"Local install" of Galaxy Tool
Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY. However, it is not found using if the <command> tag looks as follows: <command>BINARY (arguments)</command> When I put the following, it works: <command>$__root_dir__/tools/CATEGORY/BINARY</command> Am I doing something wrong? Is there a preferable way to such a "local" installation than my second try? Thanks! Manuel [1] http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial
Hi Manuel, is your XML file also under ${galaxy_root}/tools/${category}/ ? It should be. Tata, Bjoern
Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY. However, it is not found using if the <command> tag looks as follows:
<command>BINARY (arguments)</command>
When I put the following, it works:
<command>$__root_dir__/tools/CATEGORY/BINARY</command>
Am I doing something wrong? Is there a preferable way to such a "local" installation than my second try?
Thanks! Manuel
[1] http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxy
Yes, this is the case. I have: galaxy-dist/tools/${category}/BINARY galaxy-dist/tools/${category}/BINARY.xml Where BINARY.xml contains the <tool ...><command>BINARY... XML code. Is there a good way to see what Galaxy is exactly executing for the tool? I could not find a description on how to do that anywhere on the internet (*sigh* apparently one cannot find anything related to Galaxy, at least since the term Galaxy got "hijacked" by the smartphone of the same name ;). Thanks, Manuel ________________________________________ From: Björn Grüning [bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Wednesday, April 10, 2013 11:37 PM To: Holtgrewe, Manuel Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] "Local install" of Galaxy Tool Hi Manuel, is your XML file also under ${galaxy_root}/tools/${category}/ ? It should be. Tata, Bjoern
Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY. However, it is not found using if the <command> tag looks as follows:
<command>BINARY (arguments)</command>
When I put the following, it works:
<command>$__root_dir__/tools/CATEGORY/BINARY</command>
Am I doing something wrong? Is there a preferable way to such a "local" installation than my second try?
Thanks! Manuel
[1] http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxy
Hi,
I have:
galaxy-dist/tools/${category}/BINARY galaxy-dist/tools/${category}/BINARY.xml
Try to put the binary in your PATH.
Where BINARY.xml contains the <tool ...><command>BINARY... XML code.
Is there a good way to see what Galaxy is exactly executing for the tool?
In your webX.log. It is depending on your configuration, but in your log file the executed command is logged.
I could not find a description on how to do that anywhere on the internet (*sigh* apparently one cannot find anything related to Galaxy, at least since the term Galaxy got "hijacked" by the smartphone of the same name ;)
Please use these URL for searching: http://galaxyproject.org/search/web/ Cheers, Bjoern
Thanks, Manuel ________________________________________ From: Björn Grüning [bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Wednesday, April 10, 2013 11:37 PM To: Holtgrewe, Manuel Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] "Local install" of Galaxy Tool
Hi Manuel,
is your XML file also under ${galaxy_root}/tools/${category}/ ? It should be.
Tata, Bjoern
Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY. However, it is not found using if the <command> tag looks as follows:
<command>BINARY (arguments)</command>
When I put the following, it works:
<command>$__root_dir__/tools/CATEGORY/BINARY</command>
Am I doing something wrong? Is there a preferable way to such a "local" installation than my second try?
Thanks! Manuel
[1] http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxy
Adding galaxy-dist/tools/${category} to PATH before calling sh run.sh does the trick. This is not ideal but works for now... Thanks, Manuel ________________________________________ From: Björn Grüning [bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Thursday, April 11, 2013 12:19 AM To: Holtgrewe, Manuel Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] "Local install" of Galaxy Tool Hi,
I have:
galaxy-dist/tools/${category}/BINARY galaxy-dist/tools/${category}/BINARY.xml
Try to put the binary in your PATH.
Where BINARY.xml contains the <tool ...><command>BINARY... XML code.
Is there a good way to see what Galaxy is exactly executing for the tool?
In your webX.log. It is depending on your configuration, but in your log file the executed command is logged.
I could not find a description on how to do that anywhere on the internet (*sigh* apparently one cannot find anything related to Galaxy, at least since the term Galaxy got "hijacked" by the smartphone of the same name ;)
Please use these URL for searching: http://galaxyproject.org/search/web/ Cheers, Bjoern
Thanks, Manuel ________________________________________ From: Björn Grüning [bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Wednesday, April 10, 2013 11:37 PM To: Holtgrewe, Manuel Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] "Local install" of Galaxy Tool
Hi Manuel,
is your XML file also under ${galaxy_root}/tools/${category}/ ? It should be.
Tata, Bjoern
Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY. However, it is not found using if the <command> tag looks as follows:
<command>BINARY (arguments)</command>
When I put the following, it works:
<command>$__root_dir__/tools/CATEGORY/BINARY</command>
Am I doing something wrong? Is there a preferable way to such a "local" installation than my second try?
Thanks! Manuel
[1] http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxy
Hi Manuel, collect your binaries in a separate location and add to PATH and your cluster. If you want to ship your tool in the toolshed, the installation and PATH will be automatically added once you installed it from the toolshed. Have a look at: http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_too... Regards, Bjoern
Adding galaxy-dist/tools/${category} to PATH before calling sh run.sh does the trick. This is not ideal but works for now...
Thanks, Manuel ________________________________________ From: Björn Grüning [bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Thursday, April 11, 2013 12:19 AM To: Holtgrewe, Manuel Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] "Local install" of Galaxy Tool
Hi,
I have:
galaxy-dist/tools/${category}/BINARY galaxy-dist/tools/${category}/BINARY.xml
Try to put the binary in your PATH.
Where BINARY.xml contains the <tool ...><command>BINARY... XML code.
Is there a good way to see what Galaxy is exactly executing for the tool?
In your webX.log. It is depending on your configuration, but in your log file the executed command is logged.
I could not find a description on how to do that anywhere on the internet (*sigh* apparently one cannot find anything related to Galaxy, at least since the term Galaxy got "hijacked" by the smartphone of the same name ;)
Please use these URL for searching:
http://galaxyproject.org/search/web/
Cheers, Bjoern
Thanks, Manuel ________________________________________ From: Björn Grüning [bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Wednesday, April 10, 2013 11:37 PM To: Holtgrewe, Manuel Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] "Local install" of Galaxy Tool
Hi Manuel,
is your XML file also under ${galaxy_root}/tools/${category}/ ? It should be.
Tata, Bjoern
Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY. However, it is not found using if the <command> tag looks as follows:
<command>BINARY (arguments)</command>
When I put the following, it works:
<command>$__root_dir__/tools/CATEGORY/BINARY</command>
Am I doing something wrong? Is there a preferable way to such a "local" installation than my second try?
Thanks! Manuel
[1] http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial ___________________________________________________________ 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://galaxy
participants (2)
-
Björn Grüning -
Holtgrewe, Manuel