[galaxy-dev] Amazon cloud setup for galaxy training
Dear, I am setting up with my colleague Jing an Introductory Galaxy training course at the University of Cambridge due to on the 24th September. I am looking for help on how to setup the cloud to have a smooth user experience during the workshop. Would you have any links with information to recommend or any advices on how to set it up? Many thanks in advance. Kindest regards, Anne. -- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cruk.cam.ac.uk | +44 (0)1223 769 631 ___ 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] cannot start galaxy after upgade
Hi Greg, Brilliant! Thanks a lot for your advice, it worked! I do run the latest dist release that went out yesterday. Thanks again for your prompt help, it is very much appreciated. Cheers, Anne. On 15 Nov 2012, at 16:45, Greg Von Kuster wrote: > HI Anne, > > Just to confirm, you are running the latest dist release which went out > yesterday, correct? If so, perhaps you can try this: > > %sh manage_tools.sh upgrade > > The above will set the value of the migrate_tools.version column in your > database to the latest migration value. After doing this, try > > %sh run.sh > > which will start up your Galaxy server. Then you can run any of the tool > migrations you want by getting the commands from the Admin menu link. > > Let me know if this works. > > Greg Von Kuster > > On Nov 15, 2012, at 11:39 AM, Anne Pajon wrote: > >> Hi Greg, >> >> No change at all, how can I check? >> >> [webapp@uk-cri-lbio07 galaxy]$ hg status | grep -v '^?' >> M tool-data/shared/ucsc/ucsc_build_sites.txt >> >> The problem may be that I did not upgrade since 14 June 2012. Could it be >> related to the version of tools in the database? Please advice me if you >> could on the places to look at. I've looked at the code but I did not find >> yet which data/config file is causing this error. >> >> Should I revert the upgrade and try to upgrade to the previous release >> instead? Any advices would be very much appreciated. >> >> Thanks. >> Cheers, >> Anne. >> >> >> On 15 Nov 2012, at 16:12, Greg Von Kuster wrote: >> >>> Hi Anne, >>> >>> We've never seen this error before and we are not able to reproduce it, so >>> not sure we can help. Have you made any changes to your Galaxy code base >>> or to your Galaxy environment? >>> >>> Greg Von Kuster >>> >>> On Nov 15, 2012, at 9:15 AM, Anne Pajon wrote: >>> >>>> Hi, >>>> >>>> I'm having some problems restarting our galaxy server after upgrading it >>>> to the latest version today... >>>> >>>> Here is the error message: >>>> >>>> python path is: >>>> /opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, >>>> >>>> /opt/local/home/webapp/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, >>>> /opt/local/home/webapp/galaxy/eggs/boto-2.5.2-py2.7.egg, >>>> /opt/local/home/webapp/galaxy/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, >>>> /opt/local/home/webapp/galaxy/eggs/Fabric-1.4.2-py2.7.egg, >>>> /opt/local/home/webapp/galaxy/eggs/ssh-1.7.14-py2.7.egg, >>>> /opt/local/home/webapp/galaxy/eggs/Whoosh-0.3.18-py2.7.egg, >>>> /opt/local/home/webapp/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, >>>> >>>> /opt/local/home/webapp/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, >>>> >>>> /opt/local/home/webapp/galaxy/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg, >>>> /opt/local/home/webapp/galaxy/eggs/amqplib-0.6.1-py2.7.egg, >>>> /opt/local/home/webapp/galaxy/eggs/pexpect-2.4-py2.7.egg, >>>> /opt/local/home/webapp/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, >>>> /opt/local/home/webapp/galaxy/! eggs/Babel-0.9.4-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/Mako-0.4.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebHelpers-0.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/wchartype-0.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/elementtree-1.2.6_20050316-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/docutils-0.7-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebOb-0.8.5-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Routes-1.12.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/PasteDeploy-1.3.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/PasteScript-1.7.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Paste-1.6-py2.7.egg, /opt/local/home/webapp/galaxy/lib, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-pack! ages/setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/softw! are/p! >>>> ython/py >>>> thon2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg, >>>> >>>> /opt/local/home/webapp/software/python/p
Re: [galaxy-dev] cannot start galaxy after upgade
Hi Greg, No change at all, how can I check? [webapp@uk-cri-lbio07 galaxy]$ hg status | grep -v '^?' M tool-data/shared/ucsc/ucsc_build_sites.txt The problem may be that I did not upgrade since 14 June 2012. Could it be related to the version of tools in the database? Please advice me if you could on the places to look at. I've looked at the code but I did not find yet which data/config file is causing this error. Should I revert the upgrade and try to upgrade to the previous release instead? Any advices would be very much appreciated. Thanks. Cheers, Anne. On 15 Nov 2012, at 16:12, Greg Von Kuster wrote: > Hi Anne, > > We've never seen this error before and we are not able to reproduce it, so > not sure we can help. Have you made any changes to your Galaxy code base or > to your Galaxy environment? > > Greg Von Kuster > > On Nov 15, 2012, at 9:15 AM, Anne Pajon wrote: > >> Hi, >> >> I'm having some problems restarting our galaxy server after upgrading it to >> the latest version today... >> >> Here is the error message: >> >> python path is: >> /opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/boto-2.5.2-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/Fabric-1.4.2-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/ssh-1.7.14-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/Whoosh-0.3.18-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, >> >> /opt/local/home/webapp/galaxy/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/amqplib-0.6.1-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/pexpect-2.4-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, >> /opt/local/home/webapp/galaxy/eg! gs/Babel-0.9.4-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/Mako-0.4.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebHelpers-0.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/wchartype-0.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/elementtree-1.2.6_20050316-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/docutils-0.7-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebOb-0.8.5-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Routes-1.12.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/PasteDeploy-1.3.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/PasteScript-1.7.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Paste-1.6-py2.7.egg, /opt/local/home/webapp/galaxy/lib, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packag! es/setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/softwar! e/p! >> ython/py >> thon2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg, >> >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/termcolor-1.1.0-py2.7.egg, >> >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/PyYAML-3.10-py2.7-linux-x86_64.egg, >> >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/py_mysql2pgsql-0.1.3-py2.7.egg, >> >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python27.zip, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/plat-linux2, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-tk, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-old, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-dynload, >> /opt/local/home/webapp/soft! ware/mercurial/mercurial-2.1/lib/python2.7/site-packages, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages >> galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,841 Loading >> references to tool sheds from tool_sheds_conf.xml >> galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded >> reference to tool shed: Galaxy main tool shed >> ga
[galaxy-dev] cannot start galaxy after upgade
xy/tool_shed/encoding_util.py", line 15, in tool_shed_decode a, b = value.split( ":" ) ValueError: too many values to unpack Removing PID file paster.pid Any help would be greatly appreciated. Thanks! Cheers, Anne. -- Anne Pajon, Ph.D. - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cruk.cam.ac.uk | +44 (0)1223 40 4334 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 charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). 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/
[galaxy-dev] circular import in tool_shed code gives unit test failure
Dear, I've been running unit tests on the latest galaxy-central 7294:663e03e40c86 that have me this error: [localhost] out: == [localhost] out: ERROR: Failure: ImportError (cannot import name install_manager) [localhost] out: -- [localhost] out: Traceback (most recent call last): [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/loader.py", line 379, in loadTestsFromName [localhost] out: addr.filename, addr.module) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 39, in importFromPath [localhost] out: return self.importFromDir(dir_path, fqname) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/eggs/nose-0.11.1-py2.7.egg/nose/importer.py", line 86, in importFromDir [localhost] out: mod = load_module(part_fqname, fh, filename, desc) [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/lib/galaxy/tool_shed/install_manager.py", line 10, in [localhost] out: from galaxy.tool_shed.migrate.common import * [localhost] out: File "/Users/pajon01/galaxy-test/galaxy-central/lib/galaxy/tool_shed/migrate/common.py", line 9, in [localhost] out: from galaxy.tool_shed import install_manager [localhost] out: ImportError: cannot import name install_manager [localhost] out: -- I fixed it by commenting out the circular import in tool_shed/install_manager.py hg diff diff -r 663e03e40c86 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py Wed Jun 20 03:39:05 2012 -0400 +++ b/lib/galaxy/tool_shed/install_manager.py Wed Jun 20 16:37:06 2012 +0100 @@ -7,7 +7,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * from galaxy.util.odict import odict -from galaxy.tool_shed.migrate.common import * +#from galaxy.tool_shed.migrate.common import * Hope it would be useful to someone else. 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] cannot access conditional parameter in command
Hi,
I think I found the solution to my problem by googling it instead of just
searching through the dev mailing list. I found this post very useful for
debugging tips on cheetah template:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004817.html
Then I read on the galaxy wiki:
http://wiki.g2.bx.psu.edu/Admin/Tools/Data%20Tables How to use Data Tables and
found this:
"""
The script or binary will need the actual path in the command, and since the ID
is the value, some work will need to be done to extract the path. The following
line would do the trick: --ref="${ filter( lambda x: str( x[0] ) == str( $index
), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" In
this line, str( x[0] ) refers to the unique ID in column 0 and the -1 in
[0][-1] gets the path in the last column.
"""
I've changed the command to print all available parameters:
#silent sys.stderr.write(" Cheetah Template Variables \n")
#for k,v in $searchList[2].items()
#silent sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))
#end for
#silent sys.stderr.write("CRI datasets: %s\n" %
str($__app__.tool_data_tables[ 'cri_datasets' ].get_fields()))
#silent sys.stderr.write("Dataset selected: %s\n" % str($dataset.name))
#silent dataset_path = filter( lambda x: str( x[0] ) == str( $dataset.name ),
$__app__.tool_data_tables[ 'cri_datasets' ].get_fields() )[0][-1]
#silent sys.stderr.write("Dataset path: %s\n" % str(dataset_path) )
#silent sys.stderr.write(" end-of-list \n")
...
and finally got it to works!
To summary, to get the path from the cri_datasets table:
dataset_path = filter( lambda x: str( x[0] ) == str( $dataset.name ),
$__app__.tool_data_tables[ 'cri_datasets' ].get_fields() )[0][-1]
Hope it could be useful to someone else.
Anne.
On 22 May 2012, at 19:52, Anne Pajon wrote:
> Hi,
>
> I'm writing a galaxy tool xml file for an in house existing R script. I have
> a conditional parameter set for selecting the dataset to work with but I
> would like to access the path of the file from the data table I've created:
>
>
> value, name, path
>
>
>
> Here is the beginning of the xml file:
>
>
>rp.R --args $dataset.name.fields.name $dataset.name.fields.path $input
> $column $output_txt $output_html $output_html.files_path $dataset.outcome
> $dataset.receptor $dataset.treatment $dataset.er $dataset.age $dataset.grade
> $dataset.signature $dataset.margins $dataset.groups $dataset.gleason
> $dataset.tstage 2>stderr || cat stderr 1>&2
>
>
>
> help="File containing a list of gene symbols"/>
> label="Column" help="Column containing gene symbols (only available for
> tabular input file)" />
>
>
>
>
>
> ...
>
> but when running the tool, here is the error message I get:
>
> Traceback (most recent call last):
> File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/runners/local.py", line
> 59, in run_job
>job_wrapper.prepare()
> File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/__init__.py", line 429,
> in prepare
>self.command_line = self.tool.build_command_line( param_dict )
> File "/opt/local/home/webapp/galaxy/lib/galaxy/tools/__init__.py", line
> 1971, in build_command_line
>command_line = fill_template( self.command, context=param_dict )
> File "/opt/local/home/webapp/galaxy/lib/galaxy/util/template.py", line 9, in
> fill_template
>return str( Template( source=template_text, searchList=[context] ) )
> File
> "/opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py",
> line 1004, in __str__
>return getattr(self, mainMethName)()
> File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
> NotFound: cannot find 'fields' while searching for 'dataset.name.fields.name'
>
> Is it possible to access the other columns of a loc file? It seems possible
> based of what I read on the wiki
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coptions.3E_tag_set
> using from_data_table and syntax of ${param.fields.path} but I could not
> manage to make it work.
>
> Any help would be very much appreciated. Thanks!
> 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
>
>
--
Anne Pajon, Ph.D.
Cancer Research UK - Cambridge Research Institute
Li Ka Shing Centre, R
[galaxy-dev] cannot access conditional parameter in command
Hi,
I'm writing a galaxy tool xml file for an in house existing R script. I have a
conditional parameter set for selecting the dataset to work with but I would
like to access the path of the file from the data table I've created:
value, name, path
Here is the beginning of the xml file:
rp.R --args $dataset.name.fields.name $dataset.name.fields.path $input
$column $output_txt $output_html $output_html.files_path $dataset.outcome
$dataset.receptor $dataset.treatment $dataset.er $dataset.age $dataset.grade
$dataset.signature $dataset.margins $dataset.groups $dataset.gleason
$dataset.tstage 2>stderr || cat stderr 1>&2
...
but when running the tool, here is the error message I get:
Traceback (most recent call last):
File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/runners/local.py", line
59, in run_job
job_wrapper.prepare()
File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/__init__.py", line 429,
in prepare
self.command_line = self.tool.build_command_line( param_dict )
File "/opt/local/home/webapp/galaxy/lib/galaxy/tools/__init__.py", line 1971,
in build_command_line
command_line = fill_template( self.command, context=param_dict )
File "/opt/local/home/webapp/galaxy/lib/galaxy/util/template.py", line 9, in
fill_template
return str( Template( source=template_text, searchList=[context] ) )
File
"/opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py",
line 1004, in __str__
return getattr(self, mainMethName)()
File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
NotFound: cannot find 'fields' while searching for 'dataset.name.fields.name'
Is it possible to access the other columns of a loc file? It seems possible
based of what I read on the wiki
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coptions.3E_tag_set
using from_data_table and syntax of ${param.fields.path} but I could not
manage to make it work.
Any help would be very much appreciated. Thanks!
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"
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and other Galaxy lists, please use the interface at:
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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 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 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
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
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/
[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?
I'm interested too. On 27 Apr 2012, at 21:13, Ann Black-Ziegelbein wrote: > Thanks everyone! Glad to find some common interest. I will see if I can > arrange an initial call. > > Hi Tyler - I was hoping we could just do a voice conference call. It would > be great to meet those face to face at the Galaxy Conference in Chicago if > some are attending. > > Thanks! > > Ann > > On 4/27/2012 3:07 PM, JIE CHEN wrote: >> Cool idea. I am very interested in it. One question: how could we attend the >> conference since we all at different place? >> >> Cheers, >> Tyler >> >> On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian >> wrote: >> Great idea. In! >> >> Cheers, >> Mo Heydarian >> >> PhD candidate >> The Johns Hopkins School of Medicine >> Department of Biological Chemistry >> 725 Wolfe Street >> 414 Hunterian >> Baltimore, MD 21205 >> >> >> >> On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein >> 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/ >> > > ___ > 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)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] tool_conf.xml.main vs tool_conf.xml.sample
te list of unwanted sections, otherwise it will be added. WARNING: +++ peak_calling/ccat_wrapper.xml: New Tool in section peak_calling. It will be added. WARNING: +++ ngs-simulation: New Section. Please update list of unwanted sections, otherwise it will be added. WARNING: +++ vcf_tools: New Section. Please update list of unwanted sections, otherwise it will be added. Is this correct? Thanks to let me know. Cheers, Anne. On 27 Mar 2012, at 16:57, Anne Pajon wrote: > Got it. Thanks! > > On 27 Mar 2012, at 16:53, Greg Von Kuster wrote: > >> We have a buildbot set up that runs our functional tests against various >> platforms / environments. The .sample file used by the buildbot tests >> everything. The tool_conf.xml.main contains a subset of everything that is >> tested. >> >> On Mar 27, 2012, at 11:48 AM, Anne Pajon wrote: >> >>> Hi Nate, >>> >>> Thanks but I am still confused... sorry. Why these two files are different >>> then? Are you not running the functional tests on all the tools available >>> at the public server? >>> >>> Anne. >>> >>> On 27 Mar 2012, at 16:33, Nate Coraor wrote: >>> >>>> On Mar 27, 2012, at 11:17 AM, Anne Pajon wrote: >>>> >>>>> Hi, >>>>> >>>>> I would like to know which tool_conf.xml to use, and would like to know >>>>> the difference between the main and the sample one. I know that the >>>>> functional tests are running against the tool_conf.xml.sample but what >>>>> tool_conf.xml.main is used for? >>>> >>>> Hi Anne, >>>> >>>> tool_conf.xml.main is used by the public server (Galaxy Main) at >>>> usegalaxy.org. >>>> >>>> --nate >>>> >>>>> >>>>> Thanks. >>>>> 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/ >>>> >>> >>> -- >>> 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 Char
Re: [galaxy-dev] tool_conf.xml.main vs tool_conf.xml.sample
Got it. Thanks! On 27 Mar 2012, at 16:53, Greg Von Kuster wrote: > We have a buildbot set up that runs our functional tests against various > platforms / environments. The .sample file used by the buildbot tests > everything. The tool_conf.xml.main contains a subset of everything that is > tested. > > On Mar 27, 2012, at 11:48 AM, Anne Pajon wrote: > >> Hi Nate, >> >> Thanks but I am still confused... sorry. Why these two files are different >> then? Are you not running the functional tests on all the tools available at >> the public server? >> >> Anne. >> >> On 27 Mar 2012, at 16:33, Nate Coraor wrote: >> >>> On Mar 27, 2012, at 11:17 AM, Anne Pajon wrote: >>> >>>> Hi, >>>> >>>> I would like to know which tool_conf.xml to use, and would like to know >>>> the difference between the main and the sample one. I know that the >>>> functional tests are running against the tool_conf.xml.sample but what >>>> tool_conf.xml.main is used for? >>> >>> Hi Anne, >>> >>> tool_conf.xml.main is used by the public server (Galaxy Main) at >>> usegalaxy.org. >>> >>> --nate >>> >>>> >>>> Thanks. >>>> 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/ >>> >> >> -- >> 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/ > -- 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] tool_conf.xml.main vs tool_conf.xml.sample
Hi Nate, Thanks but I am still confused... sorry. Why these two files are different then? Are you not running the functional tests on all the tools available at the public server? Anne. On 27 Mar 2012, at 16:33, Nate Coraor wrote: > On Mar 27, 2012, at 11:17 AM, Anne Pajon wrote: > >> Hi, >> >> I would like to know which tool_conf.xml to use, and would like to know the >> difference between the main and the sample one. I know that the functional >> tests are running against the tool_conf.xml.sample but what >> tool_conf.xml.main is used for? > > Hi Anne, > > tool_conf.xml.main is used by the public server (Galaxy Main) at > usegalaxy.org. > > --nate > >> >> Thanks. >> 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/ > -- 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] functional test issue - PDF output file comparison
Hi Greg, I did not get any answer unfortunately. I still do have errors when running the functional tests and I do not know how the tool shed will solve the problem as Nate replied to a related email regarding functional test failures. As far as I am aware, the most used tool for comparing the test outputs is 'diff'. It is perfectly fine when comparing text file but there are plenty of tools that produce PDF files, and as you mention they differ a lot even when generated under identical circumstances. However, to temporarily solve these differences, I've generated manually these files using the export GALAXY_TEST_SAVE=/data_ls/galaxy/test-data ran the test, visually compared the files and copied them back to test-data/ directory. Not very elegant and time consuming. Anyone with better solution? Cheers, Anne. On 26 Mar 2012, at 08:27, Greg Edwards wrote: > Hi Anne, > > Just wondering if you got any response to your question, I'm interested to > know the answer myself. > > I'm not a PDF expert, but have done some work over the years with PDFs, > PostScript, fonts etc. Even a small thing like the date/time generated in the > PDF could make a diff fail, > or the encoding of the system info it was generated on. Font library info > gets included that can differ across systems. > Plus diff thinks there is binary data in the PDF, which there can be, so that > will cause diff to have hiccups. > > I printed two identical PDF's, just a few chars, on my Mac and they differ a > lot, even though created a few seconds apart under identical circumstances. > > I don;t think 'diff' is much use to do a comparison in the functional tests, > I'm surprised that they use that. Unless Galaxy has a cut down, simplified > PDF generator that doesn;t encode any variable info, which I doubt. > > Cheers, > Greg E > > > > > > On Tue, Mar 6, 2012 at 4:35 AM, Anne Pajon wrote: > Dear All, > > I have noticed that some output files of functional tests are of type PDF. > When comparing the one produced by the tool and the one stored in test-data/, > they obviously differ even if they visually look identical. > > Is there a better way to compare PDF files within Galaxy than using diff? If > not, do you have experience or suggestion at solving these functional test > failures? > > Thanks a lot in advance. > 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/ > > > > -- > Greg Edwards, > Port Jackson Bioinformatics > gedwar...@gmail.com > -- 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] functional test failures
Hi Nate, Thanks for your answer. I am looking forward at the relocation of the tools to the tool shed then. Cheers, Anne. On 26 Mar 2012, at 14:49, Nate Coraor wrote: > Hi Anne, > > We're aware that many tests require certain local data to be set up > beforehand. As such, these tests can't really be run at a local site. As > part of relocating our tools to the tool shed, we hope to fix this issue. > > Thanks, > --nate > > On Feb 20, 2012, at 1:25 PM, Anne Pajon wrote: > >> Hello, >> >> I am trying to have all functional tests on our production server >> (galaxy-dist 6621:26920e20157f) run successfully but I do still have >> failures that I do not know how to solve. >> >> Theses failures are related to unexpected differences probably due to >> versions of software that have been upgraded recently. >> >> ( Extract genomic DNA 1 ) > Test-1 >> ( Extract genomic DNA 1 ) > Test-2 >> ( Extract genomic DNA 1 ) > Test-3 >> ( Extract genomic DNA 1 ) > Test-4 >> ( Extract genomic DNA 1 ) > Test-5 >> ( GeneBed_Maf_Fasta2 ) > Test-1 >> ( Interval2Maf1 ) > Test-1 >> ( Interval2Maf1 ) > Test-3 >> ( Interval_Maf_Merged_Fasta2 ) > Test-1 >> ( Interval_Maf_Merged_Fasta2 ) > Test-2 >> ( LinearRegression1 ) > Test-1 >> ( XY_Plot_1 ) > Test-1 >> ( cca1 ) > Test-1 >> ( histogram_rpy ) > Test-1 >> ( kpca1 ) > Test-1 >> ( pca1 ) > Test-1 >> ( pca1 ) > Test-2 >> ( pca1 ) > Test-3 >> ( plot_for_lda_output1 ) > Test-1 >> ( qual_stats_boxplot ) > Test-1 >> AssertionError: History item 2 different than expected, difference (using >> diff) >> >> ( gops_join_1 ) > Test-4 >> TwillAssertionError: code is 500 != 200 >> >> I do also have failures due to missing data but I am struggling to find out >> where to download them. >> >> ( gd_select_snps ) > Test-1 >> AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset >> blurb: error >> 'bighorn' does not appear in location file >> '/opt/local/home/webapp/galaxy/tool-data/gd.chrlens.loc' >> >> ( Annotation_Profiler_0 ) > Test-1 >> ( Annotation_Profiler_0 ) > Test-2 >> AssertionError: Configuration error: Table directory is missing >> (/opt/local/home/webapp/galaxy/tool-data/annotation_profiler/hg18) >> >> ( Interval2Maf_pairwise1 ) > Test-1 >> AssertionError: Attempting to set field 'mafType' to value >> '['PAIRWISE_hg17_fr1']' in form 'tool_form' threw exception: cannot find >> value/label "PAIRWISE_hg17_fr1" in list control >> >> ( maf_stats1 ) > Test-1 >> ( maf_stats1 ) > Test-2 >> AssertionError: Attempting to set field 'maf_source_type|mafType' to value >> '['8_WAY_MULTIZ_hg17']' in form 'tool_form' threw exception: cannot find >> value/label "8_WAY_MULTIZ_hg17" in list control >> >> ( phastOdds_for_intervals ) > Test-1 >> AssertionError: Attempting to set field 'score_file' to value >> '['/galaxy/data/phastOdds_precomputed/encode_SEP-2005_\ >> tba.v2_phastOdds']' in form 'tool_form' threw exception: cannot find >> value/label "/galaxy/data/phas..2_phastOdds" in li\ >> st control >> >> ( aggregate_scores_in_intervals2 ) > Test-1 >> ( aggregate_scores_in_intervals2 ) > Test-2 >> AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset >> blurb: error >> >> ( gencode_partition1 ) > Test-1 >> Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error >> Error loading partitioning dataset. >> >> ( lda_analy1 ) > Test-1 >> AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset >> blurb: error >> >> The last failure is related to genome diversity and the fact that it calls >> python2.5. I've changed it to python for testing but the test still fails. >> >> ( gd_extract_flanking_dna ) > Test-1 >> ( gd_extract_primers ) > Test-1 >> ( gd_select_restriction_enzymes ) > Test-1 >> AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset >> blurb: error >> python2.5: command not found >>> if changed to python: ERROR: 'NoneType' object has no attribute 'rfind' >> >&g
Re: [galaxy-dev] New Galaxy look from usegalaxy.org
Hi, I have set up a brand in my universe but with the "new" look you cannot see it as it is written on top of the Tools' header. The new look is available from galaxy-central. Thanks, Anne. On 27 Mar 2012, at 15:24, James Taylor wrote: > The new look will go out with the next galaxy-dist, once we've squashed most > of the bugs. Thanks for your interest! > > On Mar 26, 2012, at 5:18 AM, Leandro Hermida wrote: > >> Dear all, >> >> How do I get the new Galaxy look enabled that you see in >> usegalaxy.org? I have two servers on the latest galaxy-dist. >> >> regards, >> Leandro >> ___ >> 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/ > > -- jt > > James Taylor, Assistant Professor, Biology / Computer Science, Emory > University > > > > > > ___ > 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/
[galaxy-dev] tool_conf.xml.main vs tool_conf.xml.sample
Hi, I would like to know which tool_conf.xml to use, and would like to know the difference between the main and the sample one. I know that the functional tests are running against the tool_conf.xml.sample but what tool_conf.xml.main is used for? Thanks. 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/
[galaxy-dev] functional test issue - PDF output file comparison
Dear All, I have noticed that some output files of functional tests are of type PDF. When comparing the one produced by the tool and the one stored in test-data/, they obviously differ even if they visually look identical. Is there a better way to compare PDF files within Galaxy than using diff? If not, do you have experience or suggestion at solving these functional test failures? Thanks a lot in advance. 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] functional test failures
dat --indexLocation=/opt/local/home/webapp/galaxy/tool-data/maf_pairwise.loc galaxy.jobs.runners.local: DEBUG: execution finished: python /opt/local/home/webapp/galaxy/tools/maf/interval2maf.py --dbkey=hg17 --chromCol=1 --startCol=2 --endCol=3 --strandCol=6 --mafType=PAIRWISE_hg17_fr1 --interval_file=/data_ls/tmp/tmpmYp_1L/database/files/000/dataset_1.dat --output_file=/data_ls/tmp/tmpmYp_1L/database/files/000/dataset_2.dat --indexLocation=/opt/local/home/webapp/galaxy/tool-data/maf_pairwise.loc galaxy.jobs: DEBUG: job 2 ended base.twilltestcase: INFO: ## files diff on /opt/local/home/webapp/galaxy/test-data/Interval2Maf_pairwise_out.maf and /data_ls/tmp/tmpmYp_1L/database/tmp/tmplBoXcFInterval2Maf_pairwise_out.maf lines_diff=0, found diff = 5256 - >> end captured logging << - -- Ran 1 test in 21.136s FAILED (failures=1) functional_tests.py INFO 2012-02-23 18:13:31,065 Shutting down functional_tests.py INFO 2012-02-23 18:13:31,065 Shutting down embedded web server functional_tests.py INFO 2012-02-23 18:13:31,068 Embedded web server stopped functional_tests.py INFO 2012-02-23 18:13:31,068 Shutting down app galaxy.jobs INFO 2012-02-23 18:13:31,068 sending stop signal to worker thread galaxy.jobs INFO 2012-02-23 18:13:31,068 job queue stopped galaxy.jobs.runners.local INFO 2012-02-23 18:13:31,069 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2012-02-23 18:13:31,069 local job runner stopped galaxy.jobs INFO 2012-02-23 18:13:31,069 sending stop signal to worker thread galaxy.jobs INFO 2012-02-23 18:13:31,069 job stopper stopped functional_tests.py INFO 2012-02-23 18:13:31,070 Embedded Universe application stopped functional_tests.py INFO 2012-02-23 18:13:31,070 Cleaning up temporary files in /data_ls/tmp/tmpmYp_1L galaxy.jobs INFO 2012-02-23 18:13:31,922 sending stop signal to worker thread galaxy.jobs INFO 2012-02-23 18:13:31,923 job queue stopped galaxy.jobs.runners.local INFO 2012-02-23 18:13:31,923 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2012-02-23 18:13:31,923 local job runner stopped galaxy.jobs INFO 2012-02-23 18:13:31,923 sending stop signal to worker thread galaxy.jobs INFO 2012-02-23 18:13:31,923 job stopper stopped Exception OSError: (2, 'No such file or directory', '/data_ls/tmp/tmpmYp_1L/database/tmp/tmpcORjQS') in ', mode 'w' at 0x2aa80780>> ignored 'run_functional_tests.sh help' for help Note: galaxy test framework uses tool_conf.xml.sample, not tool_conf.xml Thanks for your help. Anne. On 20 Feb 2012, at 18:25, Anne Pajon wrote: > Hello, > > I am trying to have all functional tests on our production server > (galaxy-dist 6621:26920e20157f) run successfully but I do still have failures > that I do not know how to solve. > > Theses failures are related to unexpected differences probably due to > versions of software that have been upgraded recently. > > ( Extract genomic DNA 1 ) > Test-1 > ( Extract genomic DNA 1 ) > Test-2 > ( Extract genomic DNA 1 ) > Test-3 > ( Extract genomic DNA 1 ) > Test-4 > ( Extract genomic DNA 1 ) > Test-5 > ( GeneBed_Maf_Fasta2 ) > Test-1 > ( Interval2Maf1 ) > Test-1 > ( Interval2Maf1 ) > Test-3 > ( Interval_Maf_Merged_Fasta2 ) > Test-1 > ( Interval_Maf_Merged_Fasta2 ) > Test-2 > ( LinearRegression1 ) > Test-1 > ( XY_Plot_1 ) > Test-1 > ( cca1 ) > Test-1 > ( histogram_rpy ) > Test-1 > ( kpca1 ) > Test-1 > ( pca1 ) > Test-1 > ( pca1 ) > Test-2 > ( pca1 ) > Test-3 > ( plot_for_lda_output1 ) > Test-1 > ( qual_stats_boxplot ) > Test-1 >AssertionError: History item 2 different than expected, difference (using > diff) > > ( gops_join_1 ) > Test-4 > TwillAssertionError: code is 500 != 200 > > I do also have failures due to missing data but I am struggling to find out > where to download them. > > ( gd_select_snps ) > Test-1 > AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset > blurb: error > 'bighorn' does not appear in location file > '/opt/local/home/webapp/galaxy/tool-data/gd.chrlens.loc' > > ( Annotation_Profiler_0 ) > Test-1 > ( Annotation_Profiler_0 ) > Test-2 > AssertionError: Configuration error: Table directory is missing > (/opt/local/home/webapp/galaxy/tool-data/annotation_profiler/hg18) > > ( Interval2Maf_pairwise1 ) > Test-1 > AssertionError: Attempting to set field 'mafType' to value > '['PAIRWISE_hg17_fr1']' in form 'tool_form' threw exception: cannot find > value/label "PAIRWISE_hg17_fr1" in list control > > ( maf_stats1 ) >
[galaxy-dev] functional test failures
Hello, I am trying to have all functional tests on our production server (galaxy-dist 6621:26920e20157f) run successfully but I do still have failures that I do not know how to solve. Theses failures are related to unexpected differences probably due to versions of software that have been upgraded recently. ( Extract genomic DNA 1 ) > Test-1 ( Extract genomic DNA 1 ) > Test-2 ( Extract genomic DNA 1 ) > Test-3 ( Extract genomic DNA 1 ) > Test-4 ( Extract genomic DNA 1 ) > Test-5 ( GeneBed_Maf_Fasta2 ) > Test-1 ( Interval2Maf1 ) > Test-1 ( Interval2Maf1 ) > Test-3 ( Interval_Maf_Merged_Fasta2 ) > Test-1 ( Interval_Maf_Merged_Fasta2 ) > Test-2 ( LinearRegression1 ) > Test-1 ( XY_Plot_1 ) > Test-1 ( cca1 ) > Test-1 ( histogram_rpy ) > Test-1 ( kpca1 ) > Test-1 ( pca1 ) > Test-1 ( pca1 ) > Test-2 ( pca1 ) > Test-3 ( plot_for_lda_output1 ) > Test-1 ( qual_stats_boxplot ) > Test-1 AssertionError: History item 2 different than expected, difference (using diff) ( gops_join_1 ) > Test-4 TwillAssertionError: code is 500 != 200 I do also have failures due to missing data but I am struggling to find out where to download them. ( gd_select_snps ) > Test-1 AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error 'bighorn' does not appear in location file '/opt/local/home/webapp/galaxy/tool-data/gd.chrlens.loc' ( Annotation_Profiler_0 ) > Test-1 ( Annotation_Profiler_0 ) > Test-2 AssertionError: Configuration error: Table directory is missing (/opt/local/home/webapp/galaxy/tool-data/annotation_profiler/hg18) ( Interval2Maf_pairwise1 ) > Test-1 AssertionError: Attempting to set field 'mafType' to value '['PAIRWISE_hg17_fr1']' in form 'tool_form' threw exception: cannot find value/label "PAIRWISE_hg17_fr1" in list control ( maf_stats1 ) > Test-1 ( maf_stats1 ) > Test-2 AssertionError: Attempting to set field 'maf_source_type|mafType' to value '['8_WAY_MULTIZ_hg17']' in form 'tool_form' threw exception: cannot find value/label "8_WAY_MULTIZ_hg17" in list control ( phastOdds_for_intervals ) > Test-1 AssertionError: Attempting to set field 'score_file' to value '['/galaxy/data/phastOdds_precomputed/encode_SEP-2005_\ tba.v2_phastOdds']' in form 'tool_form' threw exception: cannot find value/label "/galaxy/data/phas..2_phastOdds" in li\ st control ( aggregate_scores_in_intervals2 ) > Test-1 ( aggregate_scores_in_intervals2 ) > Test-2 AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error ( gencode_partition1 ) > Test-1 Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error Error loading partitioning dataset. ( lda_analy1 ) > Test-1 AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error The last failure is related to genome diversity and the fact that it calls python2.5. I've changed it to python for testing but the test still fails. ( gd_extract_flanking_dna ) > Test-1 ( gd_extract_primers ) > Test-1 ( gd_select_restriction_enzymes ) > Test-1 AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error python2.5: command not found > if changed to python: ERROR: 'NoneType' object has no attribute 'rfind' Is there a way to fix these failures? Any help would be very much appreciated. Thanks, 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] shed_tool_conf.xml not updated
Greg, Thanks for your patience and help with this too! I've upgraded to ebf72cda61e7, cleaned all up (db, tool_conf.xml and shed_tool_conf.xml, file system) and restarted galaxy. The import of tabular2html works without the version attribute in the section of the tool_conf.xml file. After installing, I've restarted again and all is working fine as expected. Thanks for the fix. I've also tested the installation of bedtools into a new tool panel section and it works fine too but I think it has never been an issue. Thanks again. Kind regards, Anne. On 30 Jan 2012, at 17:46, Greg Von Kuster wrote: > Anne, > > Thanks for all of your patience and help with this. You uncovered a problem > that is very nice to have corrected. The fix is included in change set > 6634:ebf72cda61e7 on our central repository. This change set will allow you > to have section tags in your tool_conf.xml file that do not include version > attributes. Selecting these sections to contain tools installed with a tool > shed repository will now be functionally correct. > > Thanks again! > > Greg > > On Jan 30, 2012, at 12:08 PM, Anne Pajon wrote: > >> Brilliant! It is working - no more server error and I now have a >> shed_tool_conf.xml updated: >> >> Let me know when you commit your next change set, so I will be able to test. >> Thanks a lot for your help. >> Anne. >> > > Greg Von Kuster > Galaxy Development Team > g...@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)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] shed_tool_conf.xml not updated
Hi Greg,
Sorry I forget to print everything. Here it is:
galaxy.util.shed_util DEBUG 2012-01-30 16:40:32,209 XXX shed_tool_conf_dict:
{'tool_path': '../shed_tools', 'config_filename': './shed_tool_conf.xml',
'config_elems': []}
galaxy.util.shed_util DEBUG 2012-01-30 16:40:32,210 XXX elem:
Anne.
On 30 Jan 2012, at 16:10, Greg Von Kuster wrote:
> Hi Anne,
>
> Can you replace the config_elems_to_xml_file() method on line 15 of
> ~/lib/galaxy/util/shed_util.py with the following method which contains 2
> debugging statements? You'll need to once again remove the installed
> repository from disk, remove the tow for it in the tool_shed_repository
> table, and restart your Galaxy server. Try installing the repository again
> and your paster log will include the debugging statement's output. Send your
> paster log to me with this output.
>
> Thanks!
>
> def config_elems_to_xml_file( app, shed_tool_conf_dict ):
> log.debug("XXX shed_tool_conf_dict: %s" % str( shed_tool_conf_dict ))
> # Persist the current in-memory list of config_elems in the received
> shed_tool_conf_dict
> # to a file named by the value of config_filename in the received
> shed_tool_conf_dict.
> config_filename = shed_tool_conf_dict[ 'config_filename' ]
> tool_path = shed_tool_conf_dict[ 'tool_path' ]
> config_elems = shed_tool_conf_dict[ 'config_elems' ]
> fd, filename = tempfile.mkstemp()
> os.write( fd, '\n' )
> os.write( fd, '\n' % str( tool_path ) )
> for elem in config_elems:
> log.debug("XXX elem: %s" % str( elem ))
> os.write( fd, '%s' % util.xml_to_string( elem, pretty=True ) )
> os.write( fd, '\n' )
> os.close( fd )
> shutil.move( filename, os.path.abspath( config_filename ) )
> os.chmod( config_filename, 0644 )
>
>
>
> On Jan 30, 2012, at 10:59 AM, Anne Pajon wrote:
>
>> Hi Greg,
>>
>> Please see below my inline answers to your questions.
>>
>> On 30 Jan 2012, at 15:37, Greg Von Kuster wrote:
>>
>>> Hi Anne,
>>>
>>> From your paster log it looks like the repository is installed, but for
>>> whatever reason your shed_tool_conf.xml file cannot be updated. I've tried
>>> many things, but am not able to reproduce this. Can you answer the
>>> following?
>>>
>>> Have you ever been able to install a tool from the tool shed, or is this
>>> your first attempt?
>>
>> This is my first attempt, I never been able to install any tools properly
>> from the tool shed.
>>
>>
>>>
>>> Is the tabular2html repository successfully installed on disk?
>>
>> Yes it is and the tool even works in Galaxy the problem starts when you
>> restart the server then the tool is not present in the tool menu anymore.
>>
>>
>>>
>>> Is there a row added to the tool_shed_repository database table for the
>>> tabular2html repository?
>>
>> Yes and here is what I have in this table:
>>
>> id |create_time|update_time |
>> tool_shed| name | description |
>> owner | changeset_revision | deleted |
>>
>>
>> metadata
>>
>>
>> | includes_datatypes |
>> update_available | installed_changeset_revision | uninstalled | dist_to_shed
>> +---+++--++++-+-++--+--+-+--
>>
Re: [galaxy-dev] shed_tool_conf.xml not updated
Hi Greg,
Please see below my inline answers to your questions.
On 30 Jan 2012, at 15:37, Greg Von Kuster wrote:
> Hi Anne,
>
> From your paster log it looks like the repository is installed, but for
> whatever reason your shed_tool_conf.xml file cannot be updated. I've tried
> many things, but am not able to reproduce this. Can you answer the following?
>
> Have you ever been able to install a tool from the tool shed, or is this your
> first attempt?
This is my first attempt, I never been able to install any tools properly from
the tool shed.
>
> Is the tabular2html repository successfully installed on disk?
Yes it is and the tool even works in Galaxy the problem starts when you restart
the server then the tool is not present in the tool menu anymore.
>
> Is there a row added to the tool_shed_repository database table for the
> tabular2html repository?
Yes and here is what I have in this table:
id |create_time|update_time | tool_shed
| name | description | owner |
changeset_revision | deleted |
metadata
| includes_datatypes | update_available |
installed_changeset_revision | uninstalled | dist_to_shed
+---+++--++++-+-++--+--+-+--
2 | 2012-01-30 09:54:42.31609 | 2012-01-30 09:54:42.316111 |
toolshed.g2.bx.psu.edu | tabular2html | Creates HTML tables from tabular data.
| ondovb | a5814dd5a11a | f | {"tool_panel_section": {"id":
"myTools", "name": "My Tools", "version": null}, "tools": [{"description": "for
easier table viewing", "guid":
"toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0", "id":
"tabular2HTML", "name": "Tabular-to-HTML", "requirements": [], "tests": [],
"tool_config":
"../shed_tools/toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/a5814dd5a11a/tabular2html/tabular2HTML.xml",
"version": "1.0.0", "version_string_cmd": null}]} | f | f
| a5814dd5a11a | f | f
(1 row)
>
> What database are you using for your Galaxy instance?
I am using PostgreSQL.
>
> What setting do you have for tool_config_file in your universe_wsgi.ini? For
> the file to which the setting refers, can you paste its entire contents below?
>
In the universe_wsgi.ini, I have:
tool_config_file = tool_conf.xml,shed_tool_conf.xml
shed_tool_conf.xml:
Thanks for your help.
Kind regards,
Anne.
> Thanks!
>
>
> On Jan 30, 2012, at 5:12 AM, Anne Pajon wrote:
>
>> Hi Greg,
>>
>> Thanks for your answer.
>>
>> I've deleted the row in the tool_shed_repository table, removed the
>> installed tool shed repository from disk, updated my Galaxy instance to
>> 6629:cb458aca542e from Galaxy central and restarted Galaxy server.
>>
>> I am sorry to say but I do still have the same problem (Server Error when
>> installing and shed_tool_conf.xml not updated). Any ideas on why it does not
>> work? Thanks to let me know.
>>
>> Here is my log:
>>
>> galaxy.util.shed_util DEBUG 2012-01-30 09:54:40,555 Installing repository
>> 'tabular2html'
>> galaxy.util.shed_util DEBUG 2012-01-30 09:54:40,556 Cloning
>> http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html
>> galaxy.util.shed_util DEBUG 2012-01-30 09:54:42,165 Updating cloned
>> repository to revision "a5814dd5a11a"
>> galaxy.util.shed_util DEBUG 2012-01-30 09:54:42,308 A
Re: [galaxy-dev] shed_tool_conf.xml not updated
e 695 in _write File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 827 in _escape_attrib File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 774 in _raise_serialization_error TypeError: cannot serialize None (type NoneType) Kind regards, Anne. On 27 Jan 2012, at 19:38, Greg Von Kuster wrote: > Hi Anne, > > OK, the only other thing this could be is that the metadata column in the > tool_shed_repository database table for this repository got corrupted during > the initial install when the revision of your Galaxy instance was not up to > date. So, if the repository once again got installed on disk, but the entry > for the tool didn't make it into shed_tool_conf,xml, then manually remove the > repository from disk again. Then either update the metadata column in the > tool shed repository table for this repository to be null or delete the > record from the table. > > If you're using postgres, then the update statement would be something like: > > update tool_shed_repository set metadata = null where id = is of the tabular2html tool shed repository> > > You could also delete this record from the table and it will be recreated > when you install the repository. > > After taking these 2 steps, you should be able to install the tool with no > problem. However, if there is an entry in your shed_tool_conf.xml file, > remove it manually before attempting to reinstall. > > Sorry for all of this, but once you have your environment cleared up > (following the steps above) and you're running the correct change set, > installing from the tool shed should not cause you problems. > > Let me know how this goes. > > Greg Von Kuster > > > On Jan 27, 2012, at 2:27 PM, Anne Pajon wrote: > >> Hi Greg, >> >> Thanks for your answer. I've upgraded my Galaxy instance to 56bdee21dc78 >> from Galaxy central repository. >> >> I tried again to install tabular2html from the tool shed, but I get the same >> problem (Server Error when installing and shed_tool_conf.xml not updated). >> Here is my log in case it helps. >> >> galaxy.util.shed_util DEBUG 2012-01-27 19:20:52,660 Installing repository >> 'tabular2html' >> galaxy.util.shed_util DEBUG 2012-01-27 19:20:52,660 Cloning >> http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html >> galaxy.util.shed_util DEBUG 2012-01-27 19:20:53,839 Updating cloned >> repository to revision "a5814dd5a11a" >> galaxy.util.shed_util DEBUG 2012-01-27 19:20:53,982 Adding new row (or >> updating an existing row) for repository 'tabular2html' in the >> tool_shed_repository table. >> galaxy.tools DEBUG 2012-01-27 19:20:54,050 Reloading section: My Tools >> galaxy.tools DEBUG 2012-01-27 19:20:54,078 Loaded tool id: >> toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, >> version: 1.0.0. >> 143.65.172.178 - - [27/Jan/2012:19:20:52 +0100] "POST >> /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True >> HTTP/1.1" 500 - >> "http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True"; >> "Mozilla/5.0 (Macint! osh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13" >> Error - : cannot serialize None (type NoneType) >> URL: >> http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True >> File >> '/opt/local/home/webapp/galaxy/ga
Re: [galaxy-dev] shed_tool_conf.xml not updated
ter:
paste.recursive.script_name: '/galaxy'
paste.throw_errors: True
webob._parsed_post_vars: (MultiDict([('shed_tool_conf',
'shed_tool_conf.xml'), ('new_tool_panel_section', ''), ('tool_panel_section',
'myTools'), ('select_tool_panel_section_button', 'Install')]), )
webob._parsed_query_vars: (MultiDict([('tool_shed_url',
'http://toolshed.g2.bx.psu.edu'), ('repo_info_dict',
'3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d'),
('includes_tools', 'True')]),
'tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True')
wsgi process: 'Multithreaded'
Kind regards,
Anne.
On 27 Jan 2012, at 15:55, Greg Von Kuster wrote:
> Hi Anne, see my inline comments.
>
> On Jan 27, 2012, at 10:26 AM, Anne Pajon wrote:
>
>> Hi Greg,
>>
>> Thanks a lot. I have the impression from what I read on the wiki that Galaxy
>> will be using the tool shed to provide more flexibility in choosing tools
>> instead of having them bundle in the current distribution. We are very much
>> interested by these new features because we only use a subset of the
>> available tools plus some that we have developed in house.
>
> Yes, this is correct. At some point, a subset of the tools currently in the
> Galaxy distribution will be moved to the main Galaxy tool shed from which
> they can be easily installed using Galaxy's new installation manager. You'll
> be able to very easily install any portion of the tools that will be
> eliminated from the distribution. All of this is now functional in the
> latest version of Galaxy as well as the main Galaxy tool shed, but the
> timeline for beginning to eliminate tools from the distribution is yet to be
> determined.
>
> The tip of the central repository, which will be added to the Galaxy
> distribution repository today, includes the ability to deactivate or
> uninstall repositories that you've installed from the tool shed, enabling
> much more flexibility in managing the tools that are included in your Galaxy
> tool panel. The last section of the tool shed wiki describes this new
> feature set:
>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Deactivating_and_uninstalling_tool_shed_repositories_installed_into_a_local_Galaxy_instance
>
>>
>>> From what you are saying, I have the impression that I will be better of
>>> running my Galaxy instance against the central repository instead of the
>>> distribution one if I do not want to wait for bug fixes. Am I right of
>>> thinking that? If so, I will migrate to the central repository and let you
>>> know how it goes.
>
> Although this is not ideal, it is unfortunately necessary at least for the
> current time. At some point, the communication layers between Galaxy and the
> tool shed will stabilize to the point that the distribution repository can be
> used, but in the meantime, the central repository is required. My advice for
> now would be to have your Galaxy instance track central, but not necessarily
> update it all of the time. I believe the update to the distribution going
> out today will be change set 6621:26920e20157f, which includes all new tool
> shed features. So although this is not the latest on the central repo, you
> can update to that revision if you want. To do so, change your hgrc to pull
> from Galaxy central and use the following.
>
> hg pull -u 26920e20157f
>
> If you are comfortable in updating to the latest from central, just use
>
> hg pull -u
>
>>
>> Before migrating and updating I will manually remove the installed tool shed
>> repository from disk as you advised.
>>
>> Kind regards,
>> Anne.
>>
>>
>> On 27 Jan 2012, at 14:57, Greg Von Kuster wrote:
>>
>>> Hi Anne,
>>>
>>> A new update to the Galaxy distribution repository is planned for today, I
>>> believe, so unless that changes you should be able to update your Galaxy
>>> instance either to
Re: [galaxy-dev] shed_tool_conf.xml not updated
Hi Greg, Thanks a lot. I have the impression from what I read on the wiki that Galaxy will be using the tool shed to provide more flexibility in choosing tools instead of having them bundle in the current distribution. We are very much interested by these new features because we only use a subset of the available tools plus some that we have developed in house. >From what you are saying, I have the impression that I will be better of >running my Galaxy instance against the central repository instead of the >distribution one if I do not want to wait for bug fixes. Am I right of >thinking that? If so, I will migrate to the central repository and let you >know how it goes. Before migrating and updating I will manually remove the installed tool shed repository from disk as you advised. Kind regards, Anne. On 27 Jan 2012, at 14:57, Greg Von Kuster wrote: > Hi Anne, > > A new update to the Galaxy distribution repository is planned for today, I > believe, so unless that changes you should be able to update your Galaxy > instance either today or Monday using the distribution repository. However, > this problem will continue to exist between Galaxy instances that track the > distribution repository and that also want to take advantage of the Galaxy > tool shed features that enable direct interaction between Galaxy and the tool > shed. The tool shed features are implement much more rapidly than the Galaxy > distribution is updated, resulting in this ongoing problem. > > Regarding the state of your local instance and the tool shed repository you > attempted to install - if I understand correctly, the repository was > successfully installed on disk, but the XML tag set entry for the contained > tool was not added to your shed_tool_conf.xml file. If this is the case, > then you'll need to manually remove the installed tool shed repository from > disk before you try installing it again after updating your Galaxy instance > to the new upcoming distribution. > > Sorry for the inconvenience. > > Greg > > On Jan 27, 2012, at 9:35 AM, Anne Pajon wrote: > >> Hello Greg, >> >> Thanks a lot for your answer and sorry for having sent two emails. >> >> Regarding the version of our local instance, I understand perfectly that the >> Galaxy distribution repository is behind the Galaxy central repository but >> we would like to use Galaxy on a production server and we are looking at >> stable releases not development ones. What would you advice us to do? >> >> Here is the value for tool_path in my shed_tool_conf.xml: >> >> >> >> >> I'm waiting your advice to migrate my repository from Galaxy distribution to >> Galaxy central. Thanks in advance. >> >> Kind regards, >> Anne. >> >> >> On 27 Jan 2012, at 13:03, Greg Von Kuster wrote: >> >>> Hello Anne, >>> >>> I apologize for the delay in responding to you on this. The first issue I >>> see is that the revision of your local Galaxy instance implies that your >>> repo is not being updated from the Galaxy central repository on bitbucket. >>> Unfortunately in order to use the tool shed, you local Galaxy instance must >>> be up to date with the central repository since the Galaxy distribution >>> repository generally lags 6 to 8 weeks behind the central repository, and >>> so the communication between Galaxy and the tool shed is often not >>> functionally correct. The central repository on bitbucket is current at >>> revision 6626:d8af2f7b1f35. >>> >>> For clarification what value have you set for the tool_path config setting >>> in your shed_tool_conf.xml file? >>> >>> After you update your Galaxy instance, try installing the tool again and >>> let me know if you encounter issues. >>> >>> Thanks very much! >>> >>> Greg Von Kuster >>> >>> >>> On Jan 27, 2012, at 5:55 AM, Anne Pajon wrote: >>> >>>> Hello, >>>> >>>> When installing a tool from the tool shed repository into our local >>>> instance, I've got a page with "Server error". When restarting Galaxy, >>>> the imported tool has disappeared from the blue left list of tools. After >>>> installing the tool, the file shed_tool_conf.xml has not been updated. >>>> >>>> Bellow is my previous email "server error when installing tool from tool >>>> shed repository into local instance" sent two days ago detailing what I >>>> have done and the log related to the error. >>>> >>&
Re: [galaxy-dev] shed_tool_conf.xml not updated
Hello Greg, Thanks a lot for your answer and sorry for having sent two emails. Regarding the version of our local instance, I understand perfectly that the Galaxy distribution repository is behind the Galaxy central repository but we would like to use Galaxy on a production server and we are looking at stable releases not development ones. What would you advice us to do? Here is the value for tool_path in my shed_tool_conf.xml: I'm waiting your advice to migrate my repository from Galaxy distribution to Galaxy central. Thanks in advance. Kind regards, Anne. On 27 Jan 2012, at 13:03, Greg Von Kuster wrote: > Hello Anne, > > I apologize for the delay in responding to you on this. The first issue I > see is that the revision of your local Galaxy instance implies that your repo > is not being updated from the Galaxy central repository on bitbucket. > Unfortunately in order to use the tool shed, you local Galaxy instance must > be up to date with the central repository since the Galaxy distribution > repository generally lags 6 to 8 weeks behind the central repository, and so > the communication between Galaxy and the tool shed is often not functionally > correct. The central repository on bitbucket is current at revision > 6626:d8af2f7b1f35. > > For clarification what value have you set for the tool_path config setting in > your shed_tool_conf.xml file? > > After you update your Galaxy instance, try installing the tool again and let > me know if you encounter issues. > > Thanks very much! > > Greg Von Kuster > > > On Jan 27, 2012, at 5:55 AM, Anne Pajon wrote: > >> Hello, >> >> When installing a tool from the tool shed repository into our local >> instance, I've got a page with "Server error". When restarting Galaxy, the >> imported tool has disappeared from the blue left list of tools. After >> installing the tool, the file shed_tool_conf.xml has not been updated. >> >> Bellow is my previous email "server error when installing tool from tool >> shed repository into local instance" sent two days ago detailing what I have >> done and the log related to the error. >> >> Sorry to ask again but I did not solve the problem and I am still looking >> for help. I just wanted to re-formulate the issue in a shorter way. >> >> Let me know if you have any suggestions. >> Kind regards, >> Anne. >> >> >> On 25 Jan 2012, at 16:43, Anne Pajon wrote: >> >>> Hello, >>> >>> I have the version 6528:63bc46cc73b7 of galaxy running locally on our >>> server installed from https://bitbucket.org/galaxy/galaxy-dist/. >>> >>> I've tried to bring tabular2html tool from Galaxy main tool shed repository >>> following the wiki information >>> (http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance) >>> without success. >>> >>> Here is what I've done. >>> >>> (1) I've edited my universe_wsgi.ini >>> # -- Files and directories >>> >>> # Tool config files, defines what tools are available in Galaxy. >>> # Tools can be locally developed or installed from Galaxy tool sheds. >>> tool_config_file = tool_conf.xml,shed_tool_conf.xml >>> >>> # Default path to the directory containing the tools defined in >>> tool_conf.xml. >>> # Other tool config files must include the tool_path as an attribute in the >>> tag. >>> tool_path = tools >>> >>> (2) I've created the directory shed_tools/ above the galaxy-dist/ as >>> recommended >>> >>> (3) I've restarted the server >>> >>> (4) I've logged in as "admin" user. I've clicked the "Admin" link in the >>> top Galaxy tool panel to display the Galaxy Administration interface and >>> then "Search and browse tool sheds" under "Tool sheds" from the left blue >>> section to display the Accessible Galaxy tool sheds page, click "Galaxy >>> main tool shed" to display the valid repositories and choose tabular2html >>> and click on Install to local Galaxy, select the panel section and click >>> Install. >>> >>> I get a page with "Server Error". >>> >>> Strangely, the tool appears in the list of tools and works in my Galaxy >>> instance. The tool files have been installed on disk at the directory >>> created in (2) but the shed_tool_conf.xml has not been updated. After &g
[galaxy-dev] shed_tool_conf.xml not updated
Hello, When installing a tool from the tool shed repository into our local instance, I've got a page with "Server error". When restarting Galaxy, the imported tool has disappeared from the blue left list of tools. After installing the tool, the file shed_tool_conf.xml has not been updated. Bellow is my previous email "server error when installing tool from tool shed repository into local instance" sent two days ago detailing what I have done and the log related to the error. Sorry to ask again but I did not solve the problem and I am still looking for help. I just wanted to re-formulate the issue in a shorter way. Let me know if you have any suggestions. Kind regards, Anne. On 25 Jan 2012, at 16:43, Anne Pajon wrote: > Hello, > > I have the version 6528:63bc46cc73b7 of galaxy running locally on our server > installed from https://bitbucket.org/galaxy/galaxy-dist/. > > I've tried to bring tabular2html tool from Galaxy main tool shed repository > following the wiki information > (http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance) > without success. > > Here is what I've done. > > (1) I've edited my universe_wsgi.ini > # -- Files and directories > > # Tool config files, defines what tools are available in Galaxy. > # Tools can be locally developed or installed from Galaxy tool sheds. > tool_config_file = tool_conf.xml,shed_tool_conf.xml > > # Default path to the directory containing the tools defined in tool_conf.xml. > # Other tool config files must include the tool_path as an attribute in the > tag. > tool_path = tools > > (2) I've created the directory shed_tools/ above the galaxy-dist/ as > recommended > > (3) I've restarted the server > > (4) I've logged in as "admin" user. I've clicked the "Admin" link in the top > Galaxy tool panel to display the Galaxy Administration interface and then > "Search and browse tool sheds" under "Tool sheds" from the left blue section > to display the Accessible Galaxy tool sheds page, click "Galaxy main tool > shed" to display the valid repositories and choose tabular2html and click on > Install to local Galaxy, select the panel section and click Install. > > I get a page with "Server Error". > > Strangely, the tool appears in the list of tools and works in my Galaxy > instance. The tool files have been installed on disk at the directory created > in (2) but the shed_tool_conf.xml has not been updated. After restarting my > Galaxy server, the tool is not visible anymore. > > Here is what appears in the log related to the installation of the tool: > galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Installing repository > 'tabular2html' > galaxy.util.shed_util DEBUG 2012-01-25 14:20:54,451 Cloning > http://toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html > galaxy.util.shed_util DEBUG 2012-01-25 14:20:55,486 Updating cloned > repository to revision "a5814dd5a11a" > galaxy.tools DEBUG 2012-01-25 14:20:55,652 Reloading section: My Tools > galaxy.tools DEBUG 2012-01-25 14:20:55,673 Loaded tool id: > toolshed.g2.bx.psu.edu/repos/ondovb/tabular2html/tabular2HTML/1.0.0, version: > 1.0 > .0. > 143.65.172.178 - - [25/Jan/2012:14:20:54 +0100] "POST > /galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.ps > u.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b22437265617465732048544d4c207461626c6573 > 2066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6f6e646f76622f74616275 > 6c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True > HTTP/1.1" 500 - "http://uk-cri-lbio08/galaxy/admin_toolshed/insta > ll_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=3abd29129982504350fb737085131cc07e47cc03:7b22746162756c61723268746d > 6c223a205b22437265617465732048544d4c207461626c65732066726f6d20746162756c617220646174612e222c2022687474703a2f2f746f6f6c736865642e67322e62782e > 7073752e6564752f7265706f732f6f6e646f76622f746162756c61723268746d6c222c2022613538313464643561313161225d7d&includes_tools=True" > "Mozilla/5.0 ( > Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.13) Gecko/20101203 > Firefox/3.6.13" > Error - : cannot serialize None (type NoneType) > URL: > http://uk-cri-lbio08/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu&repo_info_dict=3abd2912 > 9982504350fb737085131cc07e47cc03%3A7b22746162756c61723268746d6c223a205b224372656
[galaxy-dev] server error when installing tool from tool shed repository into local instance
'/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 275 in install_repository new_install=True ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 644 in load_repository_contents add_to_config=True ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 699 in load_altered_part_of_tool_panel add_shed_tool_conf_entry( app, shed_tool_conf, elem_entry ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 41 in add_shed_tool_conf_entry new_shed_tool_conf.write( util.xml_to_string( tool_panel_entry, pretty=True ) ) File '/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/util/__init__.py', line 113 in xml_to_string return ElementTree.tostring( pretty_print_xml( elem ) ) File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 1006 in tostring File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 660 in write File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 695 in _write File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 827 in _escape_a ttrib File '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py', line 774 in _raise_se rialization_error TypeError: cannot serialize None (type NoneType) Any help would be very welcome. Thanks a lot in advance. 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)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] unit tests failures
Hi, Thanks a lot for your answer. I've manually changed lib/galaxy/objectstore/__init__.py while waiting for the fixed to be released. All the unit tests now pass. Anne. On 23 Jan 2012, at 18:51, Nate Coraor wrote: > On Jan 23, 2012, at 6:22 AM, Anne Pajon wrote: > >> Hello, >> >> I've installed recently galaxy on one of our test server with python2.7 and >> I am running out of ideas on how to solve the issue related to this unit >> test failure: galaxy.objectstore.DiskObjectStore. Here is the output when >> running sh run_unit_tests.sh. > > Hi Anne, > > This has been fixed in changeset 8a597b83448f. Unfortunately, this changeset > is not part of the current stable release. It will be in the next one, > however. > > https://bitbucket.org/galaxy/galaxy-central/changeset/8a597b83448f > > --nate > -- 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/
[galaxy-dev] unit tests failures
.. ok InRangeValidator (galaxy.tools.parameters.validation) Doctest: galaxy.tools.parameters.validation.InRangeValidator ... ok LengthValidator (galaxy.tools.parameters.validation) Doctest: galaxy.tools.parameters.validation.LengthValidator ... ok RegexValidator (galaxy.tools.parameters.validation) Doctest: galaxy.tools.parameters.validation.RegexValidator ... ok Params (galaxy.util) Doctest: galaxy.util.Params ... ok file_iter (galaxy.util) Doctest: galaxy.util.file_iter ... ok nice_size (galaxy.util) Doctest: galaxy.util.nice_size ... ok unique_id (galaxy.util) Doctest: galaxy.util.unique_id ... ok CheckboxField (galaxy.web.form_builder) Doctest: galaxy.web.form_builder.CheckboxField ... ok DrillDownField (galaxy.web.form_builder) Doctest: galaxy.web.form_builder.DrillDownField ... ok FileField (galaxy.web.form_builder) Doctest: galaxy.web.form_builder.FileField ... ok HiddenField (galaxy.web.form_builder) Doctest: galaxy.web.form_builder.HiddenField ... ok PasswordField (galaxy.web.form_builder) Doctest: galaxy.web.form_builder.PasswordField ... ok SelectField (galaxy.web.form_builder) Doctest: galaxy.web.form_builder.SelectField ... ok TextArea (galaxy.web.form_builder) Doctest: galaxy.web.form_builder.TextArea ... ok TextField (galaxy.web.form_builder) Doctest: galaxy.web.form_builder.TextField ... ok == FAIL: DiskObjectStore (galaxy.objectstore) Doctest: galaxy.objectstore.DiskObjectStore -- Traceback (most recent call last): File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 2166, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for galaxy.objectstore.DiskObjectStore File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 190, in DiskObjectStore -- File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 198, in galaxy.objectstore.DiskObjectStore Failed example: s = DiskObjectStore(Bunch(umask=077), file_path=file_path) Exception raised: Traceback (most recent call last): File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 1254, in __run compileflags, 1) in test.globs File "", line 1, in s = DiskObjectStore(Bunch(umask=077), file_path=file_path) File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 208, in __init__ self.extra_dirs['job_work'] = config.job_working_directory AttributeError: 'Bunch' object has no attribute 'job_working_directory' -- File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 199, in galaxy.objectstore.DiskObjectStore Failed example: s.create(1) Exception raised: Traceback (most recent call last): File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 1254, in __run compileflags, 1) in test.globs File "", line 1, in s.create(1) NameError: name 's' is not defined -- File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 200, in galaxy.objectstore.DiskObjectStore Failed example: s.exists(1) Exception raised: Traceback (most recent call last): File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 1254, in __run compileflags, 1) in test.globs File "", line 1, in s.exists(1) NameError: name 's' is not defined -- File "/opt/local/home/webapp/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 202, in galaxy.objectstore.DiskObjectStore Failed example: assert s.get_filename(1) == file_path + '/000/dataset_1.dat' Exception raised: Traceback (most recent call last): File "/opt/local/home/webapp/galaxy/python/lib/python2.7/doctest.py", line 1254, in __run compileflags, 1) in test.globs File "", line 1, in assert s.get_filename(1) == file_path + '/000/dataset_1.dat' NameError: name 's' is not defined -- Ran 60 tests in 3.651s FAILED (failures=1) Thanks in advance for your help. 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)7958 511 353 NOTICE AND DISCLAIME
