Computational Biology Lab Wiki

We have installed the program SEQenv version 1.30. It's intalled in a virtual environment of python 2.7.

To work with SEQenv users must activate the virtual environment first. Example of a job script:

#!/bin/bash

source /home/soft/virtenvs/python2/bin/activate

sh /home/usuaris/xavier.roijals/proves/provaSeqenv2/seqenvMonegros98.sh

deactivate

The lines “source /home/soft/virtenvs/python2/bin/activate” and “deactivate” are needed to activate the python virtual environment (and deactivate it when the work is finished).

This script will let you connect to the virtual environment and execute the example script seqenvMonegros.sh. We can see in this script:

#!/bin/bash

### rsync fitxers en local
now=`date +%d.%m.%Y`
rsync -arh --delete /home/usuaris/ceab/blastdb/nt* /tmp/blastdb_$now

export PATH=/home/soft/ncbi-blast-2.2.28+/bin:$PATH

cd /home/usuaris/xavier.roijals/proves/provaSeqenv


seqenv /home/usuaris/xavier.roijals/proves/provaSeqenv/otus_nch_16S_def_ed_mod.fasta --abundances /home/usuaris/xavier.roijals/proves/provaSeqenv/otutable_Monegros_16S_sorted_wt_filtered_ed2_freqs.tsv --min_identity 0.98 --max_targets 500 --num_threads 10 --search_db=/tmp/blastdb_08.10.2018/nt --out_dir=/home/usuaris/xavier.roijals/proves/provaSeqenv/outputdirMonegros98 2> /home/usuaris/xavier.roijals/proves/provaSeqenv/errorsSeqenv98.txt > /home/usuaris/xavier.roijals/proves/provaSeqenv/sortidaSeqenv98.txt

(It's important that these last script has execution permissions (chmod +x).)