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Merge pull request #13 from pgdurand/prepV5
Prep v5
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| # Provide here the path to the home directory of an | ||
| # Oracle JRE release 1.7 or above | ||
| # | ||
| JAVA_HOME=/usr/local/jre1.7 [update as needed] | ||
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| export JAVA_HOME | ||
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| # Provide here the path to the home directory of a Ant | ||
| # 1.6.5 or above. By default, DBMS installer will use its | ||
| # 1.9 or above. By default, DBMS installer will use its | ||
| # own Ant. | ||
| # | ||
| ANT_HOME=$PWD/ant | ||
| export ANT_HOME | ||
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| PATH=$JAVA_HOME/bin:$ANT_HOME/bin:$PATH | ||
| PATH=$ANT_HOME/bin:$PATH | ||
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| export PATH | ||
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| @@ -0,0 +1,62 @@ | ||
| #!/usr/bin/env bash | ||
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| # ================================================= | ||
| # Test script for BeeDeeM legacy installer. | ||
| # To be used directly on the command-line. | ||
| # DO NOT use for Singularity/Docker installations. | ||
| # | ||
| # How to? | ||
| # | ||
| # Step 1: install BeeDeeM as stated at: | ||
| # https://pgdurand.gitbook.io/beedeem/installation/installation#legacy-installation | ||
| # | ||
| # Step 2: run test as follows: | ||
| # ./test_bdm.sh | ||
| # -- | ||
| # P. Durand (SeBiMER, Ifremer), last updated on Jan 2023 | ||
| # ================================================= | ||
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| # == TEST 1 =========================================== | ||
| echo "*** TEST 1: Start simple bank installation" | ||
| # set log mode to console (otherwise default is a log file located in KL_WORKING_DIR | ||
| export KL_LOG_TYPE=console | ||
| # Set the bank to install | ||
| # This is a '.dsc' file located in BeeDeeM installation path at ${beedeem-home}/conf/descriptors | ||
| DESCRIPTOR="SwissProt_human" | ||
| # start BeeDeeM with 'install' command | ||
| ./bdm install -desc ${DESCRIPTOR} | ||
| # check whether command succeeded or not | ||
| if [ $? -eq 0 ]; then | ||
| echo "TEST 1: SUCCESS" | ||
| else | ||
| echo "TEST 1: FAILED." | ||
| exit 1 | ||
| fi | ||
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| # == TEST 2 =========================================== | ||
| echo "*** TEST 2: list installed bank" | ||
| # reset log mode to file | ||
| export KL_LOG_TYPE=file | ||
| # start BeeDeeM with 'info' command | ||
| ./bdm info -d all -f txt | ||
| if [ $? -eq 0 ]; then | ||
| echo "TEST 2: SUCCESS" | ||
| else | ||
| echo "TEST 2: FAILED. Review log file in: @KL_WORKING_DIR@" | ||
| exit 1 | ||
| fi | ||
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| # == TEST 3 =========================================== | ||
| # Change default log file name to something else | ||
| export KL_LOG_FILE=query.log | ||
| SW_ENTRY="ZZZ3_HUMAN" | ||
| echo "*** TEST 3: query bank for entry: $SW_ENTRY" | ||
| # start BeeDeeM with 'query' command | ||
| ./bdm query -d protein -f txt -i $SW_ENTRY | ||
| if [ $? -eq 0 ]; then | ||
| echo "TEST 3: SUCCESS" | ||
| else | ||
| echo "TEST 3: FAILED. Review log file: @KL_WORKING_DIR@" | ||
| exit 1 | ||
| fi | ||
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