Recommended method to pull from ToolShed ?
Hi, with the new ToolShed inplace, and support for cloning/pulling tools directly: What's the recommend way to organize the repositories ? For example, I want to use Peter's Venn tool: hg clone http://toolshed.g2.bx.psu.edu/repos/peterjc/venn_list If I clone, I get the following folder hierarchy: venn_list -> tools -> plotting -> xml/py . So I can't directly clone into the <galaxy>/tools folder. Even if I could (somehow skipping the "venn_list" directory), cloning multiple tools would override the ".hg" folder of each other. so is it still a manual process of cloning to a temporary directory, then manually copy the files to the <galaxy>/tools folder ? or am I missing something ? being able to automagically "pull -u" tools from the toolshed would be really cool. thanks, -gordon
On Thu, Jun 9, 2011 at 7:15 PM, Assaf Gordon <gordon@cshl.edu> wrote:
Hi,
with the new ToolShed inplace, and support for cloning/pulling tools directly: What's the recommend way to organize the repositories ?
For example, I want to use Peter's Venn tool: hg clone http://toolshed.g2.bx.psu.edu/repos/peterjc/venn_list
If I clone, I get the following folder hierarchy: venn_list -> tools -> plotting -> xml/py .
So I can't directly clone into the <galaxy>/tools folder. Even if I could (somehow skipping the "venn_list" directory), cloning multiple tools would override the ".hg" folder of each other.
so is it still a manual process of cloning to a temporary directory, then manually copy the files to the <galaxy>/tools folder ? or am I missing something ?
being able to automagically "pull -u" tools from the toolshed would be really cool.
thanks, -gordon
Good question Gordon, Back on the old tar-ball based Tool Shed, the guidelines were quite loose about directory structures - at least one folder was recommended though. I used to do things expecting the user to be able to untar it in the root Galaxy folder. Consider we might have test files, configuration files (e.g. a sample loc file), as well as the core XML file and any associated scripts. I'm happy to restructure if there are clear guidelines. In this case, you could probably clone the Venn diagram tool anywhere, and reference it in tool_conf.xml with an absolute path (or relative with a few .. entries). This should be fine in this case as there are no other data files. Peter
In addition to cloning, you can also download the tarball for each tool just like you used to - see the Repository Options popup menu for each repo. On Jun 9, 2011, at 2:55 PM, Peter Cock wrote:
On Thu, Jun 9, 2011 at 7:15 PM, Assaf Gordon <gordon@cshl.edu> wrote:
Hi,
with the new ToolShed inplace, and support for cloning/pulling tools directly: What's the recommend way to organize the repositories ?
For example, I want to use Peter's Venn tool: hg clone http://toolshed.g2.bx.psu.edu/repos/peterjc/venn_list
If I clone, I get the following folder hierarchy: venn_list -> tools -> plotting -> xml/py .
So I can't directly clone into the <galaxy>/tools folder. Even if I could (somehow skipping the "venn_list" directory), cloning multiple tools would override the ".hg" folder of each other.
so is it still a manual process of cloning to a temporary directory, then manually copy the files to the <galaxy>/tools folder ? or am I missing something ?
being able to automagically "pull -u" tools from the toolshed would be really cool.
thanks, -gordon
Good question Gordon,
Back on the old tar-ball based Tool Shed, the guidelines were quite loose about directory structures - at least one folder was recommended though.
I used to do things expecting the user to be able to untar it in the root Galaxy folder. Consider we might have test files, configuration files (e.g. a sample loc file), as well as the core XML file and any associated scripts.
I'm happy to restructure if there are clear guidelines.
In this case, you could probably clone the Venn diagram tool anywhere, and reference it in tool_conf.xml with an absolute path (or relative with a few .. entries). This should be fine in this case as there are no other data files.
Peter
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
participants (3)
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Assaf Gordon -
Greg Von Kuster -
Peter Cock