Manually adding new tools from toolshed
Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes. Along with the new data types is python class file. I'm referring to the exist datatypes_conf.xml.sample but don't see a reference to datatype_files as is coded in the RSEM tool. So my question is, how can I manually install a tool such as RSEM from the toolshed? I've cloned it but not sure where to put the files and what to modify in Galaxy's configuration to see the new files. I can modify the datatypes_conf.xml and include the datatypes, but I get the sense this is not correct. Ryan
On Thu, Jan 15, 2015 at 6:57 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes.
Along with the new data types is python class file. I'm referring to the exist datatypes_conf.xml.sample but don't see a reference to datatype_files as is coded in the RSEM tool.
So my question is, how can I manually install a tool such as RSEM from the toolshed? I've cloned it but not sure where to put the files and what to modify in Galaxy's configuration to see the new files. I can modify the datatypes_conf.xml and include the datatypes, but I get the sense this is not correct.
Ryan
The old pre-ToolShed way to add a new datatype was indeed to add it to datatypes_conf.xml and put any Python file into the galaxy-dist/lib/galaxy/datatypes/ I'm still doing this on some of my locally developed tools, but now they are in the ToolShed perhaps I should switch to using that... Regards, Peter P.S. You also used to need to add an import line to the galaxy-dist/lib/galaxy/datatypes/registry.py but that is not longer required as of this bug fix: https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015...
Hi Ryan, what about a local bootstrapped ToolShed which is in sync with the public one (at least for the users you are interested on). Than you can install from this ToolShed. I guess this is less annoying than maintaining everything on your own. Cheers, Bjoern Am 16.01.2015 um 08:22 schrieb Peter Cock:
On Thu, Jan 15, 2015 at 6:57 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes.
Along with the new data types is python class file. I'm referring to the exist datatypes_conf.xml.sample but don't see a reference to datatype_files as is coded in the RSEM tool.
So my question is, how can I manually install a tool such as RSEM from the toolshed? I've cloned it but not sure where to put the files and what to modify in Galaxy's configuration to see the new files. I can modify the datatypes_conf.xml and include the datatypes, but I get the sense this is not correct.
Ryan
The old pre-ToolShed way to add a new datatype was indeed to add it to datatypes_conf.xml and put any Python file into the galaxy-dist/lib/galaxy/datatypes/
I'm still doing this on some of my locally developed tools, but now they are in the ToolShed perhaps I should switch to using that...
Regards,
Peter
P.S. You also used to need to add an import line to the galaxy-dist/lib/galaxy/datatypes/registry.py but that is not longer required as of this bug fix: https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015... ___________________________________________________________ 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/
I can try a local toolshed, but the organization I work at frowns upon automatic installation for various reasons. That and it lets me see exactly how a tool is installed and works within my local instance. When a tool is installed from the toolshed, how does Galaxy know about it?
From a DB entry, or from the XML file(s) being present somewhere? I sort of like the idea of how /etc/profile.d gets scanned by /etc/bashrc when a user logs into a linux machine. This way, there is no modification of files, just placing the right files in the right directory is all that is needed. Anyway, I need to understand how Galaxy works with the toolshed.
On Fri, Jan 16, 2015 at 3:08 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Ryan,
what about a local bootstrapped ToolShed which is in sync with the public one (at least for the users you are interested on). Than you can install from this ToolShed. I guess this is less annoying than maintaining everything on your own.
Cheers, Bjoern
On Thu, Jan 15, 2015 at 6:57 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes.
Along with the new data types is python class file. I'm referring to
exist datatypes_conf.xml.sample but don't see a reference to datatype_files as is coded in the RSEM tool.
So my question is, how can I manually install a tool such as RSEM from
Am 16.01.2015 um 08:22 schrieb Peter Cock: the the
toolshed? I've cloned it but not sure where to put the files and what to modify in Galaxy's configuration to see the new files. I can modify the datatypes_conf.xml and include the datatypes, but I get the sense this is not correct.
Ryan
The old pre-ToolShed way to add a new datatype was indeed to add it to datatypes_conf.xml and put any Python file into the galaxy-dist/lib/galaxy/datatypes/
I'm still doing this on some of my locally developed tools, but now they are in the ToolShed perhaps I should switch to using that...
Regards,
Peter
P.S. You also used to need to add an import line to the galaxy-dist/lib/galaxy/datatypes/registry.py but that is not longer required as of this bug fix:
https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015...
___________________________________________________________ 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/
I am skeptical that setting up a local tool shed is worth the effort - it seems like overkill. I think just downloading the tar balls, manually modifying the datatypes_conf.xml is fine. If you set the tool_dependencies_dir in your Galaxy configuration - you can also create a isolated environments for tool requirements (https://wiki.galaxyproject.org/Admin/Config/ToolDependencies) allowing multiple versions of requirements like samtools to be installed simultaneously. I recently added the ability to have multiple versions of tools themselves installed like the tool shed but without the tool shed (https://bitbucket.org/galaxy/galaxy-central/commits/08f8850853d004bf8a456a14...) - it is pretty experimental but it might help if you go down this road. As for how Galaxy knows about the tool shed installs - it is a combination of file system files and database modifications (Galaxy installs the dependencies into tool_dependencies_dir, the tool files into the directory specified in shed_tools_conf.xml, updates the file integrated_tool_panel_conf.xml, and registers tool lineages and installation status in the Galaxy database). It should certainly be possible to install tools from a different server than Galaxy is running on - but you will need to run a Galaxy process on that server that can access all the same files and the Galaxy database. Hope this helps, -John On Fri, Jan 16, 2015 at 10:39 AM, Ryan G <ngsbioinformatics@gmail.com> wrote:
I can try a local toolshed, but the organization I work at frowns upon automatic installation for various reasons. That and it lets me see exactly how a tool is installed and works within my local instance.
When a tool is installed from the toolshed, how does Galaxy know about it? From a DB entry, or from the XML file(s) being present somewhere? I sort of like the idea of how /etc/profile.d gets scanned by /etc/bashrc when a user logs into a linux machine. This way, there is no modification of files, just placing the right files in the right directory is all that is needed. Anyway, I need to understand how Galaxy works with the toolshed.
On Fri, Jan 16, 2015 at 3:08 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Ryan,
what about a local bootstrapped ToolShed which is in sync with the public one (at least for the users you are interested on). Than you can install from this ToolShed. I guess this is less annoying than maintaining everything on your own.
Cheers, Bjoern
Am 16.01.2015 um 08:22 schrieb Peter Cock:
On Thu, Jan 15, 2015 at 6:57 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes.
Along with the new data types is python class file. I'm referring to the exist datatypes_conf.xml.sample but don't see a reference to datatype_files as is coded in the RSEM tool.
So my question is, how can I manually install a tool such as RSEM from the toolshed? I've cloned it but not sure where to put the files and what to modify in Galaxy's configuration to see the new files. I can modify the datatypes_conf.xml and include the datatypes, but I get the sense this is not correct.
Ryan
The old pre-ToolShed way to add a new datatype was indeed to add it to datatypes_conf.xml and put any Python file into the galaxy-dist/lib/galaxy/datatypes/
I'm still doing this on some of my locally developed tools, but now they are in the ToolShed perhaps I should switch to using that...
Regards,
Peter
P.S. You also used to need to add an import line to the galaxy-dist/lib/galaxy/datatypes/registry.py but that is not longer required as of this bug fix:
https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015... ___________________________________________________________ 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 (4)
-
Björn Grüning -
John Chilton -
Peter Cock -
Ryan G