Mercurial > repos > iuc > busco
changeset 3:f18f0b887c31 draft
planemo upload commit 99b8e51a68074a214ca4415a635a426e80e4129b
| author | iuc |
|---|---|
| date | Fri, 14 Dec 2018 08:13:25 -0500 |
| parents | 382a4c19007f |
| children | 5ecdeca79a0d |
| files | busco.xml tool-data/busco.loc.sample |
| diffstat | 2 files changed, 12 insertions(+), 7 deletions(-) [+] |
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--- a/busco.xml Fri Oct 20 03:54:35 2017 -0400 +++ b/busco.xml Fri Dec 14 08:13:25 2018 -0500 @@ -9,16 +9,16 @@ && + if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi && + cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && + export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && + #if $adv.aug_prediction.augustus_mode == 'history': ## Using an augustus model from history, we need to unzip it and let augustus find it - cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && - mkdir -p 'augustus_dir/species/' && tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null && - - export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && #end if run_BUSCO.py
--- a/tool-data/busco.loc.sample Fri Oct 20 03:54:35 2017 -0400 +++ b/tool-data/busco.loc.sample Fri Dec 14 08:13:25 2018 -0500 @@ -5,9 +5,14 @@ # # Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html # -# "/some/path/arthropoda/" would be the last column in the line -# If this were for the mm10 mouse genome, the resulting entry would look like: +# "/some/path/datasets/" would be the last column in the line +# If this were for the /some/path/lineage/cyanobacteria_odb9/ reference dataset: # -#arthropoda_2.0 arthropoda_2.0 /some/path/arthropoda/ +# $ ls /some/path/datasets/cyanobacteria_odb9/ +# ancestral ancestral_variants dataset.cfg hmms info lengths_cutoff prfl scores_cutoff +# +# the resulting entry would look like: +# +#cyanobacteria_odb9 cyanobacteria /some/path/datasets/ # #