Mercurial > repos > iuc > ebi_metagenomics_run_downloader
annotate download_ebi_metagenomics_run_data @ 2:6155fa39a899 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
author | iuc |
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date | Sat, 21 Jan 2017 14:40:54 -0500 |
parents | e2e9fae080ad |
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e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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1 #!/usr/bin/env bash |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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2 set -e |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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3 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
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4 python_script=$1 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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5 run_id=$2 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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changeset
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6 information_type=$3 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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7 information_to_download=$4 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
changeset
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8 chunk_type=$5 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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9 output_file=$6 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
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10 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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11 touch $output_file |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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12 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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13 run_link=$(python $python_script getRunLink $run_id) |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
changeset
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14 run_link="$run_link/$information_type/$information_to_download" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
changeset
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15 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
changeset
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16 if [[ $chunk_type == 'multiple_chunks' ]]; then |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
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17 chunk_nb=$(curl "$run_link/chunks") |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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18 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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19 if [[ "$chunk_nb" < 1 ]]; then |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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20 >&2 echo "-----" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
changeset
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21 >&2 echo "ERROR" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
changeset
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22 >&2 echo "-----" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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23 >&2 echo "No data are found for this link:" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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changeset
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24 >&2 echo "$run_link/chunks" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
changeset
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25 >&2 echo "-----" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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26 exit 6 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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changeset
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27 fi |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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changeset
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28 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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29 for i in $(seq "$chunk_nb"); do |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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30 curl "$run_link/chunks/$i" | gunzip >> $output_file |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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31 done |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
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32 else |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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33 curl "$run_link" >> $output_file |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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34 fi |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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35 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
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36 if [ ! -s $output_file ]; then |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
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37 >&2 echo "-----" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
changeset
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38 >&2 echo "ERROR" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
diff
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39 >&2 echo "-----" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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40 >&2 echo "The output file is empty probably because the following link is not working:" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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41 >&2 echo "$run_link" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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42 >&2 echo "-----" |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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43 exit 6 |
e2e9fae080ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
iuc
parents:
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44 fi |