On 9/17/13 7:08 AM, Bjoern Gruening wrote:
Hi JJ,

I've had occasion to use some of the samtools misc utilities in galaxy
tools.
Should those also be copied to the $INSTALL_DIR/bin when
package_samtools is installed?
Sorry, I do not get the question :(
Are you asking to enhance the existing samtools definition?

Thanks,

JJ


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James E. Johnson, Minnesota Supercomputing Institute, University of
Minnesota
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Yes.    I would enhance the existing samtools definition.

I added in: 
http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_samtools_0_1_19

                <action type="shell_command">chmod ugo+rx misc/*.p?</action>
                <action type="shell_command">mkdir misc/bin</action>
                <action type="shell_command">cp -p `find misc -type f -perm -555` 
misc/bin/</action>
                <action type="move_file">
                    <source>samtools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bcftools/bcftools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bcftools/vcfutils.pl</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>misc/bin</source_directory>
                    
<destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>

The other option would be to create additional packages that download the same 
samtools source, but install bcftools and misc.



--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
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