Re: [galaxy-dev] [galaxy-iuc] package_samtools_0_1_19 - bcftools and misc utilities
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-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] package_samtools_0_1_19 - bcftools and misc utilities
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 $INSTALL_DIR/bin when package_samtools is installed? Sorry, I do not get the question :( Are you asking to enhance the existing samtools definition? Thanks, JJ -- James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota ___ galaxy-iuc mailing list galaxy-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc Yes.I would enhance the existing samtools definition. I added in: http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_samtools_0_1_19 action type=shell_commandchmod ugo+rx misc/*.p?/action action type=shell_commandmkdir misc/bin/action action type=shell_commandcp -p `find misc -type f -perm -555` misc/bin//action action type=move_file sourcesamtools/source destination$INSTALL_DIR/bin/destination /action action type=move_file sourcebcftools/bcftools/source destination$INSTALL_DIR/bin/destination /action action type=move_file sourcebcftools/vcfutils.pl/source destination$INSTALL_DIR/bin/destination /action action type=move_directory_files source_directorymisc/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 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] package_samtools_0_1_19 - bcftools and misc utilities
Hi, oh I see. Great! I would vote to include them in the main samtools package and extend the help text a little bit, so that the search will find it. If you like you can add it to: https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_samtools_0_1_19 I have granted jjohnson write permission to the IUC samtools account. Thanks, Bjoern 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 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [galaxy-iuc] package_samtools_0_1_19 - bcftools and misc utilities
On Tue, Sep 17, 2013 at 7:43 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi, oh I see. Great! I would vote to include them in the main samtools package and extend the help text a little bit, so that the search will find it. Seconded, this would be helpful for some stuff I have been working on as well. -John If you like you can add it to: https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_samtools_0_1_19 I have granted jjohnson write permission to the IUC samtools account. Thanks, Bjoern 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 ___ galaxy-iuc mailing list galaxy-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
