bowtie2 toolshed installation
Hi there, I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml ) I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't... Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2. Is there a way to add bowtie2 manually? Best wishes, Alex
Hi Alex, there is a difference in http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0 and http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers The package_* is installing the binary for you and can be used by other programs as well. bowtie_wrappers contains the actual wrappers and is depending on package_*. To make it short. You need to install http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers and both packages will be installed and you should see your wrapper. Ciao, Bjoern 2014-01-31 Alexander Kurze <alexander.kurze@bioch.ox.ac.uk>:
Hi there,
I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml )
I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't...
Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2.
Is there a way to add bowtie2 manually?
Best wishes,
Alex
___________________________________________________________ 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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Thanks for your quick answers. I actually have installed the dependencies first and then I have tried to add bowtie2 http://toolshed.g2.bx.psu.edu/view/devteam/bowtie2. But this is where the problem lies: I get following error message: "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" Meanwhile, I have downloaded the bowtie2.xml and added it to the ./tools/sr_mapping/ folder and added it to the tool_config.xml and it now works. Any clue why I get the error message? Is there something wrong with my server or do is it the repository? Cheers, Alex On Fri, Jan 31, 2014 at 1:18 PM, bjoern.gruening@googlemail.com < bjoern.gruening@gmail.com> wrote:
Hi Alex,
there is a difference in http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0 and http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers The package_* is installing the binary for you and can be used by other programs as well. bowtie_wrappers contains the actual wrappers and is depending on package_*. To make it short. You need to install http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers and both packages will be installed and you should see your wrapper.
Ciao, Bjoern
2014-01-31 Alexander Kurze <alexander.kurze@bioch.ox.ac.uk>:
Hi there,
I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml )
I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't...
Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2.
Is there a way to add bowtie2 manually?
Best wishes,
Alex
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341
Alex, To help determine the cause of this, could you paste the output of the following commands run from the root of your Galaxy installation? hg heads hg id --Dave B. On 01/31/2014 09:05 AM, Alexander Kurze wrote:
Thanks for your quick answers.
I actually have installed the dependencies first and then I have tried to add bowtie2 http://toolshed.g2.bx.psu.edu/view/devteam/bowtie2.
But this is where the problem lies: I get following error message:
"Server Error
An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)"
Meanwhile, I have downloaded the bowtie2.xml and added it to the ./tools/sr_mapping/ folder and added it to the tool_config.xml and it now works.
Any clue why I get the error message? Is there something wrong with my server or do is it the repository?
Cheers,
Alex
On Fri, Jan 31, 2014 at 1:18 PM, bjoern.gruening@googlemail.com <mailto:bjoern.gruening@googlemail.com> <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> wrote:
Hi Alex,
there is a difference in http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0 and http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers The package_* is installing the binary for you and can be used by other programs as well. bowtie_wrappers contains the actual wrappers and is depending on package_*. To make it short. You need to install http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers and both packages will be installed and you should see your wrapper.
Ciao, Bjoern
2014-01-31 Alexander Kurze <alexander.kurze@bioch.ox.ac.uk <mailto:alexander.kurze@bioch.ox.ac.uk>>:
Hi there,
I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml <http://testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml>)
I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't...
Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2.
Is there a way to add bowtie2 manually?
Best wishes,
Alex
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 Fax:+44 1865 613 341
Here we go changeset: 8796:961ae35ba612 branch: stable tag: tip parent: 8794:1c7174911392 user: Nate Coraor <nate@bx.psu.edu> date: Fri Feb 08 11:23:04 2013 -0500 summary: Added tag release_2013.02.08 for changeset 1c7174911392 changeset: 8795:9fd7fe0c5712 parent: 8785:25bd9d387135 parent: 8794:1c7174911392 user: Nate Coraor <nate@bx.psu.edu> date: Fri Feb 08 11:22:54 2013 -0500 summary: merge from stable 961ae35ba612+ (stable) tip Alex On Fri, Jan 31, 2014 at 2:09 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Alex,
To help determine the cause of this, could you paste the output of the following commands run from the root of your Galaxy installation?
hg heads hg id
--Dave B.
On 01/31/2014 09:05 AM, Alexander Kurze wrote:
Thanks for your quick answers.
I actually have installed the dependencies first and then I have tried to add bowtie2 http://toolshed.g2.bx.psu.edu/view/devteam/bowtie2.
But this is where the problem lies: I get following error message:
"Server Error
An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)"
Meanwhile, I have downloaded the bowtie2.xml and added it to the ./tools/sr_mapping/ folder and added it to the tool_config.xml and it now works.
Any clue why I get the error message? Is there something wrong with my server or do is it the repository?
Cheers,
Alex
On Fri, Jan 31, 2014 at 1:18 PM, bjoern.gruening@googlemail.com <mailto:bjoern.gruening@googlemail.com> <bjoern.gruening@gmail.com
<mailto:bjoern.gruening@gmail.com>> wrote:
Hi Alex,
there is a difference in http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0 and http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers The package_* is installing the binary for you and can be used by other programs as well. bowtie_wrappers contains the actual wrappers and is depending on package_*. To make it short. You need to install http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers and both packages will be installed and you should see your wrapper.
Ciao, Bjoern
2014-01-31 Alexander Kurze <alexander.kurze@bioch.ox.ac.uk <mailto:alexander.kurze@bioch.ox.ac.uk>>:
Hi there,
I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/jjohnson/ package_bowtie_2_1_0/38652b57e057/package_bowtie_2_ 1_0/tool_dependencies.xml <http://testtoolshed.g2.bx.psu.edu/repos/jjohnson/ package_bowtie_2_1_0/38652b57e057/package_bowtie_2_ 1_0/tool_dependencies.xml>)
I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't...
Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2.
Is there a way to add bowtie2 manually?
Best wishes,
Alex
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 Fax:+44 1865 613 341
-- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX Tel: +44 1865-243-609 Mobile: +44 7962-425-865
Alex, It is likely that the error you're encountering may have been resolved in the current stable branch. A description of the steps required to update your installation can be found on the following page: https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date Be advised that there is at least one database upgrade between the 2013-02-08 release and the current stable branch, so the paragraph describing database migration does apply. Additionally, a number of tools were migrated to the tool shed from the Galaxy distribution since that release. A detailed explanation of this process and instructions for installing the repositories containing migrated tools can be found at the following page: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution --Dave B. On 01/31/2014 09:14 AM, Alexander Kurze wrote:
Here we go
changeset: 8796:961ae35ba612 branch: stable tag: tip parent: 8794:1c7174911392 user: Nate Coraor <nate@bx.psu.edu <mailto:nate@bx.psu.edu>> date: Fri Feb 08 11:23:04 2013 -0500 summary: Added tag release_2013.02.08 for changeset 1c7174911392
changeset: 8795:9fd7fe0c5712 parent: 8785:25bd9d387135 parent: 8794:1c7174911392 user: Nate Coraor <nate@bx.psu.edu <mailto:nate@bx.psu.edu>> date: Fri Feb 08 11:22:54 2013 -0500 summary: merge from stable
961ae35ba612+ (stable) tip
Alex
On Fri, Jan 31, 2014 at 2:09 PM, Dave Bouvier <dave@bx.psu.edu <mailto:dave@bx.psu.edu>> wrote:
Alex,
To help determine the cause of this, could you paste the output of the following commands run from the root of your Galaxy installation?
hg heads hg id
--Dave B.
On 01/31/2014 09:05 AM, Alexander Kurze wrote:
Thanks for your quick answers.
I actually have installed the dependencies first and then I have tried to add bowtie2 http://toolshed.g2.bx.psu.edu/__view/devteam/bowtie2 <http://toolshed.g2.bx.psu.edu/view/devteam/bowtie2>.
But this is where the problem lies: I get following error message:
"Server Error
An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)"
Meanwhile, I have downloaded the bowtie2.xml and added it to the ./tools/sr_mapping/ folder and added it to the tool_config.xml and it now works.
Any clue why I get the error message? Is there something wrong with my server or do is it the repository?
Cheers,
Alex
On Fri, Jan 31, 2014 at 1:18 PM, bjoern.gruening@googlemail.com <mailto:bjoern.gruening@googlemail.com> <mailto:bjoern.gruening@__googlemail.com <mailto:bjoern.gruening@googlemail.com>> <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>
<mailto:bjoern.gruening@gmail.__com <mailto:bjoern.gruening@gmail.com>>> wrote:
Hi Alex,
there is a difference in http://toolshed.g2.bx.psu.edu/__view/devteam/package_bowtie2___2_1_0 <http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0> and http://toolshed.g2.bx.psu.edu/__view/devteam/bowtie_wrappers <http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers> The package_* is installing the binary for you and can be used by other programs as well. bowtie_wrappers contains the actual wrappers and is depending on package_*. To make it short. You need to install http://toolshed.g2.bx.psu.edu/__view/devteam/bowtie_wrappers <http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers> and both packages will be installed and you should see your wrapper.
Ciao, Bjoern
2014-01-31 Alexander Kurze <alexander.kurze@bioch.ox.ac.__uk <mailto:alexander.kurze@bioch.ox.ac.uk> <mailto:alexander.kurze@bioch.__ox.ac.uk <mailto:alexander.kurze@bioch.ox.ac.uk>>>:
Hi there,
I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg
galaxy/shed_tools/testtoolshed__.g2.bx.psu.edu/repos/jjohnson/__package_bowtie_2_1_0/__38652b57e057/package_bowtie_2___1_0/tool_dependencies.xml <http://testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml>
<http://testtoolshed.g2.bx.__psu.edu/repos/jjohnson/__package_bowtie_2_1_0/__... <http://testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml>>)
I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't...
Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2.
Is there a way to add bowtie2 manually?
Best wishes,
Alex
_____________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/__search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 <tel:%2B44%201865%20613%20230> Fax:+44 1865 613 341 <tel:%2B44%201865%20613%20341>
-- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX
Tel: +44 1865-243-609 Mobile: +44 7962-425-865
participants (4)
-
Alexander Kurze -
Alexander Kurze -
bjoern.gruening＠googlemail.com -
Dave Bouvier