Re: [galaxy-dev] Tool.xml : correct way to define an environment_variable ?
Thanks Peter, it works, now I've moved my xml to the way you've suggested **and** I had to change the name of my environment_variable. I don't know why but I suspect there is a 'ghost/persistent' (?) version of my variable that still exists(!?) somewhere from a previous attempt. Thank you again. P. ___ 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/
Re: [galaxy-dev] Tool.xml : correct way to define an environment_variable ?
On 10/20/2016 11:06 AM, Peter Cock wrote: Hi Pierre, The first example looks OK, very similar to this one of mine for example, so I am not sure what is breaking: https://github.com/peterjc/pico_galaxy/blob/133aea82c02adf5509134c415565ada99c519312/tools/effectiveT3/tool_dependencies.xml I would try adding more shell actions to debug this with echo statements? Hi Peter, Thanks , your xml is inspiring, I'll have a look at this. Best, Pierre ___ 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/
Re: [galaxy-dev] Tool.xml : correct way to define an environment_variable ?
Hi Pierre,
The first example looks OK, very similar to this one of mine for example,
so I am not sure what is breaking:
https://github.com/peterjc/pico_galaxy/blob/133aea82c02adf5509134c415565ada99c519312/tools/effectiveT3/tool_dependencies.xml
I would try adding more shell actions to debug this with echo statements?
However, rather than using wget you could use the download_file
action which can verify the checksum, and will also work on a Mac
where wget is usually missing.
Peter
On Thu, Oct 20, 2016 at 8:03 AM, Pierre Lindenbaum
wrote:
> (cross-posted at https://biostar.usegalaxy.org/p/20220/ )
>
>
> I'm trying to create some `tools.xml` that use java.
>
> Those tools need to download some library (*.jar) files from
> http://central.maven.org/ and I want to create a variable $MYTOOLCLASSPATH
> containing the jars. I've tried the following xml :
>
>
>
>
>
>
> wget -P
> "$REPOSITORY_INSTALL_DIR" "http://central.maven.org/lib1.jar";
> "http://central.maven.org/lib2.jar";
>
> action="set_to">$REPOSITORY_INSTALL_DIR/lib1.jar:$REPOSITORY_INSTALL_DIR/lib2.jar
>
>
>
>
>
>
> the base java command is defined as a token in macro.xml:
>
> (...)
>
> java -cp "\${MYTOOLCLASSPATH}"
>
> (...)
>
> and called in my tool.xml:
>
> @MYJAVA@ tool.Tool ${input} > ${out}
>
> but It seems that $MYTOOLCLASSPATH is empty.
>
> I've also tried to create a set_environment under :
>
>
> action="set_to">$REPOSITORY_INSTALL_DIR/lib1.jar:$REPOSITORY_INSTALL_DIR/lib2.jar
>
>
>
> same problem: the $MYTOOLCLASSPATH remains empty
>
> Where Am i wrong ? What's the correct way to define MYTOOLCLASSPATH ?
>
>
>
> Thanks,
>
> Pierre
>
>
> ___
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[galaxy-dev] Tool.xml : correct way to define an environment_variable ?
(cross-posted at https://biostar.usegalaxy.org/p/20220/ )
I'm trying to create some `tools.xml` that use java.
Those tools need to download some library (*.jar) files from
http://central.maven.org/ and I want to create a variable
$MYTOOLCLASSPATH containing the jars. I've tried the following xml :
wget -P
"$REPOSITORY_INSTALL_DIR" "http://central.maven.org/lib1.jar";
"http://central.maven.org/lib2.jar";
action="set_to">$REPOSITORY_INSTALL_DIR/lib1.jar:$REPOSITORY_INSTALL_DIR/lib2.jar
the base java command is defined as a token in macro.xml:
(...)
java -cp "\${MYTOOLCLASSPATH}"
(...)
and called in my tool.xml:
@MYJAVA@ tool.Tool ${input} > ${out}
but It seems that $MYTOOLCLASSPATH is empty.
I've also tried to create a set_environment under :
action="set_to">$REPOSITORY_INSTALL_DIR/lib1.jar:$REPOSITORY_INSTALL_DIR/lib2.jar
same problem: the $MYTOOLCLASSPATH remains empty
Where Am i wrong ? What's the correct way to define MYTOOLCLASSPATH ?
Thanks,
Pierre
___
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and other Galaxy lists, please use the interface at:
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