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install-notes-ryan-mclaughlin.txt
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# Notes for installing and running MP 3.0
######################################################################
######################## Clone from BitBucket ########################
######################################################################
git clone --recurse-submodules https://[email protected]/BCB2/metapathways_engcyc.git
######################################################################
######################################################################
########################## Create Conde Env ##########################
######################################################################
conda create -n mpath3_demo python=3
conda activate mpath3_demo
######################################################################
######################################################################
######################## Install Dependencies ########################
######################################################################
MP_HOME=~/dev/metapathways_engcyc
# BLAST
conda install -c bioconda blast
cp ~/anaconda3/envs/mpath3_demo/bin/blastn ${MP_HOME}/executables/linux/
cp ~/anaconda3/envs/mpath3_demo/bin/blastp ${MP_HOME}/executables/linux/
cp ~/anaconda3/envs/mpath3_demo/bin/makeblastdb ${MP_HOME}/executables/linux/
# Create directory to store binaries
mkdir ${MP_HOME}/executables/linux
### Build some binaires that are packaged with MP 3.0 ###
### BWA
cd ${MP_HOME}/executables/source/bwa
make
cp bwa ${MP_HOME}/executables/linux/
### FAST
cd ${MP_HOME}/executables/source/FAST
make
cp fastal ${MP_HOME}/executables/linux/
cp fastdb ${MP_HOME}/executables/linux/
### Prodigal
cd ${MP_HOME}/executables/source/prodigal
make
cp prodigal ${MP_HOME}/executables/linux/
### RPKM
cd ${MP_HOME}/executables/source/rpkm
make
cp rpkm ${MP_HOME}/executables/linux/
### t-RNAScan
cd ${MP_HOME}/executables/source/trnascan
make
cp trnascan-1.4 ${MP_HOME}/executables/linux/
######################################################################
######################################################################
#################### Edit Config and Params files ####################
######################################################################
# Templates located in ${MP_HOME}/resources/
# Stored in ${MP_HOME}/config/
######################################################################
######################################################################
############################## Run Demo ##############################
######################################################################
source ~/dev/metapathways_engcyc/MetaPathwaysrc
mkdir ~/Projects/MP3_Demo
cd ~/Projects/MP3_Demo
~/dev/metapathways_engcyc/MetaPathways.py -i ~/dev/metapathways_engcyc/regtests/input/B1.fasta -o B1_MPout/ -p template_param.txt -c template_config.txt
# NOTE: PATHOLOGIC INPUT Failed!
# Go to `./libs/python_scripts/MetaPathways_create_genbank_ptinput_sequin.py` line 889
# Comment out `and plain_or_gz_file_exists(options.protein_sequences):`
# Re-Run all.
~/dev/metapathways_engcyc/MetaPathways.py -i ~/dev/metapathways_engcyc/regtests/input/B2.fas -o B2_MPout/ -p template_param.txt -c template_config.txt
~/dev/metapathways_engcyc/MetaPathways.py -i ~/dev/metapathways_engcyc/regtests/input/B3.fasta -o B3_MPout/ -p template_param.txt -c template_config.txt
# PATHOLOGIC gets skipped.
# Try running this:
/home/ryan/dev/metapathways_engcyc//libs/python_scripts/MetaPathways_run_pathologic.py --reactions /home/ryan/Projects/MP3_Demo/B3_MPout/B3/results//annotation_table//B3.metacyc.orf.annots.txt --ptoolsExec /home/ryan/pathway-tools/pathway-tools -i /home/ryan/Projects/MP3_Demo/B3_MPout/B3/ptools// -p /home/ryan/ptools-local/pgdbs/user/b3cyc -s B3 --wtd --annotation-table /home/ryan/Projects/MP3_Demo/B3_MPout/B3/results//annotation_table//B3.functional_and_taxonomic_table.txt --ncbi-tree /home/ryan/dev/MetaPathways_DBs///ncbi_tree/ncbi_taxonomy_tree.txt --ncbi-megan-map /home/ryan/dev/MetaPathways_DBs///ncbi_tree/ncbi.map --output-pwy-table /home/ryan/Projects/MP3_Demo/B3_MPout/B3/results//pgdb//b3.pwy.txt
######################################################################
1. git clone from Engcyc BitBucket
2. example data in MP/regtests
3. Use A1.fasta
4. Set MP Path:
source MP/MetaPathwaysrc
5. Main script is MetaPathways.py
6. MetaPathways.py -i ../input/ -o ../output/ -p [parameter_file] -c [config_file]
7. Template config and params are in MP/resources
8. yes = run if not run
skip = don't run
redo = re-run no matter what
9. MP executables are in MP/executables/
10. `-v` prints out all individual commands
11. make a ghost (place-holder) of pathway-tools exec
12. inputs are only assembled (meta)genomes
13. for RPKM you needs a `reads` directory in input dir containing PE `_R1.fastq.gz` `_R2.fastq.gz`
they can be gzipped or not
must be fastqs
14. MakeFile is not functional