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comparison busco.xml @ 3:f18f0b887c31 draft

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planemo upload commit 99b8e51a68074a214ca4415a635a426e80e4129b
author iuc
date Fri, 14 Dec 2018 08:13:25 -0500
parents 382a4c19007f
children 5ecdeca79a0d
comparison
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2:382a4c19007f 3:f18f0b887c31
7 <command><![CDATA[ 7 <command><![CDATA[
8 export BUSCO_CONFIG_FILE='busco_config.ini' 8 export BUSCO_CONFIG_FILE='busco_config.ini'
9 9
10 && 10 &&
11 11
12 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
13 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
14 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
15
12 #if $adv.aug_prediction.augustus_mode == 'history': 16 #if $adv.aug_prediction.augustus_mode == 'history':
13 ## Using an augustus model from history, we need to unzip it and let augustus find it 17 ## Using an augustus model from history, we need to unzip it and let augustus find it
14 18
15 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
16
17 mkdir -p 'augustus_dir/species/' && 19 mkdir -p 'augustus_dir/species/' &&
18 20
19 tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null && 21 tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null &&
20
21 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
22 #end if 22 #end if
23 23
24 run_BUSCO.py 24 run_BUSCO.py
25 --in '${input}' 25 --in '${input}'
26 --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}' 26 --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}'