Mercurial > repos > petrn > repeatexplorer
comparison fetch_databases.sh @ 0:f6ebec6e235e draft
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| author | petrn |
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| date | Thu, 19 Dec 2019 13:46:43 +0000 |
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| -1:000000000000 | 0:f6ebec6e235e |
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| 1 #!/bin/bash | |
| 2 #set -euo pipefail | |
| 3 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" | |
| 4 echo "protein databases necessary for full clustering analysis" | |
| 5 echo "are downloaded from bitbucket repository using git" | |
| 6 echo "" | |
| 7 cd $DIR | |
| 8 git clone https://bitbucket.org/petrnovak/re_databases.git 2> $DIR/.fetchdb.log | |
| 9 GITEXIT=$? | |
| 10 if [ $GITEXIT -eq "0" ] | |
| 11 then | |
| 12 echo "databases successfully downloaded" | |
| 13 ln -sf $DIR/re_databases/* $DIR/databases/ | |
| 14 fi | |
| 15 # cat $DIR/.fetchdb.log | |
| 16 if [ $GITEXIT -eq "128" ] | |
| 17 then | |
| 18 if grep -q -F "Authentication failed" $DIR/.fetchdb.log | |
| 19 then | |
| 20 echo "get login credential from (neumann at umbr.cas.cz)!" | |
| 21 fi | |
| 22 if grep -q -F "already exist" $DIR/.fetchdb.log | |
| 23 then | |
| 24 echo "repository alredy exists, updating..." | |
| 25 cd $DIR/re_databases | |
| 26 git pull && ln -f -s $DIR/re_databases/* $DIR/databases/ && find . -type f -exec touch {} + | |
| 27 fi | |
| 28 | |
| 29 fi | |
| 30 | |
| 31 | |
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