Commit a0721117 authored by peguerin's avatar peguerin
Browse files

singularity container obitools

parent c2c2d5c2
# Build a reference database
## load an environment with obitools
SINGULARITY_SIMG="/media/superdisk/utils/conteneurs/obitools.simg"
singularity shell --bind /media/superdisk:/media/superdisk $SINGULARITY_SIMG
# configure arguments value
source ./config.sh
# download the sequences
......@@ -43,3 +50,7 @@ obiannotate --uniq-id v_"${rd_prefix}"_clean_uniq_clean.fasta > db_"${rd_prefix}
#add spygen taxonomy [doesn't seems to work]
#obitaxonomy -d "${rd_prefix}" -a 'Cnasus_Ctoxo_Tsouffia':'species':10000087
#obitaxonomy -d "${rd_prefix}" -a 'Cidella_Hmolitrix':'species':10000088
obiconvert --skip-on-error --fasta -t ./TAXO --ecopcrdb-output=mitofish/"${rd_prefix}" mitofish/mitogene_12S.fasta
obiconvert --skip-on-error --embl -t ./TAXO --ecopcrdb-output="${rd_prefix}" EMBL/rel_std_*.dat
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