Question: How To Add A Tool To Cloud Galaxy
gravatar for Greg Edwards
6.9 years ago by
Greg Edwards190
Greg Edwards190 wrote:
Hi Folks, I could use some help on adding a tool to the cloud version of Galaxy. The Cloud startup process creates, among other things, /mnt/galaxyTools/galaxy-central which has tools_conf.xml, and subdir tools etc. This seems not accessible before starting the cloud. I assume I need to add my tool into the structure as per a local Galaxy instance, and then get Galaxy to restart, or re-read it's config ? Would appreciate some advice there. Just as background .. I have got a custom proteomics Perl script running ok under a local version of Galaxy on Mac. Added in to tools_conf.xml, tools etc. Made several mods to the Perl to stop any writing to stderr except for fatal show-stopper errors, everyone seems to hit that one, and other small things to make it play better with Galaxy. Also quite familiar with AWS EC2, have been using that for a while. I have Galaxy Cloudman running well, start/stop extra servers etc. Using the free t1.micro AMI for now, slowish but ok for testing. Or a Spot Instance of m1.large when I'm impatient. I couldn't find the answer in a search of Galaxy archives, apologies if it's there, or obvious in some other way. Thanks! -- Greg Edwards, Port Jackson Bioinformatics Consulting.
galaxy • 792 views
ADD COMMENTlink modified 6.9 years ago by Dannon Baker3.7k • written 6.9 years ago by Greg Edwards190
gravatar for Dannon Baker
6.9 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:
Hi Greg, In order to install custom tools you'll need to SSH into a running instance, install your tool and make any modifications to Galaxy you need in order to use it, and then use the "Persist changes to file system" option in the Cloudman administration panel. By default, Cloudman discards and simply recreates from snapshot the galaxyTools and galaxyData volumes when an instance is relaunched, but this persistence command will make a snapshot specific to your instance that will be used going forward. Here's a wiki link for more info: Let me know if you have any other questions, and good luck! -Dannon
ADD COMMENTlink written 6.9 years ago by Dannon Baker3.7k
Dannon, Thanks. I can't believe I didn;t see that, I've read the Cloud setup page a dozen times while getting familiar with Cloudman. I guess you skip what you don;t need at the time :=( Greg -- Greg Edwards, Port Jackson Bioinformatics Consulting.
ADD REPLYlink written 6.9 years ago by Greg Edwards190
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