tool shed differences local vs web
Yesterday, I noticed that there are some packages in http://toolshed.g2.bx.psu.edu that I can't find when I search the main tool shed on my local instance. I would have thought that the "Search and browse tool sheds" options under "Admin" is just a front-end for the search on the main tool shed on the web, so I was surprised to find differences. How can I install e.g. the RSEM package (http://toolshed.g2.bx.psu.edu/view/victor/rsem) on my local instance then? Is there a way to "pull" from the main tool shed so that I see the same data locally that's on the web? Thanks in advance, Ben -- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics ☎ +44 1865 617481 ✉ benjamin.schuster-boeckler@ludwig.ox.ac.uk Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom
Hi Ben, is a bug! Can you fill a trello card about that? http://galaxyproject.org/trello I would recommend to install that tool manually. The toolshed integration is not very good and even if you can install it through the toolshed you need to create the *.loc file and so on by hand. Just follow the installation instructions in the repository, copy the XML file under ./tools/somewhere/ and add the file to your tool_conf.xml file. Cheers, Bjoern
Yesterday, I noticed that there are some packages in http://toolshed.g2.bx.psu.edu that I can't find when I search the main tool shed on my local instance. I would have thought that the "Search and browse tool sheds" options under "Admin" is just a front-end for the search on the main tool shed on the web, so I was surprised to find differences. How can I install e.g. the RSEM package (http://toolshed.g2.bx.psu.edu/view/victor/rsem) on my local instance then? Is there a way to "pull" from the main tool shed so that I see the same data locally that's on the web?
Thanks in advance, Ben
-- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics
☎ +44 1865 617481 ✉ benjamin.schuster-boeckler@ludwig.ox.ac.uk
Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom
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Ben, In the specific case of the RSEM repository, the tool shed code has determined that the rsem-1.1.17.xml tool definition file will not load correctly into Galaxy, and for that reason the repository is not considered to be installable. The 'Search and browse tool sheds' feature on the Galaxy side filters the list of repositories to those that are determined to be installable. For more details, see the wiki page for the tool shed at: http://wiki.galaxyproject.org/RepositoryRevisions#What_does_it_mean_when_rep... --Dave B. On 8/16/13 07:25:33.000, Benjamin Schuster-Boeckler wrote:
Yesterday, I noticed that there are some packages in http://toolshed.g2.bx.psu.edu that I can't find when I search the main tool shed on my local instance. I would have thought that the "Search and browse tool sheds" options under "Admin" is just a front-end for the search on the main tool shed on the web, so I was surprised to find differences. How can I install e.g. the RSEM package (http://toolshed.g2.bx.psu.edu/view/victor/rsem) on my local instance then? Is there a way to "pull" from the main tool shed so that I see the same data locally that's on the web?
Thanks in advance, Ben
-- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics
☎ +44 1865 617481 ✉ benjamin.schuster-boeckler@ludwig.ox.ac.uk
Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom
___________________________________________________________ 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/
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Ah, ok, I see, makes sense, but it's a bit confusing :-) Thanks for the explanation, anyway, I'll manually install it in that case. Best, Ben -- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics ☎ +44 1865 617481 ✉ benjamin.schuster-boeckler@ludwig.ox.ac.uk Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom On 16 Aug 2013, at 14:55, Dave Bouvier <dave@bx.psu.edu> wrote:
Ben,
In the specific case of the RSEM repository, the tool shed code has determined that the rsem-1.1.17.xml tool definition file will not load correctly into Galaxy, and for that reason the repository is not considered to be installable. The 'Search and browse tool sheds' feature on the Galaxy side filters the list of repositories to those that are determined to be installable.
For more details, see the wiki page for the tool shed at:
http://wiki.galaxyproject.org/RepositoryRevisions#What_does_it_mean_when_rep...
--Dave B.
On 8/16/13 07:25:33.000, Benjamin Schuster-Boeckler wrote:
Yesterday, I noticed that there are some packages in http://toolshed.g2.bx.psu.edu that I can't find when I search the main tool shed on my local instance. I would have thought that the "Search and browse tool sheds" options under "Admin" is just a front-end for the search on the main tool shed on the web, so I was surprised to find differences. How can I install e.g. the RSEM package (http://toolshed.g2.bx.psu.edu/view/victor/rsem) on my local instance then? Is there a way to "pull" from the main tool shed so that I see the same data locally that's on the web?
Thanks in advance, Ben
-- Benjamin Schuster-Böckler Leadership Fellow for Bioinformatics
☎ +44 1865 617481 ✉ benjamin.schuster-boeckler@ludwig.ox.ac.uk
Ludwig Institute for Cancer Research University of Oxford Old Road Campus Research Building Oxford OX3 7DQ United Kingdom
___________________________________________________________ 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/
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participants (3)
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Benjamin Schuster-Boeckler -
Bjoern Gruening -
Dave Bouvier