk Thanks, -John On Wed, Feb 5, 2014 at 9:11 AM, Renato Alves wrote: > I'm trying to run functional tests on the stable branch of galaxy using: > > GALAXY_TEST_EXTERNAL=1 GALAXY_TEST_HOST=galaxy GALAXY_TEST_PORT=80 > ./run_functional_tests.sh > > But I'm getting the error: > > Traceback (most recent call last): > File "./scripts/functional_tests.py", line 457, in > sys.exit( main() ) > File "./scripts/functional_tests.py", line 362, in main > if galaxy_test_proxy_port: > UnboundLocalError: local variable 'galaxy_test_proxy_port' referenced > before assignment > 'run_functional_tests.sh help' for help > > Am I doing something wrong? I'm following the instructions at > https://wiki.galaxyproject.org/Admin/Running Tests > > Renato > > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] html output with javascript
Hi Laure,
This is intentional behavior; galaxy sanitizes all html output as a
security measure by default. You can turn this off on your instance by
changing "sanitize_all_html" to False in your universe_wsgi.ini.
There's a Trello card to track implementation of allowing administrators to
individually pick which tools to trust, which you can see (and vote for, or
follow) here: https://trello.com/c/8iMhKlPX
-Dannon
On Wed, Feb 5, 2014 at 9:44 AM, Laure QUINTRIC wrote:
> Hello galaxy users,
>
> one of my tools returns an html output in which I have links to images and
> javascripts.
> Images and Javascripts of the dataset_XXX.dat file are located in a
> dataset_XXX_files directory. Images are well displayed in galaxy output but
> javascripts aren't executed. Even an alert('foo') cannot be retrieved.
>
> Has somebody already experiment this ? In other related posts, it's said
> to look at rgenetics fastqc wrapper but no javascript fonctions are called
> in the fastqc_report.html.
>
> Thanks,
> Laure
> ___
> 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/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
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[galaxy-dev] html output with javascript
Hello galaxy users,
one of my tools returns an html output in which I have links to images
and javascripts.
Images and Javascripts of the dataset_XXX.dat file are located in a
dataset_XXX_files directory. Images are well displayed in galaxy output
but javascripts aren't executed. Even an alert('foo') cannot be retrieved.
Has somebody already experiment this ? In other related posts, it's said
to look at rgenetics fastqc wrapper but no javascript fonctions are
called in the fastqc_report.html.
Thanks,
Laure
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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[galaxy-dev] Launching External functional tests fails with: local variable 'galaxy_test_proxy_port' referenced before assignment
I'm trying to run functional tests on the stable branch of galaxy using: GALAXY_TEST_EXTERNAL=1 GALAXY_TEST_HOST=galaxy GALAXY_TEST_PORT=80 ./run_functional_tests.sh But I'm getting the error: Traceback (most recent call last): File "./scripts/functional_tests.py", line 457, in sys.exit( main() ) File "./scripts/functional_tests.py", line 362, in main if galaxy_test_proxy_port: UnboundLocalError: local variable 'galaxy_test_proxy_port' referenced before assignment 'run_functional_tests.sh help' for help Am I doing something wrong? I'm following the instructions at https://wiki.galaxyproject.org/Admin/Running Tests Renato signature.asc Description: OpenPGP digital signature ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool dependencies - how to reinstall manually via command line
Hi everyone, I've just recently decided to try out the automatic installation of dependencies but ran into a few problems. The first is that the machine that currently runs the web component lacks most libraries which would be required for compilation. I realize that this will make it hard/impossible to install anything using this approach. The current setup uses Torque to dispatch to workers behind the scenes. What I would like to know is how to trigger installation (and re-installation in case of errors) of dependencies on the workers. I'm ok with doing this manually directly in the shell of the workers, but would also like to know if the compilation can be setup to happen as job via Torque, therefore compiling in the computing nodes. Furthermore, I'm having some problems with a few dependencies that failed to compile but are still reported as "Installed". One of such tools is: package_r_2_11_0 Which failed to compile with the errors: (from INSTALLATION.log) STDERR configure: WARNING: you cannot build DVI versions of the R manuals configure: WARNING: you cannot build DVI versions of all the help pages configure: WARNING: you cannot build PDF versions of the R manuals configure: WARNING: you cannot build PDF versions of all the help pages configure: error: No F77 compiler found # but still reports: NameVersion TypeInstallation status R 2.11.0 package Installed Thanks, Renato signature.asc Description: OpenPGP digital signature ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] IGV display_application configuration failed with require_login=TRUE
Thks Thomas,
Indeed the configuration you provide is the one we use here.
However we do not use the nginx proxy (yet ;-))
We are waiting for the next galaxy-dist release to see if it will fix
our problem.
Vincent
Vincent Navratil, PhD
IR UCBL - PRABI
http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard -- Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826
My 'ome' page http://vinavratil.free.fr
Le 2/4/14 5:06 PM, Thomas Bellembois a écrit :
On 04/02/2014 16:37, navratil wrote:
Dear galaxy-dev team,
We have configured a galaxy-dist server (stable release) behind an
Apache2 proxy (with mod_xsendfile) by following the galaxy wiki.
We would like to use the galaxy embeded user authentification with
require_login=True option instead of a remote_user configuration on
the proxy side.
With require_login = False it works but with require_login=True
configuration we fail to load .bam files into IGV (local) :
The IGV (Version 2.3.18) send this error:
*/INFO [2014-02-04 16:05:56,660] [MessageUtils.java:60] [Thread-9]
Error loading
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam:
An error occurred while accessing:
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bamInvalid
GZIP/**/header/**/
/*
and the galaxy-server send this error_log:
*//**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] "HEAD
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"/**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] "HEAD /root HTTP/1.1" 200
- "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"/**/
/**//**/
/**/Exception happened during processing of request from
('127.0.0.1', 46142)/**/
/**/Traceback (most recent call last):/**/
/**/ File
"/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread/**/
/**/self.finish_request(request, client_address)/**/
/**/ File "/usr/lib/python2.7/SocketServer.py", line 334, in
finish_request/**/
/**/self.RequestHandlerClass(request, client_address, self)/**/
/**/ File "/usr/lib/python2.7/SocketServer.py", line 651, in
__init__/**/
/**/self.finish()/**/
/**/ File "/usr/lib/python2.7/SocketServer.py", line 710, in finish/**/
/**/self.wfile.close()/**/
/**/ File "/usr/lib/python2.7/socket.py", line 279, in close/**/
/**/self.flush()/**/
/**/ File "/usr/lib/python2.7/socket.py", line 303, in flush/**/
/**/self._sock.sendall(view[write_offset:write_offset+buffer_size])/**/
/**/error: [Errno 32] Broken pipe/**/
/**//**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] "GET
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"/**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] "GET /root HTTP/1.1" 200
- "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM/*
Any idea ?
Vincent
--
Vincent Navratil, PhD
IR UCBL - PRABI
http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard -- Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826
My 'ome' pagehttp://vinavratil.free.fr
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Hi Vincent,
I had the same issue with NGINX.
Ensure that "#filter-with = gzip" is commented out in your
universe_wsgi.ini.
I also have "upstream_gzip = False"
Hope this helps,
Regards,
Thomas
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