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 <your_galaxy_instace> -a <your_api_key> -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 <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/yyyy. >> >> 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 <tool_shed> 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 > >
___________________________________________________________ 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/
