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 $INSTALL_DIR/bin when package_samtools is installed? Sorry, I do not get the question :( Are you asking to enhance the existing samtools definition?
Thanks,
JJ
-- James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota _______________________________________________ galaxy-iuc mailing list galaxy-iuc@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc
Yes. I would enhance the existing samtools definition. I added in: http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_samtools_0_1_19 <action type="shell_command">chmod ugo+rx misc/*.p?</action> <action type="shell_command">mkdir misc/bin</action> <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action> <action type="move_file"> <source>samtools</source> <destination>$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