Dear all, I think I made a really stupid mistake. I edited the shed_tool_con.xml file to change the order and section of tools. Doing this I might have introduced an error I cannot locate. However (now comes the stupidity), I didn't save the old version of the shed_tool_conf.xml file... Is there a way to fix this or do I have to reinstall all tools again? Thank you for your help. cheers, Philipp
I would try validating the broken XML file (e.g. using an online tool, or an XML aware editor). That might be enough to find the error and fix it by hand. I don't know if there is a clever way to regenerate the file instead... Peter On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de> wrote:
Dear all,
I think I made a really stupid mistake. I edited the shed_tool_con.xml file to change the order and section of tools.
Doing this I might have introduced an error I cannot locate. However (now comes the stupidity), I didn't save the old version of the shed_tool_conf.xml file...
Is there a way to fix this or do I have to reinstall all tools again?
Thank you for your help.
cheers,
Philipp
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A stupid way to do that is to remove the half bottom of your xml and open it using Firefox for example. If OK Add the half top of the half bottom -> firefox If OK … If KO Remove the half bottom of the remain -> firefox .. It’s stupid but it’s often work :) Gildas ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/> Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------
Le 22 mars 2016 à 12:56, Peter Cock <p.j.a.cock@googlemail.com> a écrit :
I would try validating the broken XML file (e.g. using an online tool, or an XML aware editor). That might be enough to find the error and fix it by hand.
I don't know if there is a clever way to regenerate the file instead...
Peter
On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de> wrote:
Dear all,
I think I made a really stupid mistake. I edited the shed_tool_con.xml file to change the order and section of tools.
Doing this I might have introduced an error I cannot locate. However (now comes the stupidity), I didn't save the old version of the shed_tool_conf.xml file...
Is there a way to fix this or do I have to reinstall all tools again?
Thank you for your help.
cheers,
Philipp
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As Peter already mentioned a XML validator is a nice tool for this purpose. For example this one: http://www.xmlvalidation.com
A stupid way to do that is to remove the half bottom of your xml and open it using Firefox for example. If OK
Add the half top of the half bottom -> firefox If OK
…
If KO
Remove the half bottom of the remain -> firefox ..
It’s stupid but it’s often work :)
Gildas
----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr
Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/>
Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------
Le 22 mars 2016 à 12:56, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>> a écrit :
I would try validating the broken XML file (e.g. using an online tool, or an XML aware editor). That might be enough to find the error and fix it by hand.
I don't know if there is a clever way to regenerate the file instead...
Peter
On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de <mailto:philipp.rathert@ibc.uni-stuttgart.de>> wrote:
Dear all,
I think I made a really stupid mistake. I edited the shed_tool_con.xml file to change the order and section of tools.
Doing this I might have introduced an error I cannot locate. However (now comes the stupidity), I didn't save the old version of the shed_tool_conf.xml file...
Is there a way to fix this or do I have to reinstall all tools again?
Thank you for your help.
cheers,
Philipp
___________________________________________________________ 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: https://lists.galaxyproject.org/
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: https://lists.galaxyproject.org/
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On 03/22/2016 12:56 PM, Peter Cock wrote:
I would try validating the broken XML file (e.g. using an online tool, or an XML aware editor). That might be enough to find the error and fix it by hand.
I don't know if there is a clever way to regenerate the file instead...
probably a lot of 'manual' work including comparing with the admin page 'Installed tool shed repositories'. Also, look at the file "integrated_tool_panel.xml". all tools listed there which are not listed in "tool_conf.xml" need an entry in shed_tool_conf.xml....as far as I know. Hans-Rudolf
Peter
On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de> wrote:
Dear all,
I think I made a really stupid mistake. I edited the shed_tool_con.xml file to change the order and section of tools.
Doing this I might have introduced an error I cannot locate. However (now comes the stupidity), I didn't save the old version of the shed_tool_conf.xml file...
Is there a way to fix this or do I have to reinstall all tools again?
Thank you for your help.
cheers,
Philipp
___________________________________________________________ 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: https://lists.galaxyproject.org/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (5)
-
Bjoern Gruening -
Gildas Le Corguillé -
Hans-Rudolf Hotz -
Peter Cock -
Rathert, Philipp, Dr.