comparison README.rst @ 56:1beff3ddce58 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75"

55:bb0130ff73ce

General Requirements
--------------------

To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:

    export _JAVA_OPTIONS='-Xmx1500M'

On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example:

	export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M'

It is also possible to set this on a per tool basis using advanced features of the galaxy job config system.

MSAmanda on linux
-----------------

For more help on installing Mono please see http://www.mono-project.com/download.

Note
----

- Requires Galaxy release v16.01 or later.

See:

* <http://compomics.github.io/projects/peptide-shaker.html/>
* <http://compomics.github.io/projects/searchgui.html/>

56:1beff3ddce58

General Requirements
--------------------

To avoid out of memory errors you may need to set the maximum heapspace for java processes if the default is too small for the data you are going to process (4gb for SearchGUI, 1GB for PeptideShaker).
For example, to set this in your shell:

    export _JAVA_OPTIONS='-Xmx8192m'

On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example:

	export _JAVA_OPTIONS='-Xmx8192m -XX:MaxPermSize=1024m'

It is also possible to set this on a per tool basis using advanced features of the galaxy job config system.

MSAmanda on linux
-----------------

For more help on installing Mono please see http://www.mono-project.com/download.

Note
----

- Requires Galaxy release v20.01 or later.

See:

* <http://compomics.github.io/projects/peptide-shaker.html/>
* <http://compomics.github.io/projects/searchgui.html/>