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build steps incomplete #36

Closed argoat closed 5 years ago

argoat commented 6 years ago

@iontorrent-dev while i'm trying to compile TVC following REAME file from the link you provide http://updates.iontorrent.com/tvc_standalone/README* i found step 6 and step 9 are missing in versions 5.xx.xx of TS. Can someone explain why and offer some nice guidance? thanks :D

chenliangomc commented 6 years ago

According to v4.6.0 ReadMe, step 6 is build vcftools, and step 9 is build/install GATK.

I have not tried to build from source for TVC, but will do it later.

ipan commented 6 years ago

In TSS 5.x, we have removed the GATK dependency. That's why the instructions would be different.

Please see this for list of the links for tvc standalone for 5.x releases:

http://updates.iontorrent.com/tvc_standalone/

I would recommend to run docker image for build. The example is for centos7 and should product a tar.gz file like this: tvc-5.8.0-CentOS_7.3.1611_x86_64-binary.tar.gz.

wget http://updates.iontorrent.com/tvc_standalone/tvc-5.8.0.tar.gz
tar xvf tvc-5.8.0.tar.gz
docker run -t -v $(pwd):/src iontorrent/tvcbuild:centos7 bash -c 'build.sh tvc-5.8.0'

You can build with trusty, xenial, and jesse.