diff --git a/deploy/alpha_6.2_58_vcellservice.include b/deploy/alpha_6.2_58_vcellservice.include index 913897942b..36245e37a3 100755 --- a/deploy/alpha_6.2_58_vcellservice.include +++ b/deploy/alpha_6.2_58_vcellservice.include @@ -95,7 +95,7 @@ vcell_I4J_pathto_secretsDir=/usr/local/deploy vcell_I4J_use_vagrant=false vcell_I4J_install_jres_into_user_home=false vcell_I4J_updateSiteBaseUrl=http://vcell.org/webstart/$vcell_site_camel -vcell_I4J_pathto_mavenRootDir=/opt/build/VCell +vcell_I4J_pathto_mavenRootDir=/opt/build/vcell vcell_I4J_pathto_installerFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/VCell.install4j vcell_I4J_pathto_vcellIcnsFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/icons/vcell.icns vcell_I4J_pathto_jreDir=$HOME/.install4j6/jres diff --git a/deploy/alpha_6.2_59_vcellservice.include b/deploy/alpha_6.2_59_vcellservice.include new file mode 100755 index 0000000000..60acd511ac --- /dev/null +++ b/deploy/alpha_6.2_59_vcellservice.include @@ -0,0 +1,118 @@ +#!/usr/bin/env bash + +shopt -s -o nounset + +_site="alpha" +_version="6.2" +_build="59" +vcell_server_os="linux64" + +vcell_site_lower=`echo $_site | tr '[:upper:]' '[:lower:]'` +vcell_site_upper=`echo $_site | tr '[:lower:]' '[:upper:]'` +vcell_site_camel="${vcell_site_upper:0:1}${vcell_site_lower:1:100}" +vcell_version=${_version} +vcell_build=${_build} +vcell_softwareVersionString="${vcell_site_camel}_Version_${vcell_version}_build_${vcell_build}" +unset _site +unset _version +unset _build + +vcell_applicationId="1471-8022-1038-5554" +vcell_server_sitedir="/share/apps/vcell2/deployed_new/$vcell_site_lower" +vcell_pathto_sitedir="/share/apps/vcell2/deployed_new/$vcell_site_lower" + +vcell_user="vcell" +vcell_servicehost="vcell-service.cam.uchc.edu" +vcell_apihost="vcellapi.cam.uchc.edu" +vcell_apiport=8080 + +# +# Nagios monitor port +# (rel=33330, beta=33331, alpha=33332, test=-33333, test2=-33334, test3=-33335, test4=-33336) +# +vcell_monitor_queryport=33332 + +vcell_rmihost="vcell-rmi-alpha.cam.uchc.edu" +vcell_rmiport_low=-1 +vcell_rmiport_high=40106 +vcell_rmihosts="vcell-rmi-alpha.cam.uchc.edu:40106" +# still using bioformats_ALPHA_6_2_54.jar for later versions ... need to replace with ImageJ support. +vcell_bioformatsJarFile="bioformats_ALPHA_6_2_54.jar" +vcell_bioformatsJarDownloadURL="http://vcell.org/webstart/$vcell_site_camel/$vcell_bioformatsJarFile" + +vcell_vcellClientJarFileName="vcell-client-0.0.1-SNAPSHOT.jar" +vcell_vcellServerJarFileName="vcell-server-0.0.1-SNAPSHOT.jar" +vcell_vcellApiJarFileName="vcell-api-0.0.1-SNAPSHOT.jar" +vcell_vcellAdminJarFileName="vcell-admin-0.0.1-SNAPSHOT.jar" + +vcell_jms_url="failover:(tcp://code2.cam.uchc.edu:61617)?timeout=120000" +vcell_jms_user=clientUser + +# +# Oracle on server +# +vcell_database_url="jdbc:oracle:thin:@VCELL-DB.cam.uchc.edu:1521/vcelldborcl.cam.uchc.edu" +vcell_database_driver=oracle.jdbc.driver.OracleDriver +vcell_database_user=vcell + +# +# Postgres on locahost +# +#vcell_database_url="jdbc:postgresql://localhost:5432/schaff" +#vcell_database_driver=org.postgresql.Driver +#vcell_database_user=schaff + +vcell_amplistor_url="http://obj1.cam.uchc.edu:8080/namespace/service_vcell/" +vcell_amplistor_user=vcell + +vcell_mongodb_host=mongo.cam.uchc.edu +vcell_mongodb_port=27017 +vcell_mongodb_database=$vcell_site_upper +vcell_mongodb_collection=logging + +vcell_smtp_host=vdsmtp.cam.uchc.edu +vcell_smtp_port=25 +vcell_smtp_email="VCell_Support@uchc.edu" + +vcell_common_jre=/share/apps/vcell2/java/jdk1.8.0_66/bin/java +vcell_common_jre_rmi=/usr/java/jdk1.8.0_66/jre/bin/java + +vcell_rmiservice_high_jmxport=12305 +vcell_rmiservice_http_jmxport=12304 +vcell_vcellservice_jmxport=12360 + +vcell_primary_datadir=/share/apps/vcell3/users/ +vcell_secondary_datadir=/share/apps/vcell3/users/ +vcell_parallel_datadir=/state/partition1/vcelltemp/ +vcell_export_dir=/share/apps/vcell2/export/ +vcell_export_url=http://vcell.org/export/ + +vcell_mpich_homedir="/share/apps/vcell2/mpich/" + +vcell_secretsDir=/usr/local/deploy +vcell_I4J_pathto_secretsDir=/usr/local/deploy + +vcell_I4J_use_vagrant=false +vcell_I4J_install_jres_into_user_home=false +vcell_I4J_updateSiteBaseUrl=http://vcell.org/webstart/$vcell_site_camel +vcell_I4J_pathto_mavenRootDir=/opt/build/vcell +vcell_I4J_pathto_installerFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/VCell.install4j +vcell_I4J_pathto_vcellIcnsFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/icons/vcell.icns +vcell_I4J_pathto_jreDir=$HOME/.install4j6/jres +vcell_I4J_jreDir=$HOME/.install4j6/jres +vcell_I4J_pathto_install4jc=/opt/install4j6/bin/install4jc + +vcell_htc_usessh=false +# +#if [ "$vcell_htc_usessh" = true ]; then +# # +# # only define these if using ssh to invoke the htc processes +# # +# # DSA Keystore is for password-less authentication to HTC host +# # +# vcell_htc_sshhost="vcell-service.cam.uchc.edu" +# vcell_htc_sshuser="vcell" +# vcell_htc_sshDsaKeyFile="/Users/schaff/.ssh/schaff_dsa" +#fi +# + diff --git a/deploy/deploy.sh b/deploy/deploy.sh old mode 100644 new mode 100755 index 95339c65d8..016e75d903 --- a/deploy/deploy.sh +++ b/deploy/deploy.sh @@ -13,8 +13,10 @@ includefile=$1 . $vcell_secretsDir/deploySecrets.include DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +echo "deploy directory is ${DIR}" projectRootDir=`dirname $DIR` +echo "project root directory is ${projectRootDir}" projectTargetDir=$projectRootDir/target serverTargetDir=$projectRootDir/vcell-server/target @@ -34,8 +36,8 @@ skip_build=false skip_download_solvers=false if [ "$skip_download_solvers" = false ]; then - installSolversScript="../localsolvers/installSolvers.sh" - . $installSolvers + installSolversScript="${projectRootDir}/localsolvers/installSolvers.sh" + $installSolversScript fi #-------------------------------------------------------------------------- @@ -570,4 +572,4 @@ else echo "" echo " then, don't forget to update symbolic links to installers" echo "" -fi \ No newline at end of file +fi diff --git a/localsolvers/mac64/libzip.3.dylib b/localsolvers/mac64/libzip.3.dylib deleted file mode 120000 index d04d27ab2e..0000000000 --- a/localsolvers/mac64/libzip.3.dylib +++ /dev/null @@ -1 +0,0 @@ -libzip.3.0.dylib \ No newline at end of file diff --git a/localsolvers/mac64/libzip.dylib b/localsolvers/mac64/libzip.dylib deleted file mode 120000 index ddb5edfcfa..0000000000 --- a/localsolvers/mac64/libzip.dylib +++ /dev/null @@ -1 +0,0 @@ -libzip.3.dylib \ No newline at end of file diff --git a/localsolvers/win32/README.txt b/localsolvers/win32/README.txt deleted file mode 100644 index 45e61a1214..0000000000 --- a/localsolvers/win32/README.txt +++ /dev/null @@ -1 +0,0 @@ -32 bit windows solvers \ No newline at end of file