Mercurial > repos > bebatut > group_humann2_uniref_abundances_to_go

annotate download_datasets.sh @ 0:13df6c6647fb draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
author bebatut
date Mon, 22 Feb 2016 07:11:20 -0500
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13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
bebatut
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1 #!/bin/bash
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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3 MY_PATH=`dirname "$0"`
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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4 data_dir=$MY_PATH"/data/"
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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6 if [ ! -d $data_dir ]; then
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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7 mkdir $data_dir
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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8 fi
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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10 cd $data_dir
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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12 echo "Download required databases"
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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13 echo "==========================="
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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15 if [ ! -f "go.obo" ]; then
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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16 echo "Download basic Gene Ontology..."
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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17 wget http://geneontology.org/ontology/go.obo
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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18 fi
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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19 if [ ! -f "goslim_metagenomics.obo" ]; then
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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20 echo "Download metagenomic slim Gene Ontology..."
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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21 wget http://www.geneontology.org/ontology/subsets/goslim_metagenomics.obo
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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22 fi
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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24 if [ ! -f "map_infogo1000_uniref50.txt" ]; then
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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25 echo "Download humann2 correspondance between Uniref50 and GO"
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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26 wget https://bitbucket.org/biobakery/humann2/raw/d1ac153083d48a5384e3b3d3597b9e36b1a4606e/humann2/data/misc/map_infogo1000_uniref50.txt.gz
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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27 gunzip map_infogo1000_uniref50.txt.gz
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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28 fi
13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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13df6c6647fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719
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30 echo ""