Differences

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

--- users:catalogue:seqenv [2018/10/10 07:50] – 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_$now
-The lines "source /home/soft/virtenvs/python2/bin/activate" and "deactivate" are needed to activate the python virtual environment (and deactivate it when the work is finished).
+export PATH=/home/soft/ncbi-blast-2.2.28+/bin:$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).)