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Comands used to build the Rust Expression Browser

These commands follow from those described for initial set up at https://github.com/JIC-CSB/expvip-ansible, particularly ensure that activate.sh has been sourced Commands are all run from the expvip_web directory

Set up BLAST server that is on the homepage of the browser

sequenceserver -p 3000 -m -d /home/expvip/data
sequenceserver -p 3000 -d /home/expvip/data # Quit this after the message appears saying sequenceserver has started

Set up MySQL databases

These contain information on the samples

rake db:setup
rake db:migrate

Initial provision of databases

This adds information on used fields and which are shown by default

rake load_data:factor[../custom_config/FactorOrder.tsv]
rake load_data:default_factor_order[../custom_config/default_factor_order.txt]

Load the metadata files

for file in $(ls ../metadata_files/*metadata.txt)
do
    rake load_data:metadata["$file"]
done

Load gene sets

This adds the transcripts to the MySQL databases

rake load_data:de_novo_genes[PST-130,../data/PST130_transcripts.fan]

rake load_data:de_novo_genes[PST-104E,../data/Pucstr1_GeneCatalog_CDS_20170922.fasta]

rake load_data:gff_produced_genes[IWGSCv1.1,../data/IWGSC_v1.1_20170706_cds.fasta]

Load in homology data for wheat genes

This allows the visualtion of gene homoeologues and the creation of ternary plots

rake load_data:homology_pairs[IWGSCv1.1,../custom_config/homologies_ta_compara_plants_41_94.txt]

Load default genes

This controls what genes are suggested to users as examples

rake load_data:sample_genes[../custom_config/default_genes.csv]

Start the mongodb service

This requires sudo rights

sudo service mongod start

Load in expression values

This adds the expression data to the mongodb, a log file is removed periodically due to storage limitations

# Adams et al., in press

rake load_data:values_mongo["Adams\ et\ al.\,\ in\ press",PST-130,tpm,../PST130_expression/merged_Adams_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Adams\ et\ al.\,\ in\ press",PST-130,count,../PST130_expression/merged_Adams_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Adams\ et\ al.\,\ in\ press",PST-104E,tpm,../PST_104E_expression/merged_Adams_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Adams\ et\ al.\,\ in\ press",PST-104E,count,../PST_104E_expression/merged_Adams_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Adams\ et\ al.\,\ in\ press",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Adams_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Adams\ et\ al.\,\ in\ press",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Adams_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# Boshoff et al., 2020

rake load_data:values_mongo["Boshoff\ et\ al.\,\ 2020",PST-130,tpm,../PST130_expression/merged_Boshoff_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Boshoff\ et\ al.\,\ 2020",PST-130,count,../PST130_expression/merged_Boshoff_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Boshoff\ et\ al.\,\ 2020",PST-104E,tpm,../PST_104E_expression/merged_Boshoff_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Boshoff\ et\ al.\,\ 2020",PST-104E,count,../PST_104E_expression/merged_Boshoff_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Boshoff\ et\ al.\,\ 2020",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Boshoff_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Boshoff\ et\ al.\,\ 2020",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Boshoff_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# Bueno-Sancho et al., 2017

rake load_data:values_mongo["Bueno-Sancho\ et\ al.\,\ 2017",PST-130,tpm,../PST130_expression/merged_Bueno-Sancho_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Bueno-Sancho\ et\ al.\,\ 2017",PST-130,count,../PST130_expression/merged_Bueno-Sancho_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Bueno-Sancho\ et\ al.\,\ 2017",PST-104E,tpm,../PST_104E_expression/merged_Bueno-Sancho_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Bueno-Sancho\ et\ al.\,\ 2017",PST-104E,count,../PST_104E_expression/merged_Bueno-Sancho_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Bueno-Sancho\ et\ al.\,\ 2017",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Bueno-Sancho_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Bueno-Sancho\ et\ al.\,\ 2017",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Bueno-Sancho_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# Cantu et al., 2013

rake load_data:values_mongo["Cantu\ et\ al.\,\ 2013",PST-130,tpm,../PST130_expression/merged_Cantu_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Cantu\ et\ al.\,\ 2013",PST-130,count,../PST130_expression/merged_Cantu_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Cantu\ et\ al.\,\ 2013",PST-104E,tpm,../PST_104E_expression/merged_Cantu_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Cantu\ et\ al.\,\ 2013",PST-104E,count,../PST_104E_expression/merged_Cantu_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Cantu\ et\ al.\,\ 2013",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Cantu_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Cantu\ et\ al.\,\ 2013",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Cantu_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# Corredor-Moreno et al., in press

rake load_data:values_mongo["Corredor-Moreno\ et\ al.\,\ in\ press",PST-130,tpm,../PST130_expression/merged_Corredor-Moreno_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Corredor-Moreno\ et\ al.\,\ in\ press",PST-130,count,../PST130_expression/merged_Corredor-Moreno_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Corredor-Moreno\ et\ al.\,\ in\ press",PST-104E,tpm,../PST_104E_expression/merged_Corredor-Moreno_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Corredor-Moreno\ et\ al.\,\ in\ press",PST-104E,count,../PST_104E_expression/merged_Corredor-Moreno_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Corredor-Moreno\ et\ al.\,\ in\ press",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Corredor-Moreno_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Corredor-Moreno\ et\ al.\,\ in\ press",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Corredor-Moreno_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# Dobon et al., 2016

rake load_data:values_mongo["Dobon\ et\ al.\,\ 2016",PST-130,tpm,../PST130_expression/merged_Dobon_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Dobon\ et\ al.\,\ 2016",PST-130,count,../PST130_expression/merged_Dobon_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Dobon\ et\ al.\,\ 2016",PST-104E,tpm,../PST_104E_expression/merged_Dobon_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Dobon\ et\ al.\,\ 2016",PST-104E,count,../PST_104E_expression/merged_Dobon_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Dobon\ et\ al.\,\ 2016",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Dobon_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Dobon\ et\ al.\,\ 2016",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Dobon_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# Garnica et al., 2013

rake load_data:values_mongo["Garnica\ et\ al.\,\ 2013",PST-130,tpm,../PST130_expression/merged_Garnica_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Garnica\ et\ al.\,\ 2013",PST-130,count,../PST130_expression/merged_Garnica_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Garnica\ et\ al.\,\ 2013",PST-104E,tpm,../PST_104E_expression/merged_Garnica_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Garnica\ et\ al.\,\ 2013",PST-104E,count,../PST_104E_expression/merged_Garnica_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Garnica\ et\ al.\,\ 2013",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Garnica_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Garnica\ et\ al.\,\ 2013",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Garnica_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# Hubbard et al., 2015

rake load_data:values_mongo["Hubbard\ et\ al.\,\ 2015",PST-130,tpm,../PST130_expression/merged_Hubbard_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Hubbard\ et\ al.\,\ 2015",PST-130,count,../PST130_expression/merged_Hubbard_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Hubbard\ et\ al.\,\ 2015",PST-104E,tpm,../PST_104E_expression/merged_Hubbard_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Hubbard\ et\ al.\,\ 2015",PST-104E,count,../PST_104E_expression/merged_Hubbard_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Hubbard\ et\ al.\,\ 2015",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Hubbard_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Hubbard\ et\ al.\,\ 2015",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Hubbard_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# Radhakrishnan et al., 2013

rake load_data:values_mongo["Radhakrishnan\ et\ al.\,\ 2019",PST-130,tpm,../PST130_expression/merged_Radhakrishnan_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Radhakrishnan\ et\ al.\,\ 2019",PST-130,count,../PST130_expression/merged_Radhakrishnan_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Radhakrishnan\ et\ al.\,\ 2019",PST-104E,tpm,../PST_104E_expression/merged_Radhakrishnan_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Radhakrishnan\ et\ al.\,\ 2019",PST-104E,count,../PST_104E_expression/merged_Radhakrishnan_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Radhakrishnan\ et\ al.\,\ 2019",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Radhakrishnan_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Radhakrishnan\ et\ al.\,\ 2019",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Radhakrishnan_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# Schwessinger et al., 2018

rake load_data:values_mongo["Schwessinger\ et\ al.\,\ 2018",PST-130,tpm,../PST130_expression/merged_Schwessinger_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["Schwessinger\ et\ al.\,\ 2018",PST-130,count,../PST130_expression/merged_Schwessinger_exp_PST130_count_0.tsv]

rake load_data:values_mongo["Schwessinger\ et\ al.\,\ 2018",PST-104E,tpm,../PST_104E_expression/merged_Schwessinger_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["Schwessinger\ et\ al.\,\ 2018",PST-104E,count,../PST_104E_expression/merged_Schwessinger_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["Schwessinger\ et\ al.\,\ 2018",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_Schwessinger_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["Schwessinger\ et\ al.\,\ 2018",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_Schwessinger_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log

# van Schalwyk et al., in press

rake load_data:values_mongo["van\ Schalwyk\ et\ al.\,\ in\ press",PST-130,tpm,../PST130_expression/merged_van_Schalwyk_exp_PST130_tpm_0.tsv]
rake load_data:values_mongo["van\ Schalwyk\ et\ al.\,\ in\ press",PST-130,count,../PST130_expression/merged_van_Schalwyk_exp_PST130_count_0.tsv]

rake load_data:values_mongo["van\ Schalwyk\ et\ al.\,\ in\ press",PST-104E,tpm,../PST_104E_expression/merged_van_Schalwyk_exp_PST_104E_tpm_0.tsv]
rake load_data:values_mongo["van\ Schalwyk\ et\ al.\,\ in\ press",PST-104E,count,../PST_104E_expression/merged_van_Schalwyk_exp_PST_104E_count_0.tsv]

rake load_data:values_mongo["van\ Schalwyk\ et\ al.\,\ in\ press",IWGSCv1.1,tpm,../IWGSC_v1_1_expression/merged_van_Schalwyk_exp_IWGSC_v1_1_tpm_0.tsv]
rake load_data:values_mongo["van\ Schalwyk\ et\ al.\,\ in\ press",IWGSCv1.1,count,../IWGSC_v1_1_expression/merged_van_Schalwyk_exp_IWGSC_v1_1_count_0.tsv]

rm /home/expvip/expvip_web/log/development.log