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genome / gms

The Genome Modeling System installer
https://github.com/genome/gms/wiki
GNU Lesser General Public License v3.0
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genome sample create command doesnt exist #192

Closed shu2010 closed 8 years ago

shu2010 commented 8 years ago

Dear authors,

The run with downsampled demo data on both AWS instance as well as local installation were successful. However, the command "genome sample create" to add external data doesnt exist on either the community ami SGMS_INSTALL_V3 or locally installed SGMS !! Any work around this will be greatly appreciated.

Cheers

GrubLord commented 8 years ago

This commit seems to resolve your issue: https://github.com/genome/genome/commit/4a2e39d8cd43d1ff819b35144d1dac7576a97381

However, it is not yet in the "gms-pub" branch, which is used in the install process.

gatoravi commented 8 years ago

Hi, Thanks for the message, that is a little strange. Were you following the tutorial referenced here Could you please post the command and the error that you get when you try to run the command? Thanks, Avi

shu2010 commented 8 years ago

Thanks!! Error with SGMS_INSTALL_V3:

screen shot 2015-11-20 at 2 33 47 pm

gatoravi commented 8 years ago

@GrubLord is right, this commit https://github.com/genome/genome/commit/f3ea92e8f3d7978b4a27954004d3a174db5ade80 from @mkiwala seems to have somehow gotten clobbered while merging branches. Thanks for reporting this.

I've cherry-picked the commit onto the gms-pub branch. To pull this change into your AWS instance, please try to cd /opt/gms/${GMS_ID}/sw/genome and run git pull. Alternatively, the target "update-repos" in the Makefile should do the same thing, so you could run make update-repos from the same directory where you ran the install step(the directory that has the Makefile in it). Thanks again for reporting this and do let us know if you run into more issues.