Closed hyphaltip closed 3 years ago
hyphaltip
commented
4 years ago I see now that when trinity conda is installed we have the tool in
bin/insilico_read_normalization.pl -> ../opt/trinity-2.8.5/util/insilico_read_normalization.pl
Whereas a Trinity source install would have left it in the folder util/insilico_read_normalization.pl
I can solve this by doing this to set my Trinity path instead.
TRINITY=$(realpath `which Trinity`)
TRINITYHOMEPATH=$(dirname $TRINITY)
nextgenusfs
commented
4 years ago So with Conda it should be setting your TRINITY_HOME to that /path/to/conda/opt/trinity-2.8.5. Funannotate looks first for TRINITYHOME and then TRINITY_HOME. Per Trinity usage, all of the commands are called using the $TRINITY_HOME location -- if the conda install is not doing this, then I'll fix the conda install as that is the way the Trinity developers have used the code.
hyphaltip
commented
4 years ago No this then was a carry over from previous run scripts where I had to set this variable in earlier versions of funannotate. I’ll remove setting those variables. Prob same for pasa too!
Jason Stajich, PhD jasonstajich.phd@gmail.com On Dec 15, 2019, 9:17 PM -0800, Jon Palmer notifications@github.com, wrote:
So with Conda it should be setting your TRINITY_HOME to that /path/to/conda/opt/trinity-2.8.5. Funannotate looks first for TRINITYHOME and then TRINITY_HOME. Per Trinity usage, all of the commands are called using the $TRINITY_HOME location -- if the conda install is not doing this, then I'll fix the conda install as that is the way the Trinity developers have used the code. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.
nextgenusfs
commented
4 years ago yeah, worth checking which build of conda though as well -- so for trinity only build5 I believe has the proper ENV variable exported into the environment. I don't understand the conda solver, but I do know it doesn't always grab the most recent build.
hyphaltip
commented
4 years ago Now i have problems that transdecoder plugin not installed in PASA in conda - do you have it in yours - looks like it is 2.4.1 installed.
[Mon Dec 16 14:08:44 2019] Running CMD: /opt/linux/centos/7.x/x86_64/pkgs/anaconda3/4.5.4/envs/funannotate/opt/pasa-2.4.1/pasa-plugins/transdecoder/TransDecoder.LongOrfs -t __all_transcripts.fasta -S
Can't exec "/opt/linux/centos/7.x/x86_64/pkgs/anaconda3/4.5.4/envs/funannotate/opt/pasa-2.4.1/pasa-plugins/transdecoder/TransDecoder.LongOrfs": No such file or directory Huh -- which funannotate version and which script? I thought I got rid of the separate transdecoder call.
In
train- expecting to find bin/util/insilico_read_normalization.pl But its installed in bin/insilico_read_normalization.pl in conda install so I assume should fix the train step to use the path as installed by conda version but just wanted to check if this is your intention of what goes in the bin path with the conda install?