Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
Hi Peter, I've created the following Trello card for this. I know what the problems are, but I won't have time to get fixes for them for a while. Please continue to reposrt issues you discover and I'll make sure to get fixes as soon as I get time. https://trello.com/c/M1rwVWhI/143-nightly-test-runs-1 Thanks Greg Von Kuster On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Jan 29, 2014, at 1:18 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter wrote: http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-29 missing blast_datatypes dependency (why?) 2014-01-28 showing failed tests for sambamba_filter (wrong tool) I'll have to take a look at the above issue. I'm completely swamped though, so it will be a while. I believe I have the above issue resolved in 12331:fd4936ae8219 ( at least I took a step in the right direction ). We'll have to wait for tonight's test run to make sure everything is handled correctly. Hi again Greg, That one is still weird - was that fix deployed to the main toolshed? http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr Moreover there is a similar problem with the matching repository on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-04 showing failed tests for proteomics_search_tandem_1 2013-12-20 showing failed tests for proteomics_search_tandem_1 2013-12-18 tests for blastxml_to_top_descr passed 2013-12-17 tests for blastxml_to_top_descr passed -- Returning to the MIRA4 problem, I got a meaningful test failure which I fixed (I hadn't set an environment variable in the install script), but I now get only partial test output: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Not datestamped (a glitch if there is only one test entry?): Automated tool test results Automated test environment Time tested: 2014-02-03 16:25:08 System: Architecture: Python version: Galaxy revision: Galaxy database version: Tool shed revision: 12332:d9f6f3f24671 Tool shed database version: 22 Tool shed mercurial version: 2.2.3 Tools missing tests or test data Tool id: mira_4_0_mapping Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2 Missing components: Functional test definitions missing for mira_4_0_mapping. Tool id: mira_4_0_de_novo Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo/0.0.2 Missing components: Functional test definitions missing for mira_4_0_de_novo. That's all fine, but where are the test results for mira_bait which I would expect to pass? Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
Hi Peter, I've created the following Trello card for this. I know what the problems are, but I won't have time to get fixes for them for a while. Please continue to reposrt issues you discover and I'll make sure to get fixes as soon as I get time. https://trello.com/c/M1rwVWhI/143-nightly-test-runs-1 Thanks Greg Von Kuster On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Jan 29, 2014, at 1:18 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter wrote: http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-29 missing blast_datatypes dependency (why?) 2014-01-28 showing failed tests for sambamba_filter (wrong tool) I'll have to take a look at the above issue. I'm completely swamped though, so it will be a while. I believe I have the above issue resolved in 12331:fd4936ae8219 ( at least I took a step in the right direction ). We'll have to wait for tonight's test run to make sure everything is handled correctly. Hi again Greg, That one is still weird - was that fix deployed to the main toolshed? http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr Moreover there is a similar problem with the matching repository on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-04 showing failed tests for proteomics_search_tandem_1 2013-12-20 showing failed tests for proteomics_search_tandem_1 2013-12-18 tests for blastxml_to_top_descr passed 2013-12-17 tests for blastxml_to_top_descr passed -- Returning to the MIRA4 problem, I got a meaningful test failure which I fixed (I hadn't set an environment variable in the install script), but I now get only partial test output: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Not datestamped (a glitch if there is only one test entry?): Automated tool test results Automated test environment Time tested: 2014-02-03 16:25:08 System: Architecture: Python version: Galaxy revision: Galaxy database version: Tool shed revision: 12332:d9f6f3f24671 Tool shed database version: 22 Tool shed mercurial version: 2.2.3 Tools missing tests or test data Tool id: mira_4_0_mapping Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2 Missing components: Functional test definitions missing for mira_4_0_mapping. Tool id: mira_4_0_de_novo Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo/0.0.2 Missing components: Functional test definitions missing for mira_4_0_de_novo. That's all fine, but where are the test results for mira_bait which I would expect to pass? Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] IGV display_application configuration failed with require_login=TRUE
Dear galaxy-dev team,
We have configured a galaxy-dist server (stable release) behind an
Apache2 proxy (with mod_xsendfile) by following the galaxy wiki.
We would like to use the galaxy embeded user authentification with
require_login=True option instead of a remote_user configuration on the
proxy side.
With require_login = False it works but with require_login=True
configuration we fail to load .bam files into IGV (local) :
The IGV (Version 2.3.18) send this error:
*/INFO [2014-02-04 16:05:56,660] [MessageUtils.java:60] [Thread-9]
Error loading
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam:
An error occurred while accessing:
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bambrInvalid
GZIP/**/header/**/
/*
and the galaxy-server send this error_log:
*//**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] HEAD
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1 302 - - IGV Version 2.3.18 (20)09/05/2013 12:24 PM/**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] HEAD /root HTTP/1.1 200 -
- IGV Version 2.3.18 (20)09/05/2013 12:24 PM/**/
/**//**/
/**/Exception happened during processing of request from ('127.0.0.1',
46142)/**/
/**/Traceback (most recent call last):/**/
/**/ File
/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py,
line 1068, in process_request_in_thread/**/
/**/self.finish_request(request, client_address)/**/
/**/ File /usr/lib/python2.7/SocketServer.py, line 334, in
finish_request/**/
/**/self.RequestHandlerClass(request, client_address, self)/**/
/**/ File /usr/lib/python2.7/SocketServer.py, line 651, in __init__/**/
/**/self.finish()/**/
/**/ File /usr/lib/python2.7/SocketServer.py, line 710, in finish/**/
/**/self.wfile.close()/**/
/**/ File /usr/lib/python2.7/socket.py, line 279, in close/**/
/**/self.flush()/**/
/**/ File /usr/lib/python2.7/socket.py, line 303, in flush/**/
/**/self._sock.sendall(view[write_offset:write_offset+buffer_size])/**/
/**/error: [Errno 32] Broken pipe/**/
/**//**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] GET
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1 302 - - IGV Version 2.3.18 (20)09/05/2013 12:24 PM/**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] GET /root HTTP/1.1 200 -
- IGV Version 2.3.18 (20)09/05/2013 12:24 PM/*
Any idea ?
Vincent
--
Vincent Navratil, PhD
IR UCBL - PRABI
http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard -- Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826
My 'ome' page http://vinavratil.free.fr
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Re: [galaxy-dev] IGV display_application configuration failed with require_login=TRUE
Hi Vincent,
I think there was an error that was fixed recently. If you can, please try
yo upgrade or wait a few more days until the new galaxy-dist version is
released.
Bjoern
2014-02-04 navratil navra...@prabi.fr:
Dear galaxy-dev team,
We have configured a galaxy-dist server (stable release) behind an
Apache2 proxy (with mod_xsendfile) by following the galaxy wiki.
We would like to use the galaxy embeded user authentification with
require_login=True option instead of a remote_user configuration on the
proxy side.
With require_login = False it works but with require_login=True
configuration we fail to load .bam files into IGV (local) :
The IGV (Version 2.3.18) send this error:
*INFO [2014-02-04 16:05:56,660] [MessageUtils.java:60] [Thread-9] Error
loading
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam:
An error occurred while accessing:
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bambrInvalid
GZIP** header*
and the galaxy-server send this error_log:
**
*XX - - [04/Feb/2014:16:05:40 +0200] HEAD
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1 302 - - IGV Version 2.3.18 (20)09/05/2013 12:24 PM*
*XX - - [04/Feb/2014:16:05:40 +0200] HEAD /root HTTP/1.1 200 - -
IGV Version 2.3.18 (20)09/05/2013 12:24 PM*
**
*Exception happened during processing of request from ('127.0.0.1', 46142)*
*Traceback (most recent call last):*
* File
/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py,
line 1068, in process_request_in_thread*
*self.finish_request(request, client_address)*
* File /usr/lib/python2.7/SocketServer.py, line 334, in finish_request*
*self.RequestHandlerClass(request, client_address, self)*
* File /usr/lib/python2.7/SocketServer.py, line 651, in __init__*
*self.finish()*
* File /usr/lib/python2.7/SocketServer.py, line 710, in finish*
*self.wfile.close()*
* File /usr/lib/python2.7/socket.py, line 279, in close*
*self.flush()*
* File /usr/lib/python2.7/socket.py, line 303, in flush*
*self._sock.sendall(view[write_offset:write_offset+buffer_size])*
*error: [Errno 32] Broken pipe*
**
*XX - - [04/Feb/2014:16:05:40 +0200] GET
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1 302 - - IGV Version 2.3.18 (20)09/05/2013 12:24 PM*
*XX - - [04/Feb/2014:16:05:40 +0200] GET /root HTTP/1.1 200 - -
IGV Version 2.3.18 (20)09/05/2013 12:24 PM*
Any idea ?
Vincent
--
Vincent Navratil, PhD
IR UCBL - PRABI http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard - Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826
My 'ome' page http://vinavratil.free.fr
___
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
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To search Galaxy mailing lists use the unified search at:
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[galaxy-dev] Cheetah code issue
Hi,
While developing a tool, I am facing Cheetah code issue. I looked up the
mailing list archive and found many similar issues reported earlier but
could not debug this. Any tips in debugging is appreciated.
File cheetah_DynamicallyCompiledCheetahTemplate_1391530084_29_71368.py,
line 97, in respond
NotFound: cannot find 'rngstart'
Attached is the xml tool definition file.
Best,
Ketan
tool id=swiftforeach name=foreach
descriptionA generic tool to run executable via Swift foreach parallel construct/description
command interpreter=bash
#if $rangeorlist.rl == rng
swiftforeachrange.sh
$site
$interpret
$exec
$rngstart
$rend
$stepsize
$outloc
$logfile
$outlist
#for $a in $arg
${a.argname}
#end for
#else
swiftforeachlist.sh
$site
$interpret
$exec
$listfile
$outloc
$logfile
$outlist
#for $a in $arg
${a.argname}
#end for
#end if
/command
inputs
param name=site type=select label=Execution Location
option value=localhostLocalhost/option
option value=midwayMidway/option
option value=uc3UC3/option
option value=stampedeStampede/option
/param
param name=interpret type=select label=Execution interpreter
option value=shsh/option
option value=pythonpython/option
option value=javajava/option
option value=RR/option
option value=matlabmatlab/option
/param
param format=sh,binexec name=exec type=data label=Executable/
conditional name=rangeorlist
param name=rl type=select label=Select range or list
option value=rngnumeric range/option
option value=lstitems list/option
/param
when value=rng
param name=rngstart size=2 type=integer value=0 label=start/
param name=rend size=2 type=integer value=9 label=end/
param name=stepsize size=2 type=integer value=1 label=stepsize/
/when
when value=lst
param format=data name=listfile type=data label=List file/
/when
/conditional
repeat name=arg title=arg
param name=argname type=text label=arg /
/repeat
param name=outloc size=50 type=text value=$HOME/swift-sandbox label=location for output files help=Swift will write output files here on disc
sanitizer sanitize=False /
/param
conditional name=configuration
param name=mode type=select label=Swift configuration
option value=defaultdefault configuration/option
option value=advancedadvanced configuration/option
/param
when value=default
/when
when value=advanced
param name=remoteurl size=50 type=text value=midway.swift.rcc.uchicago.edu label=remote url help=remote resource to run jobs on/param
param name=throttle size=5 type=float value=0.07 label=job throttle help=number of parallel jobs to run/param
param name=project type=text value=TG-STA110005S label=Project allocation help=name/code of project/param
param name=slots size=5 type=integer value=1 label=slots help=number of scheduler jobs/param
param name=queue size=5 type=text value=normal label=queue help=queue to run jobs on/param
param name=nodes size=5 type=integer value=1 label=nodes help=number of nodes requested/param
param name=nodegranularity size=5 type=integer value=1 label=node granularity help=node granularity/param
param name=jobspernode size=5 type=integer value=8 label=jobs per node help=number of jobs per node requested/param
param name=ppn size=5 type=integer value=8 label=ppn help=processes per node requested/param
param name=walltime size=5 type=text value=00:10:00 label=Job walltime help=time in hh:mm:ss to request to scheduler for this job/param
param name=maxtime size=5 type=integer value=700 label=application maxtime help=Application maxtime in seconds for this job/param
/when
/conditional
/inputs
outputs
data format=txt name=logfile type=data label=Swift output /
data format=txt name=outlist type=data label=Output list /
/outputs
!--
code file=postprocess.py
hook postprocess=writeoutlist /
/code
--
help
.. class:: warningmark
**TIP**. Add args to provide additional arguments to your executable.
-
**What it does**
This is a generic Swift tool that runs an executable over a range of numbers with arbitrary stepsize.
Execution location allows user to declare where to run the tool. Executable can be any arbitrary executable of type binexec uploaded by user.
Start, end and stepsize are integer values. Note that the stepsize cannot be less than 1. Optionally,
Re: [galaxy-dev] IGV display_application configuration failed with require_login=TRUE
On 04/02/2014 16:37, navratil wrote:
Dear galaxy-dev team,
We have configured a galaxy-dist server (stable release) behind an
Apache2 proxy (with mod_xsendfile) by following the galaxy wiki.
We would like to use the galaxy embeded user authentification with
require_login=True option instead of a remote_user configuration on
the proxy side.
With require_login = False it works but with require_login=True
configuration we fail to load .bam files into IGV (local) :
The IGV (Version 2.3.18) send this error:
*/INFO [2014-02-04 16:05:56,660] [MessageUtils.java:60] [Thread-9]
Error loading
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam:
An error occurred while accessing:
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bambrInvalid
GZIP/**/header/**/
/*
and the galaxy-server send this error_log:
*//**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] HEAD
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1 302 - - IGV Version 2.3.18 (20)09/05/2013 12:24 PM/**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] HEAD /root HTTP/1.1 200
- - IGV Version 2.3.18 (20)09/05/2013 12:24 PM/**/
/**//**/
/**/Exception happened during processing of request from ('127.0.0.1',
46142)/**/
/**/Traceback (most recent call last):/**/
/**/ File
/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py,
line 1068, in process_request_in_thread/**/
/**/self.finish_request(request, client_address)/**/
/**/ File /usr/lib/python2.7/SocketServer.py, line 334, in
finish_request/**/
/**/self.RequestHandlerClass(request, client_address, self)/**/
/**/ File /usr/lib/python2.7/SocketServer.py, line 651, in __init__/**/
/**/self.finish()/**/
/**/ File /usr/lib/python2.7/SocketServer.py, line 710, in finish/**/
/**/self.wfile.close()/**/
/**/ File /usr/lib/python2.7/socket.py, line 279, in close/**/
/**/self.flush()/**/
/**/ File /usr/lib/python2.7/socket.py, line 303, in flush/**/
/**/self._sock.sendall(view[write_offset:write_offset+buffer_size])/**/
/**/error: [Errno 32] Broken pipe/**/
/**//**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] GET
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1 302 - - IGV Version 2.3.18 (20)09/05/2013 12:24 PM/**/
/**/XX - - [04/Feb/2014:16:05:40 +0200] GET /root HTTP/1.1 200 -
- IGV Version 2.3.18 (20)09/05/2013 12:24 PM/*
Any idea ?
Vincent
--
Vincent Navratil, PhD
IR UCBL - PRABI
http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard -- Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826
My 'ome' pagehttp://vinavratil.free.fr
___
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Hi Vincent,
I had the same issue with NGINX.
Ensure that #filter-with = gzip is commented out in your
universe_wsgi.ini.
I also have upstream_gzip = False
Hope this helps,
Regards,
Thomas
--
Thomas Bellembois, network and system administrator
ENS-Lyon/IGFL - 46, Allée d'Italie 69364 LYON CEDEX 07 FRANCE
+33 4 26 73 13 67
.The IGFL is a member of the portail-labos project
(https://portail-labos.ens-lyon.fr/site/).
.IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc
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Re: [galaxy-dev] Cheetah code issue
Hi, to access variables in a conditional you need to write something like that: $rangeorlist.rngstart $rangeorlist.rend $rangeorlist.stepsize Cheers, Bjoern 2014-02-04 Ketan Maheshwari ketancmaheshw...@gmail.com: Hi, While developing a tool, I am facing Cheetah code issue. I looked up the mailing list archive and found many similar issues reported earlier but could not debug this. Any tips in debugging is appreciated. File cheetah_DynamicallyCompiledCheetahTemplate_1391530084_29_71368.py, line 97, in respond NotFound: cannot find 'rngstart' Attached is the xml tool definition file. Best, Ketan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cheetah code issue
That did the trick! Thanks! On Tue, Feb 4, 2014 at 10:26 AM, bjoern.gruen...@googlemail.com bjoern.gruen...@gmail.com wrote: Hi, to access variables in a conditional you need to write something like that: $rangeorlist.rngstart $rangeorlist.rend $rangeorlist.stepsize Cheers, Bjoern 2014-02-04 Ketan Maheshwari ketancmaheshw...@gmail.com: Hi, While developing a tool, I am facing Cheetah code issue. I looked up the mailing list archive and found many similar issues reported earlier but could not debug this. Any tips in debugging is appreciated. File cheetah_DynamicallyCompiledCheetahTemplate_1391530084_29_71368.py, line 97, in respond NotFound: cannot find 'rngstart' Attached is the xml tool definition file. Best, Ketan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Ketan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] tools fails only in workflow
Dear all, I developed a tool which allows an optional selection as input amongst others. It works quite neat if I run it via Analyse Data. Actually, it only breaks in one condition: If I try to run it as a Workflow and set the multiple selection input to be set at runtime AND do not select anything at runtime it'll raise a Cheetah error. Even if I select nothing but prior to runtime as workflow it works fine again. The multiple selection is based on a data table/ loc-file. Any ideas? Cheers, Christan relevant tool specification snippet: - [...] param [...] type=select optional=true multiple=true display=checkboxes [...] options from_data_table=fmi_[...]/ /param [...] Cheetah error: Traceback (most recent call last): File [...]/galaxy/galaxy_dist/lib/galaxy/jobs/runners/__init__.py, line 123, in prepare_job job_wrapper.prepare() File [...]/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py, line 702, in prepare self.command_line = self.tool.build_command_line( param_dict ) File [...]/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py, line 2639, in build_command_line command_line = fill_template( self.command, context=param_dict ) File [...]/galaxy/galaxy_dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File [...]/galaxy/galaxy_dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1391423600_85_54475.py, line 89, in respond File cheetah_DynamicallyCompiledCheetahTemplate_1391423600_85_54475.py, line 89, in lambda IndexError: list index out of range Galaxy: -- changeset: 11219:5c789ab4144a branch: stable ___ 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] Upload via FTP - Assertion Error on Change ownership of working dictory
Thanks for the tip Eric. I was able to figure it out. The key to this,
was you suggested was permission issue.
I had to modify sudoers so tty was not required. This will allow
scripts to change ownership to the correct user so SGE can submit
them.
Thanks!
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
System Administrator, HPC Cluster
Office of Information Technology
http://hpc.oit.uci.edu/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu
On Mon, Feb 3, 2014 at 9:57 AM, Eric Rasche rasche.e...@yandex.ru wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Looks like a permission issue. Is your FTP server set to use the same
user/group as galaxy?
For reference: my proftpd is configured to use LDAP user information,
but then it forces the user/group id of uploaded files to be that of galaxy
# Force those numbers even if LDAP finds a valid UID/GID
LDAPDefaultUID {galaxy's UID}
LDAPDefaultGID {galaxy group GID}
Hope that helps
On 02/03/2014 11:23 AM, Adam Brenner wrote:
Anyone have any ideas on this?
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
System Administrator, HPC Cluster
Office of Information Technology
http://hpc.oit.uci.edu/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu
On Thu, Jan 30, 2014 at 2:33 PM, Adam Brenner aebre...@uci.edu wrote:
Howdy,
I am having trouble uploading data on our local instance of Galaxy
here. The method is via FTP and here is the error I am seeing in the
logs:
galaxy.jobs.runners DEBUG 2014-01-30 14:29:31,987 execution of
external set_meta for job 1367 finished
galaxy.jobs DEBUG 2014-01-30 14:29:32,016 (1367) Changing ownership of
working directory with: /usr/bin/sudo -E
scripts/external_chown_script.py
/som/galaxy/database/job_working_directory/001/1367 root 0
galaxy.jobs ERROR 2014-01-30 14:29:32,058 (1367) Failed to change
ownership of /som/galaxy/database/job_working_directory/001/1367,
failing
Traceback (most recent call last):
File /data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py, line 870, in
finish
self.reclaim_ownership()
File /data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py, line
1316, in reclaim_ownership
self._change_ownership( self.galaxy_system_pwent[0], str(
self.galaxy_system_pwent[3] ) )
File /data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py, line
1302, in _change_ownership
assert p.returncode == 0
AssertionError
Any idea on how to fix the issue?
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
System Administrator, HPC Cluster
Office of Information Technology
http://hpc.oit.uci.edu/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu
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- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas AM University
College Station, TX 77843
404-692-2048
e...@tamu.edu
rasche.e...@yandex.ru
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[galaxy-dev] Running tools from within a tool
Hi, This is a question I posted to galaxy user mailing list a while back and was redirected to dev for possible answers: Is it possible in Galaxy to design a tool whose sole purpose is to run other tools. This is motivated by our desire to enhance execution capabilities of existing tools via a generic tool which acts as a wrapper. Thanks, Ketan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cluster nodes without NFS access to galaxy-dev.
Hello Luca, This is an active area of development for the core team. It is fairly ingrained in Galaxy that workers and the the web server share a networked file system - so this is a real challenge. I would review the following recent thread: http://dev.list.galaxyproject.org/Managing-Data-Locality-td4662438.html If you are interested in pushing the cutting edge of Galaxy job running development - you can consider setting up an LWR server on your cluster login node - but I wouldn't say this is well documented and I would only recommend this for a few tools at a time - I am not convinced it is a general purpose replacement for traditional job runners at this time. For instance, there is no integration with the tool shed at this time. Hope this helps, -John On Sat, Feb 1, 2014 at 3:23 AM, Luca Toldo lucato...@gmail.com wrote: dear All, my galaxy server can NFS share its disks with the head of the cluster, however the compute nodes cannot see those disks since they can see only what the head of the cluster provides. My cluster nodes are diskless. I'd appreciate advice, if someone had already installed galaxy in such configuration. Unfortunately installing galaxy-dev on the head of the cluster is not an option. Looking forward your advice. Luca ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] running tools within tool
Hi, This is a question I posted to galaxy user mailing list a while back and was redirected to dev for possible answers: Is it possible in Galaxy to design a tool whose sole purpose is to run other tools. This is motivated by our desire to enhance execution capabilities of existing tools via a generic tool which acts as a wrapper. Thanks, Ketan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] igv integration
I’m having some trouble with igv integration… it works fine for hg19, but for other this influenza genome i just added, i’m seeing from IGV [cid:9C974C45-560B-46C3-AF75-CC794D0D1ACD@neb.com] Any idea what I’m doing wrong? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist inline: PastedGraphic-1.png___ 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] Several jobs stalled in the queue: Job runner assigned but no external ID recorded
Hi guys, My list of the stalled jobs is getting longer and longer. Is there a fix of this? Cheers, Derrick On Sat, Jun 15, 2013 at 3:36 PM, Derrick Lin klin...@gmail.com wrote: Hi guys, I have several jobs have been stuck in the queue for long time, I checked the handler log and found the following message: Job runner assigned but no external ID recorded, adding to the job handler queue Is there a way that I can clean these orphan jobs out of the queue? Cheers, Derrick ___ 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/
