Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Preferred Way To Make Custom Tool Accessible Though Path
0
gravatar for Sébastien Vigneau
4.9 years ago by
Sébastien Vigneau • 50
Sébastien Vigneau • 50 wrote:
Hi, I have written a simple xml wrapper to run the UCSC *bigWigToBedGraph* tool on a custom Galaxy install on Amazon cloud. The tool works as expected in this install. The xml file itself is in /mnt/galaxy/galaxy-app/tools/myTools, but I added the bigWigToBedGraph binary to the /mnt/galaxy/tools/bin/ directory, which is by default in the PATH. Alternatively, I guess I could have modified the PATH so that it includes the myTools directory. Since I would like to contribute the tool (my contribution being the wrapper) to *Galaxy Tool Shed*, I am wondering* what is the best way to include it so that it is found in the PATH* whenever the tool is installed from the Tool Shed. Thanks for your help! Sébastien
galaxy • 754 views
ADD COMMENT • link •
modified 4.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.9 years ago by Sébastien Vigneau • 50
0
gravatar for Jennifer Hillman Jackson
4.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello, You have probably seen the Tool Shed documentation, but if not, this is the hub: https://wiki.galaxyproject.org/Tool%20Shed These are the topics about configuration: https://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_s hed_repository And this sub-section of the above covers how to define/configure dependencies so that they are part of the repository when others install it: https://wiki.galaxyproject.org/DefiningRepositoryDependencies This is a great addition, thanks for the contribution! If you run into any trouble, send the details of where you are having problems to the galaxy-dev@bx.psu.edu mailing list, to better reach the development community for troubleshooting. You can also search prior dev Q/A here: http://galaxyproject.org/search/getgalaxy/ -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENT • link written 4.9 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 179 users visited in the last hour