Re: [galaxy-dev] Changing Tool Shed URL

[Martin Čech]

Thank you very much for sharing Youssef. Very helpful.

Martin

On Fri, Oct 21, 2016 at 10:20 AM Youssef GHORBAL 
wrote:

> Hello,
>
> Two other tables need to be adapated (they reference tool_id)
> Table “job" and table “workflow_step”
>
> Youssef Ghorbal
> Institut Pasteur
> -
> > On 21 Oct 2016, at 00:36, Youssef Ghorbal 
> wrote:
> >
> > Hello,
> >
> >   What worked for us was this action sequence :
> >   - stop Galaxy
> >   - update config/tool_sheds_file.xml (change the URL from the old
> one to the new one)
> >   - “sed” shed_tool_conf.xml to change the “guid", the tool_shed and
> the “file” to replace the old prefix with the new prefix.
> >   - update the tool_version table (the tool_id column) to change the
> old prefix to the new prefix.
> >   - update the tool_shed_repositoriy table to change the tool_shed
> column to use the new tooshed prefix
> >   - update the directory shed_tools to rename the directory from the
> old prefix to the new prefix (care to adapt the subdirectories too :
> ./mytoolshed.url/xxx => ./mytoolshed2.url/)
> >   - start Galaxy (and cross your fingers)
> >
> >   Hope this help !
> >
> > Youssef Ghorbal
> > Institut Pasteur
> > -
> >> On 20 Oct 2016, at 00:16, Youssef GHORBAL 
> wrote:
> >>
> >> Hello,
> >>
> >>  I’m wondering if there is any way to change an established Tool
> Shed URL.
> >>  I have a Galaxy instance and a Tool Shed instance (
> http://mytoolshed.url/xxx) A lot of tools have beed installed from that
> Tool Shed inside Galaxy (tools referenced inside workflows etc)
> >>  I want to change the Tool Shed URL from http://mytoolshed.url/xxx
> to http://mytoolshed2.url/.
> >>
> >>  Galaxy and Tool Shed seems to use parts of the URL as a guid for
> tools.
> >>
> >>  Tool Shed does not seem to bother to be called by either URLs (it
> generates guids with the new URLs scheam for new tools though)
> >>
> >>  Galaxy does not seem to handle it, I changed the
> tool_sheds_conf.xml to point to new URL, but when I update a tool on the
> Tool Shed, Galaxy gets the new version but it generates buggy tool panel
> (the tool is cited twice)
> >>  I also tried to mess around with the shed_tool_conf.xml apdapting
> the guids and the  items with no luck.
> >>
> >>  Can someone point me to the right direction ? How the matching is
> done between shed_tool_conf.xml entries, the tool_version and
> tool_shed_repository tables.
> >>
> >>  Thank you for your help.
> >>
> >> Youssef Ghorbal
> >> Institut Pasteur
> >> ___
> >> 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/
> >
>
> ___
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Re: [galaxy-dev] Changing Tool Shed URL

[Youssef GHORBAL]

Hello,

Two other tables need to be adapated (they reference tool_id)
Table “job" and table “workflow_step”

Youssef Ghorbal
Institut Pasteur
-
> On 21 Oct 2016, at 00:36, Youssef Ghorbal  wrote:
> 
> Hello,
>   
>   What worked for us was this action sequence :
>   - stop Galaxy
>   - update config/tool_sheds_file.xml (change the URL from the old one to 
> the new one)
>   - “sed” shed_tool_conf.xml to change the “guid", the tool_shed and the 
> “file” to replace the old prefix with the new prefix.
>   - update the tool_version table (the tool_id column) to change the old 
> prefix to the new prefix.
>   - update the tool_shed_repositoriy table to change the tool_shed column 
> to use the new tooshed prefix
>   - update the directory shed_tools to rename the directory from the old 
> prefix to the new prefix (care to adapt the subdirectories too : 
> ./mytoolshed.url/xxx => ./mytoolshed2.url/) 
>   - start Galaxy (and cross your fingers)
> 
>   Hope this help !
> 
> Youssef Ghorbal
> Institut Pasteur
> -
>> On 20 Oct 2016, at 00:16, Youssef GHORBAL  wrote:
>> 
>> Hello,
>> 
>>  I’m wondering if there is any way to change an established Tool Shed 
>> URL.
>>  I have a Galaxy instance and a Tool Shed instance 
>> (http://mytoolshed.url/xxx) A lot of tools have beed installed from that 
>> Tool Shed inside Galaxy (tools referenced inside workflows etc)
>>  I want to change the Tool Shed URL from http://mytoolshed.url/xxx to 
>> http://mytoolshed2.url/. 
>> 
>>  Galaxy and Tool Shed seems to use parts of the URL as a guid for tools.
>>  
>>  Tool Shed does not seem to bother to be called by either URLs (it 
>> generates guids with the new URLs scheam for new tools though)
>> 
>>  Galaxy does not seem to handle it, I changed the tool_sheds_conf.xml to 
>> point to new URL, but when I update a tool on the Tool Shed, Galaxy gets the 
>> new version but it generates buggy tool panel (the tool is cited twice)
>>  I also tried to mess around with the shed_tool_conf.xml apdapting the 
>> guids and the  items with no luck.
>> 
>>  Can someone point me to the right direction ? How the matching is done 
>> between shed_tool_conf.xml entries, the tool_version and 
>> tool_shed_repository tables.
>> 
>>  Thank you for your help.
>> 
>> Youssef Ghorbal
>> Institut Pasteur
>> ___
>> 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/
> 

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Re: [galaxy-dev] Changing Tool Shed URL

[Youssef GHORBAL]

Hello,

What worked for us was this action sequence :
- stop Galaxy
- update config/tool_sheds_file.xml (change the URL from the old one to 
the new one)
- “sed” shed_tool_conf.xml to change the “guid", the tool_shed and the 
“file” to replace the old prefix with the new prefix.
- update the tool_version table (the tool_id column) to change the old 
prefix to the new prefix.
- update the tool_shed_repositoriy table to change the tool_shed column 
to use the new tooshed prefix
- update the directory shed_tools to rename the directory from the old 
prefix to the new prefix (care to adapt the subdirectories too : 
./mytoolshed.url/xxx => ./mytoolshed2.url/) 
- start Galaxy (and cross your fingers)

Hope this help !

Youssef Ghorbal
Institut Pasteur
-
> On 20 Oct 2016, at 00:16, Youssef GHORBAL  wrote:
> 
> Hello,
> 
>   I’m wondering if there is any way to change an established Tool Shed 
> URL.
>   I have a Galaxy instance and a Tool Shed instance 
> (http://mytoolshed.url/xxx) A lot of tools have beed installed from that Tool 
> Shed inside Galaxy (tools referenced inside workflows etc)
>   I want to change the Tool Shed URL from http://mytoolshed.url/xxx to 
> http://mytoolshed2.url/. 
> 
>   Galaxy and Tool Shed seems to use parts of the URL as a guid for tools.
>   
>   Tool Shed does not seem to bother to be called by either URLs (it 
> generates guids with the new URLs scheam for new tools though)
> 
>   Galaxy does not seem to handle it, I changed the tool_sheds_conf.xml to 
> point to new URL, but when I update a tool on the Tool Shed, Galaxy gets the 
> new version but it generates buggy tool panel (the tool is cited twice)
>   I also tried to mess around with the shed_tool_conf.xml apdapting the 
> guids and the  items with no luck.
> 
>   Can someone point me to the right direction ? How the matching is done 
> between shed_tool_conf.xml entries, the tool_version and tool_shed_repository 
> tables.
> 
>   Thank you for your help.
> 
> Youssef Ghorbal
> Institut Pasteur
> ___
> 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/

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Re: [galaxy-dev] Changing Tool Shed URL

[Marius van den Beek]

This wouldn’t be a transfer, you would uninstall the tools coming from the
old toolshed and re-install them form the new toolshed.
This is only possible if these tools are available from the second toolshed.

To illustrate the procedure, this is what you would do if you would take
all tools from usegalaxy.org,
and replace the tools coming from the main tool shed with the same tools
but coming form the testtoolshed

get-tool-list -g https://usegalaxy.org/ -o tool_list.yml
sed -i .bak 's/toolshed.g2.bx.psu.edu/testtoolshed.g2.bx.psu.edu/g'
tool_list.yml
shed-install -g  -a  -t tool_list.yml

​

On 20 October 2016 at 11:02, Olivia Doppelt-Azeroual <
olivia.dopp...@pasteur.fr> wrote:

> Hello Marius,
>
> Thank you for your answer.
>
> Are you sure that ephemeris can transfer tool from toolshed1 to toolshed2
> ? We read that it was only implemented to install tools from a toolshed on
> a Galaxy.
>
> We will try the second solution and as we already tried to manipulate the
> database, we stongly agree that it is not THE solution.
>
> Cheers,
>
> -
>
> Fabien and Olivia and Youssef
>
>
>
> Le 20/10/2016 à 10:29, Marius van den Beek a écrit :
>
> Hi Youssef,
>
> the tool shed url is also stored in the database, that's why just changing
> the shed_tool_conf.xml is not working. I think you have a bunch of options
> here:
> 1: You can make a list of tools from that toolshed and re-install them
> from the new toolshed.
> https://pypi.python.org/pypi/ephemeris/ is a nice tool to do this
> efficiently.
> Galaxy is (or should be) smart enough to recognize this and will (should)
> not break existing workflows and tool reruns.
> 2: You can setup an alias in your /etc/hosts file if only the toolshed's
> URL has changed, or you can setup a proxy to forward the requests
> if also the subdirectory has changed.
> 3. You can try to manipulate the database directly. (But I would seriously
> advise you to go with possibilities 1 or 2).
>
> Best,
> Marius
>
> On 20 October 2016 at 00:16, Youssef GHORBAL 
> wrote:
>
>> Hello,
>>
>> I’m wondering if there is any way to change an established Tool
>> Shed URL.
>> I have a Galaxy instance and a Tool Shed instance (
>> http://mytoolshed.url/xxx) A lot of tools have beed installed from that
>> Tool Shed inside Galaxy (tools referenced inside workflows etc)
>> I want to change the Tool Shed URL from http://mytoolshed.url/xxx
>> to http://mytoolshed2.url/.
>>
>> Galaxy and Tool Shed seems to use parts of the URL as a guid for
>> tools.
>>
>> Tool Shed does not seem to bother to be called by either URLs (it
>> generates guids with the new URLs scheam for new tools though)
>>
>> Galaxy does not seem to handle it, I changed the
>> tool_sheds_conf.xml to point to new URL, but when I update a tool on the
>> Tool Shed, Galaxy gets the new version but it generates buggy tool panel
>> (the tool is cited twice)
>> I also tried to mess around with the shed_tool_conf.xml apdapting
>> the guids and the  items with no luck.
>>
>> Can someone point me to the right direction ? How the matching is
>> done between shed_tool_conf.xml entries, the tool_version and
>> tool_shed_repository tables.
>>
>> Thank you for your help.
>>
>> Youssef Ghorbal
>> Institut Pasteur
>> ___
>> 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/
>
>
> --
> Olivia Doppelt-Azeroual, PhD
> Bioinformatics Engineer
> CIB - C3BI - Institut Pasteur, Paris
>
> Email: olivia.dopp...@pasteur.fr
> Tel: 01 44 38 92 15
>
>
___
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Re: [galaxy-dev] Changing Tool Shed URL

[Olivia Doppelt-Azeroual]

Hello Marius,

Thank you for your answer.

Are you sure that ephemeris can transfer tool from toolshed1 to 
toolshed2 ? We read that it was only implemented to install tools from a 
toolshed on a Galaxy.


We will try the second solution and as we already tried to manipulate 
the database, we stongly agree that it is not THE solution.


Cheers,

-

Fabien and Olivia and Youssef



Le 20/10/2016 à 10:29, Marius van den Beek a écrit :

Hi Youssef,

the tool shed url is also stored in the database, that's why just changing
the shed_tool_conf.xml is not working. I think you have a bunch of 
options here:
1: You can make a list of tools from that toolshed and re-install them 
from the new toolshed.
https://pypi.python.org/pypi/ephemeris/ 
 is a nice tool to do this 
efficiently.
Galaxy is (or should be) smart enough to recognize this and will 
(should) not break existing workflows and tool reruns.
2: You can setup an alias in your /etc/hosts file if only the 
toolshed's URL has changed, or you can setup a proxy to forward the 
requests

if also the subdirectory has changed.
3. You can try to manipulate the database directly. (But I would 
seriously advise you to go with possibilities 1 or 2).


Best,
Marius

On 20 October 2016 at 00:16, Youssef GHORBAL 
mailto:youssef.ghor...@pasteur.fr>> wrote:


Hello,

I’m wondering if there is any way to change an established
Tool Shed URL.
I have a Galaxy instance and a Tool Shed instance
(http://mytoolshed.url/xxx) A lot of tools have beed installed
from that Tool Shed inside Galaxy (tools referenced inside
workflows etc)
I want to change the Tool Shed URL from
http://mytoolshed.url/xxx to http://mytoolshed2.url/.

Galaxy and Tool Shed seems to use parts of the URL as a
guid for tools.

Tool Shed does not seem to bother to be called by either
URLs (it generates guids with the new URLs scheam for new tools
though)

Galaxy does not seem to handle it, I changed the
tool_sheds_conf.xml to point to new URL, but when I update a tool
on the Tool Shed, Galaxy gets the new version but it generates
buggy tool panel (the tool is cited twice)
I also tried to mess around with the shed_tool_conf.xml
apdapting the guids and the  items with no luck.

Can someone point me to the right direction ? How the
matching is done between shed_tool_conf.xml entries, the
tool_version and tool_shed_repository tables.

Thank you for your help.

Youssef Ghorbal
Institut Pasteur
___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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___
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--
Olivia Doppelt-Azeroual, PhD
Bioinformatics Engineer
CIB - C3BI - Institut Pasteur, Paris

Email: olivia.dopp...@pasteur.fr
Tel: 01 44 38 92 15

___
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Re: [galaxy-dev] Changing Tool Shed URL

[Marius van den Beek]

Hi Youssef,

the tool shed url is also stored in the database, that's why just changing
the shed_tool_conf.xml is not working. I think you have a bunch of options
here:
1: You can make a list of tools from that toolshed and re-install them from
the new toolshed.
https://pypi.python.org/pypi/ephemeris/ is a nice tool to do this
efficiently.
Galaxy is (or should be) smart enough to recognize this and will (should)
not break existing workflows and tool reruns.
2: You can setup an alias in your /etc/hosts file if only the toolshed's
URL has changed, or you can setup a proxy to forward the requests
if also the subdirectory has changed.
3. You can try to manipulate the database directly. (But I would seriously
advise you to go with possibilities 1 or 2).

Best,
Marius

On 20 October 2016 at 00:16, Youssef GHORBAL 
wrote:

> Hello,
>
> I’m wondering if there is any way to change an established Tool
> Shed URL.
> I have a Galaxy instance and a Tool Shed instance (
> http://mytoolshed.url/xxx) A lot of tools have beed installed from that
> Tool Shed inside Galaxy (tools referenced inside workflows etc)
> I want to change the Tool Shed URL from http://mytoolshed.url/xxx
> to http://mytoolshed2.url/.
>
> Galaxy and Tool Shed seems to use parts of the URL as a guid for
> tools.
>
> Tool Shed does not seem to bother to be called by either URLs (it
> generates guids with the new URLs scheam for new tools though)
>
> Galaxy does not seem to handle it, I changed the
> tool_sheds_conf.xml to point to new URL, but when I update a tool on the
> Tool Shed, Galaxy gets the new version but it generates buggy tool panel
> (the tool is cited twice)
> I also tried to mess around with the shed_tool_conf.xml apdapting
> the guids and the  items with no luck.
>
> Can someone point me to the right direction ? How the matching is
> done between shed_tool_conf.xml entries, the tool_version and
> tool_shed_repository tables.
>
> Thank you for your help.
>
> Youssef Ghorbal
> Institut Pasteur
> ___
> 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:
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[galaxy-dev] Changing Tool Shed URL

[Youssef GHORBAL]

Hello,

I’m wondering if there is any way to change an established Tool Shed 
URL.
I have a Galaxy instance and a Tool Shed instance 
(http://mytoolshed.url/xxx) A lot of tools have beed installed from that Tool 
Shed inside Galaxy (tools referenced inside workflows etc)
I want to change the Tool Shed URL from http://mytoolshed.url/xxx to 
http://mytoolshed2.url/. 

Galaxy and Tool Shed seems to use parts of the URL as a guid for tools.

Tool Shed does not seem to bother to be called by either URLs (it 
generates guids with the new URLs scheam for new tools though)

Galaxy does not seem to handle it, I changed the tool_sheds_conf.xml to 
point to new URL, but when I update a tool on the Tool Shed, Galaxy gets the 
new version but it generates buggy tool panel (the tool is cited twice)
I also tried to mess around with the shed_tool_conf.xml apdapting the 
guids and the  items with no luck.

Can someone point me to the right direction ? How the matching is done 
between shed_tool_conf.xml entries, the tool_version and tool_shed_repository 
tables.

Thank you for your help.

Youssef Ghorbal
Institut Pasteur
___
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:
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