Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message:
mytool.sh: line 14: mytool: unknown command
It seems that the PATH was not correctly set. What am I doing wrong ?
My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml
Here is my tool_dependencies.xml file content:
<?xml version="1.0"?> <tool_dependency> <package name="mytool" version="1.0"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> </readme> </package> </tool_dependency>
Thank you, AK
Do you have a matching dependency declaration in mytool.xml?
Peter
On Mon, Dec 22, 2014 at 9:56 AM, KRESS Arnaud (ESP) akress@unistra.fr wrote:
Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message:
mytool.sh: line 14: mytool: unknown command
It seems that the PATH was not correctly set. What am I doing wrong ?
My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml
Here is my tool_dependencies.xml file content:
<?xml version="1.0"?>
<tool_dependency> <package name="mytool" version="1.0"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> </readme> </package> </tool_dependency>
Thank you, AK ___________________________________________________________ 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/
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Hi AK,
Am 22.12.2014 um 10:56 schrieb KRESS Arnaud (ESP):
Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message:
mytool.sh: line 14: mytool: unknown command
It seems that the PATH was not correctly set. What am I doing wrong ?
My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml
Here is my tool_dependencies.xml file content:
<?xml version="1.0"?>
<tool_dependency> <package name="mytool" version="1.0"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action>
INSTALL_DIR is not the directory where your XML file is located. The correct way would be if you download/compile your binary and move it to INSTALL_DIR.
An alternative would be to put $REPOSITORY_INSTALL_DIR/bin in your path.
Ciao, Bjoern
</actions> </install> <readme> </readme> </package></tool_dependency>
Thank you, AK ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Thank you for your answer. I think I've grasped the logic. I have modified the tool_dependencies.xml to make it download and move the binary to INSTALL_DIR: the file is now correctly installed and a env.sh file is created. But I'm still getting the same error message, at what condition is this env.sh sourced at execution time ?
AK
Le Lundi 22 Décembre 2014 11:26 CET, Björn Grüning bjoern.gruening@gmail.com a écrit:
Hi AK,
Am 22.12.2014 um 10:56 schrieb KRESS Arnaud (ESP):
Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message:
mytool.sh: line 14: mytool: unknown command
It seems that the PATH was not correctly set. What am I doing wrong ?
My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml
Here is my tool_dependencies.xml file content:
<?xml version="1.0"?>
<tool_dependency> <package name="mytool" version="1.0"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action>
INSTALL_DIR is not the directory where your XML file is located. The correct way would be if you download/compile your binary and move it to INSTALL_DIR.
An alternative would be to put $REPOSITORY_INSTALL_DIR/bin in your path.
Ciao, Bjoern
</actions> </install> <readme> </readme> </package></tool_dependency>
Thank you, AK ___________________________________________________________ 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/
The env.sh file is source if you have specified a requirement tag in your tool that matches your tool_dependencies.xml file.
If you have name="mytool" version="1.0" in your tool_dependencies.xml file you need to have:
<requirement type="package" version="1.0">mytool</requirement>
in your tool.xml. Please make the package name more meaningful :)
Cheers, Bjoern
Am 22.12.2014 um 15:57 schrieb KRESS Arnaud (ESP):
Thank you for your answer. I think I've grasped the logic. I have modified the tool_dependencies.xml to make it download and move the binary to INSTALL_DIR: the file is now correctly installed and a env.sh file is created. But I'm still getting the same error message, at what condition is this env.sh sourced at execution time ?
AK
Le Lundi 22 Décembre 2014 11:26 CET, Björn Grüning bjoern.gruening@gmail.com a écrit:
Hi AK,
Am 22.12.2014 um 10:56 schrieb KRESS Arnaud (ESP):
Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message:
mytool.sh: line 14: mytool: unknown command
It seems that the PATH was not correctly set. What am I doing wrong ?
My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml
Here is my tool_dependencies.xml file content:
<?xml version="1.0"?>
<tool_dependency> <package name="mytool" version="1.0"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action>
INSTALL_DIR is not the directory where your XML file is located. The correct way would be if you download/compile your binary and move it to INSTALL_DIR.
An alternative would be to put $REPOSITORY_INSTALL_DIR/bin in your path.
Ciao, Bjoern
</actions> </install> <readme> </readme> </package></tool_dependency>
Thank you, AK ___________________________________________________________ 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/
galaxy-dev@lists.galaxyproject.org
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Björn Grüning -
KRESS Arnaud (ESP) -
Peter Cock