Broken published history in a local installation
Hi all, Since the last pull from galaxy-central (6056), whenever I try to access published histories, I get a file not found error; see the attached screenshot. I have not changed any configuration. Thanks for any pointers, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------
Nico, Does this happen when publishing new histories or just for histories that have been published previously? If you're pulling from galaxy-central, you're running a very old version of Galaxy. Currently tip is 6292:9b7d5c1c0be6 ; updating your instance to tip may solve the problem as well. J. On Nov 17, 2011, at 8:00 AM, Nicolas Delhomme wrote:
Hi all,
Since the last pull from galaxy-central (6056), whenever I try to access published histories, I get a file not found error; see the attached screenshot. I have not changed any configuration.
Thanks for any pointers,
Nico
--------------------------------------------------------------- Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------
<Screen shot 2011-11-17 at 13.56.18.png><ATT00001.txt>___________________________________________________________ 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:
Hi Jeremy, That's occuring for both. I'm pulling from galaxy-dist (sorry, my mistake). It's our production environment that we've updated a couple of weeks ago. To look up the tip, I just ran an 'hg summary' in the galaxy root directory: [galaxy@ouzhou galaxy]$ hg summary parent: 6056:338ead4737ba tip Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On 17 Nov 2011, at 14:59, Jeremy Goecks wrote:
Nico,
Does this happen when publishing new histories or just for histories that have been published previously?
If you're pulling from galaxy-central, you're running a very old version of Galaxy. Currently tip is 6292:9b7d5c1c0be6 ; updating your instance to tip may solve the problem as well.
J.
On Nov 17, 2011, at 8:00 AM, Nicolas Delhomme wrote:
Hi all,
Since the last pull from galaxy-central (6056), whenever I try to access published histories, I get a file not found error; see the attached screenshot. I have not changed any configuration.
Thanks for any pointers,
Nico
--------------------------------------------------------------- Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------
<Screen shot 2011-11-17 at 13.56.18.png><ATT00001.txt>___________________________________________________________ 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:
Nico, That's odd. I can't reproduce your issues on my local instance using that rev. We're releasing a new dist in the next week; the simplest thing is do is hope that updating to the new dist fixes the problem. If not, let me know and we'll try something else. Best, J. On Nov 17, 2011, at 9:22 AM, Nicolas Delhomme wrote:
Hi Jeremy,
That's occuring for both. I'm pulling from galaxy-dist (sorry, my mistake). It's our production environment that we've updated a couple of weeks ago. To look up the tip, I just ran an 'hg summary' in the galaxy root directory:
[galaxy@ouzhou galaxy]$ hg summary parent: 6056:338ead4737ba tip
Nico
--------------------------------------------------------------- Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------
On 17 Nov 2011, at 14:59, Jeremy Goecks wrote:
Nico,
Does this happen when publishing new histories or just for histories that have been published previously?
If you're pulling from galaxy-central, you're running a very old version of Galaxy. Currently tip is 6292:9b7d5c1c0be6 ; updating your instance to tip may solve the problem as well.
J.
On Nov 17, 2011, at 8:00 AM, Nicolas Delhomme wrote:
Hi all,
Since the last pull from galaxy-central (6056), whenever I try to access published histories, I get a file not found error; see the attached screenshot. I have not changed any configuration.
Thanks for any pointers,
Nico
--------------------------------------------------------------- Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------
<Screen shot 2011-11-17 at 13.56.18.png><ATT00001.txt>___________________________________________________________ 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:
Hi, I have a tool where the user selects their datasets from a drop-down list. The drop down list obviously contains the names of the suitable datasets as shown in the history and not that which is stored in the Galaxy database (e.g. ../database/files/011/dataset_11377.dat) I'm trying to access and pass the name of a history item to the command line parameters in the tool xml so I can use the dataset name as a column-header in an output file. Given the following fictitious xml snippet... <command interpreter="R"> /home/galaxy/software/galaxy-central/tools/test_dir/test.R --args $ctl #for $i in $inputs ${i.input} #end for </command> <inputs> <repeat name="inputs" title="Input Files"> <param name="input" type="data" format="txt" label="Dataset"/> </repeat> </inputs> <outputs> <data format="tabular" name="ctl" /> </outputs> ...if the name of the history item selected in <parma name='input'> was "Dataset 1" how would I access that information, instead of only being able to access the name of the file in the Galaxy database (e.g. dataset_11377.dat)? I'm presuming I have to do something like: #for $i in $inputs ${i.input} ${i.input.history_item_name} #end for but I don't seem able to identify the correct syntax to get what I want. Any suggestions? Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 17/11/2011 13:59, "Jeremy Goecks" <jeremy.goecks@emory.edu> wrote:
Nico,
Does this happen when publishing new histories or just for histories that have been published previously?
If you're pulling from galaxy-central, you're running a very old version of Galaxy. Currently tip is 6292:9b7d5c1c0be6 ; updating your instance to tip may solve the problem as well.
J.
On Nov 17, 2011, at 8:00 AM, Nicolas Delhomme wrote:
Hi all,
Since the last pull from galaxy-central (6056), whenever I try to access published histories, I get a file not found error; see the attached screenshot. I have not changed any configuration.
Thanks for any pointers,
Nico
--------------------------------------------------------------- Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------
<Screen shot 2011-11-17 at 13.56.18.png><ATT00001.txt>______________________________________________ _____________ 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:
___________________________________________________________ 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:
Hi Graham, Instead of ${i.input.history_item_name} Use "${i.input.name}"; I would also suggest using quotes around your argument values that are being passed to the command line. Thanks for using Galaxy, Dan On Nov 17, 2011, at 9:37 AM, graham etherington (TSL) wrote:
Hi, I have a tool where the user selects their datasets from a drop-down list. The drop down list obviously contains the names of the suitable datasets as shown in the history and not that which is stored in the Galaxy database (e.g. ../database/files/011/dataset_11377.dat) I'm trying to access and pass the name of a history item to the command line parameters in the tool xml so I can use the dataset name as a column-header in an output file. Given the following fictitious xml snippet...
<command interpreter="R"> /home/galaxy/software/galaxy-central/tools/test_dir/test.R --args $ctl #for $i in $inputs ${i.input} #end for </command> <inputs> <repeat name="inputs" title="Input Files"> <param name="input" type="data" format="txt" label="Dataset"/> </repeat> </inputs> <outputs> <data format="tabular" name="ctl" /> </outputs>
...if the name of the history item selected in <parma name='input'> was "Dataset 1" how would I access that information, instead of only being able to access the name of the file in the Galaxy database (e.g. dataset_11377.dat)? I'm presuming I have to do something like: #for $i in $inputs ${i.input} ${i.input.history_item_name} #end for
but I don't seem able to identify the correct syntax to get what I want. Any suggestions?
Many thanks, Graham
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
On 17/11/2011 13:59, "Jeremy Goecks" <jeremy.goecks@emory.edu> wrote:
Nico,
Does this happen when publishing new histories or just for histories that have been published previously?
If you're pulling from galaxy-central, you're running a very old version of Galaxy. Currently tip is 6292:9b7d5c1c0be6 ; updating your instance to tip may solve the problem as well.
J.
On Nov 17, 2011, at 8:00 AM, Nicolas Delhomme wrote:
Hi all,
Since the last pull from galaxy-central (6056), whenever I try to access published histories, I get a file not found error; see the attached screenshot. I have not changed any configuration.
Thanks for any pointers,
Nico
--------------------------------------------------------------- Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany ---------------------------------------------------------------
<Screen shot 2011-11-17 at 13.56.18.png><ATT00001.txt>______________________________________________ _____________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
participants (5)
-
Daniel Blankenberg -
graham etherington (TSL) -
Jeremy Goecks -
Jeremy Goecks
-
Nicolas Delhomme