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vidjil
vidjil
Commits
403773ad
Commit
403773ad
authored
Feb 26, 2016
by
HERBERT Ryan
Browse files
task.py put arg_cmd back in the mixcr command
parent
ca491ad7
Changes
1
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Inline
Side-by-side
server/web2py/applications/vidjil/models/task.py
View file @
403773ad
...
...
@@ -234,7 +234,7 @@ def run_mixcr(id_file, id_config, id_data, id_fuse, clean_before=False, clean_af
mixcr
=
defs
.
DIR_MIXCR
+
'mixcr'
cmd
=
mixcr
+
' align --save-reads -t 1 -r '
+
report
+
'.aln'
#+ output_filename
cmd
+=
' '
+
seq_file
+
' '
+
out_alignments
cmd
+=
' '
+
arg_cmd
+
' '
+
seq_file
+
' '
+
out_alignments
cmd
+=
' && '
+
mixcr
+
' assemble -t 1 -r '
+
report
+
'.asmbl '
+
out_alignments
+
' '
+
out_clones
cmd
+=
' && '
+
mixcr
+
' exportClones -t 1 --format vidjil -germline -id -name -reads -sequence -top -seg -s '
+
out_clones
+
' '
+
out_results
...
...
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