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#-----Gene Prediction
snaphmm= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species= #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff= #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
est2genome=01 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=01 #infer predictions from protein homology, 1 = yes, 0 = no
trna=1 #find tRNAs with tRNAscan, 1 = yes, 0 = no
snoscan_rrna=./test_data/Os-rRNA.fa #rRNA file to have Snoscan find snoRNAs
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no

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Once you have logged in to your instance using Web Shell or ssh of your MAKER-P instance, you must mount your attached volume to access it

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 Code Block
# Check to see if the volume is mounted or not. As you can see, the volume is mounted on /dev/vdc

$ df -h
Filesystem      Size  Used Avail Use% Mounted on
udev            3.9G     0  3.9G   0% /dev
tmpfs           799M  8.7M  790M   2% /run
/dev/vda1        20G  8.4G   11G  44% /
tmpfs           3.9G  1.1M  3.9G   1% /dev/shm
tmpfs           5.0M     0  5.0M   0% /run/lock
tmpfs           3.9G     0  3.9G   0% /sys/fs/cgroup
/dev/vdb         79G   56M   75G   1% /scratch
tmpfs           799M     0  799M   0% /run/user/14135
/dev/vdc        197G   60M  187G   1% /vol_c
 
# You can cd into the /vol_c and run all your analyses there from now on
 
$ cd /vol_c
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