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edna
reference_database
Commits
007d10a8
Commit
007d10a8
authored
Jan 23, 2020
by
peguerin
Browse files
build rapidrun ref db
parent
e8d09b0a
Changes
1
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Inline
Side-by-side
build_bdr_rapidrun.sh
0 → 100644
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007d10a8
###############################################################################
## RAPIDRUN
SINGULARITY_SIMG
=
"/media/superdisk/utils/conteneurs/obitools.simg"
singularity shell
--bind
/media/superdisk:/media/superdisk
$SINGULARITY_SIMG
source
./config.sh
for
marker
in
`
awk
-F
,
'{ print $1}'
infos/markers.csv
`
do
primer3
=
`
grep
$marker
infos/markers.csv |
cut
-d
,
-f2
`
primer5
=
`
grep
$marker
infos/markers.csv |
cut
-d
,
-f3
`
echo
$marker
$primer3
$primer5
MARKER_REF_DB_DIR
=
"../"
${
marker
}
"_reference_database"
mkdir
-p
"
${
MARKER_REF_DB_DIR
}
"
for
DX
in
`
ls
"
${
rd_prefix
}
"
*
dx
`
do
DX_PATH
=
`
readlink
-f
$DX
`
ln
-s
$DX_PATH
$MARKER_REF_DB_DIR
/
$DX
done
cd
"
${
MARKER_REF_DB_DIR
}
"
ecoPCR
-d
"
${
rd_prefix
}
"
-e
"
${
ecoPCR_e
}
"
-l
"
${
ecoPCR_l
}
"
-L
"
${
ecoPCR_L
}
"
"
${
primer5
}
"
"
${
primer3
}
"
>
v_
"
${
rd_prefix
}
"
.ecopcr
obigrep
-d
"
${
rd_prefix
}
"
--require-rank
=
species
--require-rank
=
genus
--require-rank
=
family v_
"
${
rd_prefix
}
"
.ecopcr
>
v_
"
${
rd_prefix
}
"
_clean.fasta
obiuniq
-d
"
${
rd_prefix
}
"
v_
"
${
rd_prefix
}
"
_clean.fasta
>
v_
"
${
rd_prefix
}
"
_clean_uniq.fasta
obigrep
-d
"
${
rd_prefix
}
"
--require-rank
=
family v_
"
${
rd_prefix
}
"
_clean_uniq.fasta
>
v_
"
${
rd_prefix
}
"
_clean_uniq_clean.fasta
obiannotate
--uniq-id
v_
"
${
rd_prefix
}
"
_clean_uniq_clean.fasta
>
db_
"
${
rd_prefix
}
"
.fasta
cd
../reference_database
done
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