annocomba/HOWTO.setup at master · reslp/annocomba · GitHub

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# !! expects a config file at data/config.yaml
#you can make a copy of data/config.yaml.template to start with

########################

#To download genemark go here: http://topaz.gatech.edu/GeneMark/license_download.cgi
#select GeneMark-ES/ET/EP+ ver 4.72_lic - LINUX 64 kernel 3.10- 5 (last downloaded 01.11.2024)
#use 64 bit version (software and key)
#this will get you a tarball: gmes_linux_64.tar.gz
link=http://topaz.gatech.edu/GeneMark/tmp/GMtoolasdfja;fsldkjVB/gmes_linux_64_4.tar.gz
keyfile=http://topaz.gatech.edu/GeneMark/tmp/GMtoolkalsfj;alfsdk;/gm_key_64.gz
cd data/external
wget $link
wget $keyfile
cd -
#if the key every runs out replace the keyfile (gzip) and rerun setup
# !!! update genemark path in config file - in the case of the example: data/external/gmes_linux_64_4
#################

#get maker from https://www.yandell-lab.org/software/maker.html
#you have to register and get the download link
#we have tested annocomba with maker-2.31.10.tgz

#now let's try maker-2.31.11.tgz
link=http://weatherby.genetics.utah.edu/maker_downloads/D3ED/1AD5/C6F9/79B7DA73577CC8BA3F41A0D4/maker-2.31.11.tgz
wget $link -O data/external/maker-2.31.11.tgz

# !! update maker path in config file

###############
#Repbase (optional - in this case I got the download link (Repbase-derived RepeatMasker libraries: RepBaseRepeatMaskerEdition-20181026.tar.gz ) from Repbase https://www.girinst.org/server/RepBase/index.php)
cd data/external
link=<get the link yourself>
wget $link
cd -

######################
#add physical protein evidence (optional)
#to location data/protein_evidence - is expected to be in *.gz, so be careful all files ending in *.gz in this directory will be interpreted as protein evidence

#add transcriptome evidence (optional)
#to data/transcripts/{name_of_sample} - unzipped
#if the file prefix is identical to the name of the sample to annotate it will be interpreted (by Maker) as transcript of this species, if not it will be interpreted as transcriptome of a related species

########### do dry run - expects data/confg.yaml and (because if so specified in the configfile) data/data.csv

#adjust your config file: data/config.yaml

./annocomba setup --maker

./annocomba setup --funannotate

./annocomba setup --maker --genemark --funannotate --verbose

######################################
#other things to setup - instructions pending
#######################
#not needed for setup step but during functional annotation

#Signal P ??

## get interproscan script
#rsync -avpuzP hahnc@vsc4.vsc.ac.at:/gpfs/data/fs71312/reslp/databases/interproscan-5.48-83.0 data/external/
#then specify position of interproscan.sh script in config file
#


./annocomba -t local --dry