Differences

This shows you the differences between two versions of the page.

--- users:catalogue:seqenv [2018/10/10 07:46] – created admins_ceab
+++ users:catalogue:seqenv [2018/10/15 10:56] (current) – admins_ceab
@@ Line 10: / Line 10: @@
 source /home/soft/virtenvs/python2/bin/activate
-/home/usuaris/xavier.roijals/proves/provaSeqenv2/seqenvMonegros98.sh
+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).)