If you make the correction in your local version it should install. However,
getting updates (if they become available) may require merging.
On Mar 20, 2014, at 3:19 PM, Pete Schmitt peter.r.schm...@dartmouth.edu wrote:
Can I just edit this file to point to the existing homer install on the
server? I found this in the tool shed tree.
On 3/20/14, 3:03 PM, Greg Von Kuster wrote:
Hi Pete,
Here is the recipe for installing homer from this repository:
http://toolshed.g2.bx.psu.edu/view/kevyin/homer
?xml version=1.0?
tool_dependency
package name=homer version=4.1
install version=4.1
actions
action
type=download_by_urlhttp://biowhat.ucsd.edu/homer/configureHomer.pl/action
action type=shell_commandperl ./configureHomer.pl
-install/action
!--action type=shell_commandperl ./configureHomer.pl -install
hg19/action--
action type=move_directory_files
source_directory.//source_directory
destination_directory$INSTALL_DIR/destination_directory
/action
action type=set_environment
environment_variable name=PATH
action=prepend_to$INSTALL_DIR/bin/environment_variable
/action
/actions
/install
readme
I'm sorry but this does not work
/readme
/package
/tool_dependency
The problem is tha the following tag:
install version=4.1
must be:
install version=1.0
I'm pretty sure a message was displayed when the file was uploaded, but it's
been a while since I looked at thie relevant code, so I'm not positive.
Gfreg Von Kuster
On Mar 20, 2014, at 2:52 PM, Pete Schmitt peter.r.schm...@dartmouth.edu
wrote:
I've installed homer 4.5 on the server that hosts the latest galaxy
version, and ensured that
it is in galaxy's path (in run.sh) when it starts up. When installing the
wrapper from the main toolshed
I get the following error which I don't understand:
Tool shed repository: homer
Tool shed repository changeset revision: f0b5827b6051
Tool dependency status: Error
Tool dependency installation error: Error installing tool dependency
package homer version 4.1: Only install version 1.0 is currently supported
(i.e., change your tag to be ).
Tool dependency installation directory:
/galaxy/tools/homer/4.1/kevyin/homer/f0b5827b6051
The following is the README from the homer wrapper that I installed:
Homer wrapper for Galaxy
The homer tools will need to be accessible from command line
Code repo: https://bitbucket.org/gvl/homer
=:
LICENSE for this wrapper:
=:
Kevin Ying
Garvan Institute: http://www.garvan.org.au
GVL: https://genome.edu.au/wiki/GVL
http://opensource.org/licenses/mit-license.php
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--
Pete Schmitt
Technical Director:
Discovery Cluster
NH INBRE Grid
Computational Genetics Lab
Institute for Quantitative
Biomedical Sciences
Dartmouth College, HB 6203
L12 Berry/Baker Library
Hanover, NH 03755
Phone: 603-646-8109
http://discovery.dartmouth.edu
http://columbia.dartmouth.edu/grid
http://www.epistasis.org
http://iQBS.org
dartmouth.png
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