Pipeline pilot
We license pipeline pilot. If you are just starting a project, we urge you to attempt to use Knime.
Installation
How to install ppilot:
System Requirements: http://accelrys.com/products/pipeline-pilot/system-requirements-70.html
Opened ports: First create a ppilot user. Move the ppilot tar file and the accelrys license (ppilot license) to the desired location and extract it. Then, as root run the sciseallow file. Then, as ppilot, run the sciinstall file:
-sh-4.1$ ./sciinstall Install the Pipeline Pilot Server on the following: RHEL 5 SLES 11
Unrecognized Red Hat version.
Continue with the installation? (y or n) y Your system appears to have SE Linux extensions enabled. If you have not already done so, run the sciseallow script as root in the installation directory. The installation directory is the directory the software is being installed from: /mnt/nfs/soft/ppilot/PP85_with_CU5_Linux64 Installation may fail if this is not done before product installation.
Continue with the installation? (y or n) >>>[y]y
- Pipeline Pilot Server 8.5 Installation *
1. Install a new server 2. Reinstall an existing installation 3. Upgrade an existing installation 4. Install a new server to a new location and upgrade the database from existing installation 5. Add/Remove packages from an existing installation
Choose (1-5)>>>[1]1
Enter the target directory for the server installation. >>>/nfs/soft/ppilot/
Confirm path for the server installation:
/nfs/soft/ppilot
Is this correct? (y or n)
>>>[y]y
Enter the path to your license file.
>>>/nfs/soft/ppilot/PP85_with_CU5_Linux64/Licenses/scitegic.lic
Package License Status Action 1. Core Yes Not Installed Install -. ADMET No Not Installed - -. ADMET Data No Not Installed - 4. Admin Portal Yes Not Installed Install -. Analytical Instrumentation No Not Installed - -. Biological Registration No Not Installed - -. Biological Registration Application No Not Installed - -. Biology Utilities No Not Installed - 9. Chemistry Yes Not Installed Install 10. Chemistry Advanced Yes Not Installed Install -. Direct Chemistry Cartridge No Not Installed - 12. Database Content Yes Not Installed Install 13. Chemistry Data Yes Not Installed Install 14. Chemistry Molecular Toolkit Yes Not Installed Install -. ChemMining No Not Installed - -. Chemical Registration No Not Installed - -. Chemical Registration Application No Not Installed - 18. Client SOAP SDK Yes Not Installed Install 19. Client SDK - .NET Yes Not Installed Install 20. Client SDK - Java Yes Not Installed Install 21. Client SDK - JavaScript Yes Not Installed Install 22. Core Utilities Yes Not Installed Install 23. Data Access Yes Not Installed Install -. Database Search No Not Installed - -. Decision Trees No Not Installed - 26. Platform Documentation Yes Not Installed Install -. Discovery Studio Client No Not Installed - -. Discovery Studio Core No Not Installed - -. Discovery Studio LicensePack No Not Installed - -. Discovery Studio Pharmacophore No Not Installed - -. Discovery Studio Protein Modeling No Not Installed - -. Discovery Studio QM No Not Installed - -. Discovery Studio QSAR No Not Installed - -. Discovery Studio SBD No Not Installed - -. Discovery Studio Simulation No Not Installed - -. Discovery Studio X-ray No Not Installed - -. GEMS No Not Installed - -. GEMS Application No Not Installed - -. Gene Expression No Not Installed - -. Gene Expression Data No Not Installed - 41. Generic Yes Not Installed Install -. Imaging No Not Installed - -. Imaging Advanced No Not Installed - -. Imaging Advanced Data No Not Installed - -. Imaging Data No Not Installed - 46. Integration Yes Not Installed Install 47. Java Server Yes Not Installed None -. App Launcher No Not Installed Embed -. List Management and Query Services No Not Installed - -. List Management and Query Services Application No Not Installed - -. Mass Spec Proteomics No Not Installed - -. Mass Spec Proteomics Data No Not Installed - -. Materials Studio No Not Installed - -. Data Modeling No Not Installed - -. Advanced Data Modeling No Not Installed - -. Next Gen Sequencing No Not Installed - -. Next Gen Sequencing Data No Not Installed - -. Plate Data Analytics No Not Installed - -. Polymer Properties (Synthia) No Not Installed - 60. Portlets Yes Not Installed Install 61. Pipeline Pilot Client Yes Not Installed Install -. Query Service No Not Installed - -. Registration No Not Installed - 64. Reporting Yes Not Installed Install 65. Reporting (Web Apps) Yes Not Installed Install 66. RSS Integration Yes Not Installed Install -. R Statistics No Not Installed - -. Sequence Analysis No Not Installed - -. Sequence Analysis Data No Not Installed - 70. SharePoint Bridge Yes Not Installed Install -. Text Analytics No Not Installed - -. Web Application Framework No Not Installed Embed 73. Web Port Yes Not Installed Install 74. Web Services Yes Not Installed Install
Required Space: 1.10 GB, Available Space: 1572.90 GB Choose a package number to toggle its action (1-74)>>>[y] y
The server will use the following default ports: HTTP: 9944 HTTPS: 9943 To accept these default ports, press Y. To change these ports, press N. Accept default ports? (y or n) >>>[y] y
Enter the lock file directory path. >>>[/var/tmp] ENTER
If this machine is the primary node in a cluster, select a cluster method:
1. This node is not in a cluster 2. Round Robin 3. Job Leveling
Choose (1-3)>>>[1] 1
Pipeline Pilot Server will perform the Install
Version: 8.5.5 Update ID: Collection Update 5 Target Directory: /nfs/soft/ppilot Mutex Directory: /var/tmp/scitegic-mutexes-9944 HTTP Port: 9944 HTTPS Port: 9943 Component collections to install: Core Admin Portal Chemistry Chemistry Advanced Database Content Chemistry Data Chemistry Molecular Toolkit Client SOAP SDK Client SDK - .NET Client SDK - Java Client SDK - JavaScript Core Utilities Data Access Platform Documentation Generic Integration Portlets Pipeline Pilot Client Reporting Reporting (Web Apps) RSS Integration SharePoint Bridge Web Port Web Services Component collections to embed: App Launcher Web Application Framework
Please wait while the installer initializes...
Deleting Packages
/nfs/soft/ppilot/apps/scitegic
Installing Packages
Copying Files for Core Copying Files for Admin Portal Copying Files for Chemistry Copying Files for Chemistry Advanced Copying Files for Database Content Copying Files for Chemistry Data Copying Files for Chemistry Molecular Toolkit Copying Files for Client SOAP SDK Copying Files for Client SDK - .NET Copying Files for Client SDK - Java Copying Files for Client SDK - JavaScript Copying Files for Core Utilities Copying Files for Data Access Copying Files for Platform Documentation Copying Files for Generic Copying Files for Integration Copying Files for App Launcher Copying Files for Portlets Copying Files for Pipeline Pilot Client Copying Files for Reporting Copying Files for Reporting (Web Apps) Copying Files for RSS Integration Copying Files for SharePoint Bridge Copying Files for Web Application Framework Copying Files for Web Port Copying Files for Web Services
Setting Permissions
On directory /nfs/soft/ppilot
Preparing to back up xmldb Replacing Tokens Write token configuration file /nfs/soft/ppilot/install/tokens.config Preparing to Register Components Registering Shared Libraries
libvcmath.so libvccore.so libwssoaputils.so libwsoldsoap.so libcsharpplugin.so libpcmjavaplugin.so libjpeg.so.62 libuwin32.so libitfhelp.so libpcmperlplugin.so libwslocator.so libvcbase.so libvcparser.so libvcbaseclient.so libpluginexamples.so libpilot.so libwsxmldb.so libvcssl.so libpilotcore.so libpackaging.so libwsfile.so libwsrunner.so libremotewrappers2.so libjniutils.so libplugintemplate.so libxmldb.so libwsprotocol.so libpcmcomponents.so libwslog.so libxmlio.so liblpl.so libeasysoap.so
Deactivating Package
/
Working on all packages for vendor \ : scitegic/admin scitegic/chemistry scitegic/chemistryadv scitegic/chemistrycontent scitegic/chemistrydata scitegic/chemistrytlkt scitegic/clientsdk scitegic/clientsdkdotnet scitegic/clientsdkjava scitegic/clientsdkjavascript scitegic/core scitegic/coreutils scitegic/dataaccess scitegic/docs scitegic/generic scitegic/integration scitegic/launcher scitegic/portlets scitegic/ppclient scitegic/report scitegic/reportadv scitegic/rss scitegic/sharepoint scitegic/waf scitegic/web scitegic/websvc
-- All components
Unregistering Components and Protocols for all packages
-- Package scitegic/websvc
-- Package scitegic/web
-- Package scitegic/waf
-- Package scitegic/sharepoint
-- Package scitegic/rss
-- Package scitegic/reportadv
-- Package scitegic/ppclient
-- Package scitegic/portlets
-- Package scitegic/launcher
-- Package scitegic/dataaccess
-- Package scitegic/integration
-- Package scitegic/coreutils
-- Package scitegic/clientsdkjavascript
-- Package scitegic/clientsdkjava
-- Package scitegic/clientsdkdotnet
-- Package scitegic/clientsdk
-- Package scitegic/chemistrytlkt
-- Package scitegic/chemistrydata
-- Package scitegic/chemistrycontent
-- Package scitegic/chemistryadv
-- Package scitegic/chemistry
-- Package scitegic/report
-- Package scitegic/admin
-- Package scitegic/generic
-- Package scitegic/docs
-- Package scitegic/core
/
Deactivating Package
scitegic/core
-- Package scitegic/core
scitegic/core
Activating Package
scitegic/core
++ Package scitegic/core
Perl: "/nfs/soft/ppilot/apps/scitegic/core/localbin/cleanxmldbobjects.pl" "/nfs/soft/ppilot" Command: /nfs/soft/ppilot/linux_bin/DbUtil -ssl Merging configuration files Refreshing authorization roles Package installation successful. scitegic/core
Deactivating Package
scitegic/docs
-- Package scitegic/docs
scitegic/docs
Activating Package
scitegic/docs
++ Package scitegic/docs
Copying files Command: chmod a+x "/nfs/soft/ppilot/linux_bin/Help.cgi" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmhelp.so" Merging configuration files Package installation successful. scitegic/docs
Deactivating Package
scitegic/generic
-- Package scitegic/generic
Unregistering Components and Protocols scitegic/generic
Activating Package
scitegic/generic
++ Package scitegic/generic
Copying files Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libvcmodeling.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libvcodbc.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmbasecalculators.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmbasedatamodel.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmbasegenerators.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmbaseintegration.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmbasescreens.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmbasesources.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmbaseui.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmbasewriters.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmlearn.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmrdbms.so" Merging configuration files Registering Components.......................................................................................................................................................................................................................................... Registering Protocols........................................................................ Package installation successful. scitegic/generic
Deactivating Package
scitegic/admin
-- Package scitegic/admin
scitegic/admin
Activating Package
scitegic/admin
++ Package scitegic/admin
Copying files Command: chmod a+x "/nfs/soft/ppilot/linux_bin/Admin.cgi" Merging configuration files Package installation successful. scitegic/admin
Deactivating Package
scitegic/report
-- Package scitegic/report
Unregistering Components and Protocols scitegic/report
Activating Package
scitegic/report
++ Package scitegic/report
Merging configuration files Registering Components.......................................................................................... Registering Protocols............................................... Indexing documentation Package installation successful. scitegic/report
Deactivating Package
scitegic/chemistry
-- Package scitegic/chemistry
Unregistering Components and Protocols scitegic/chemistry
Activating Package
scitegic/chemistry
++ Package scitegic/chemistry
Copying files Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmchemcalculators.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmchemgenerators.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmchemscreens.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmchemsources.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmchemwriters.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libpcmchemmdl.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libxmliochem.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libvcdm.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/libvcdmutil.so" Merging configuration files Registering Components....................................................................................................................................................................................................................................................................... Registering Protocols........................................................................ Indexing documentation Package installation successful. scitegic/chemistry
Deactivating Package
scitegic/chemistryadv
-- Package scitegic/chemistryadv
Unregistering Components and Protocols scitegic/chemistryadv
Activating Package
scitegic/chemistryadv
++ Package scitegic/chemistryadv
Merging configuration files Registering Components................................................................. Registering Protocols................................................................. Indexing documentation Package installation successful. scitegic/chemistryadv
Deactivating Package
scitegic/chemistrycontent
-- Package scitegic/chemistrycontent
Unregistering Components and Protocols scitegic/chemistrycontent
Activating Package
scitegic/chemistrycontent
++ Package scitegic/chemistrycontent
Merging configuration files Registering Components.................................. Registering Protocols................ Package installation successful. scitegic/chemistrycontent
Deactivating Package
scitegic/chemistrydata
-- Package scitegic/chemistrydata
scitegic/chemistrydata
Activating Package
scitegic/chemistrydata
++ Package scitegic/chemistrydata
Merging configuration files Package installation successful. scitegic/chemistrydata
Deactivating Package
scitegic/chemistrytlkt
-- Package scitegic/chemistrytlkt
Unregistering Components and Protocols scitegic/chemistrytlkt
Activating Package
scitegic/chemistrytlkt
++ Package scitegic/chemistrytlkt
Copying files Merging configuration files Registering Components....... Registering Protocols....................... Indexing documentation Package installation successful. scitegic/chemistrytlkt
Deactivating Package
scitegic/clientsdk
-- Package scitegic/clientsdk
scitegic/clientsdk
Activating Package
scitegic/clientsdk
++ Package scitegic/clientsdk
Merging configuration files Package installation successful. scitegic/clientsdk
Deactivating Package
scitegic/clientsdkdotnet
-- Package scitegic/clientsdkdotnet
scitegic/clientsdkdotnet
Activating Package
scitegic/clientsdkdotnet
++ Package scitegic/clientsdkdotnet
Merging configuration files Package installation successful. scitegic/clientsdkdotnet
Deactivating Package
scitegic/clientsdkjava
-- Package scitegic/clientsdkjava
scitegic/clientsdkjava
Activating Package
scitegic/clientsdkjava
++ Package scitegic/clientsdkjava
Merging configuration files Package installation successful. scitegic/clientsdkjava
Deactivating Package
scitegic/clientsdkjavascript
-- Package scitegic/clientsdkjavascript
scitegic/clientsdkjavascript
Activating Package
scitegic/clientsdkjavascript
++ Package scitegic/clientsdkjavascript
Merging configuration files Package installation successful. scitegic/clientsdkjavascript
Deactivating Package
scitegic/coreutils
-- Package scitegic/coreutils
Unregistering Components and Protocols scitegic/coreutils
Activating Package
scitegic/coreutils
++ Package scitegic/coreutils
Merging configuration files Registering Components....... Package installation successful. scitegic/coreutils
Deactivating Package
scitegic/integration
-- Package scitegic/integration
Unregistering Components and Protocols scitegic/integration
Activating Package
scitegic/integration
++ Package scitegic/integration
Merging configuration files Registering Components........................................... Registering Protocols.......................................... Package installation successful. scitegic/integration
Deactivating Package
scitegic/dataaccess
-- Package scitegic/dataaccess
Unregistering Components and Protocols scitegic/dataaccess
Activating Package
scitegic/dataaccess
++ Package scitegic/dataaccess
Command: rm -f "/nfs/soft/ppilot/xmldb/Objects/JdbcDriver.xml" Merging configuration files Registering Components..................................... Registering Protocols..................... Package installation successful. scitegic/dataaccess
Deactivating Package
scitegic/launcher
-- Package scitegic/launcher
Unregistering Components and Protocols scitegic/launcher
Embedding Package
scitegic/launcher
++ Package scitegic/launcher
Merging configuration files Registering Protocols. Package installation successful. scitegic/launcher
Deactivating Package
scitegic/portlets
-- Package scitegic/portlets
scitegic/portlets
Activating Package
scitegic/portlets
++ Package scitegic/portlets
Merging configuration files Package installation successful. scitegic/portlets
Deactivating Package
scitegic/ppclient
-- Package scitegic/ppclient
scitegic/ppclient
Activating Package
scitegic/ppclient
++ Package scitegic/ppclient
Merging configuration files Package installation successful. scitegic/ppclient
Deactivating Package
scitegic/reportadv
-- Package scitegic/reportadv
Unregistering Components and Protocols scitegic/reportadv
Activating Package
scitegic/reportadv
++ Package scitegic/reportadv
Merging configuration files Registering Components.................................... Registering Protocols..................................................... Indexing documentation Package installation successful. scitegic/reportadv
Deactivating Package
scitegic/rss
-- Package scitegic/rss
Unregistering Components and Protocols scitegic/rss
Activating Package
scitegic/rss
++ Package scitegic/rss
Merging configuration files Registering Components.......... Registering Protocols... Indexing documentation Package installation successful. scitegic/rss
Deactivating Package
scitegic/sharepoint
-- Package scitegic/sharepoint
Unregistering Components and Protocols scitegic/sharepoint
Activating Package
scitegic/sharepoint
++ Package scitegic/sharepoint
Merging configuration files Registering Protocols.. Indexing documentation Package installation successful. scitegic/sharepoint
Deactivating Package
scitegic/waf
-- Package scitegic/waf
Unregistering Components and Protocols scitegic/waf
Embedding Package
scitegic/waf
++ Package scitegic/waf
Merging configuration files Registering Components........................ Registering Protocols.............. Package installation successful. scitegic/waf
Deactivating Package
scitegic/web
-- Package scitegic/web
scitegic/web
Activating Package
scitegic/web
++ Package scitegic/web
Perl: "/nfs/soft/ppilot/apps/scitegic/web/customize/customize_webport.pl" "default" "-install" "-overwrite" Merging configuration files Refreshing authorization roles Indexing documentation Package installation successful. scitegic/web
Deactivating Package
scitegic/websvc
-- Package scitegic/websvc
Unregistering Components and Protocols scitegic/websvc
Activating Package
scitegic/websvc
++ Package scitegic/websvc
Copying files Command: chmod a+x "/nfs/soft/ppilot/linux_bin/Cache.cgi" Command: chmod a+x "/nfs/soft/ppilot/linux_bin/CgiFile.cgi" Command: chmod a+x "/nfs/soft/ppilot/linux_bin/libwsprotocoldoc.so" Command: chmod a+x "/nfs/soft/ppilot/linux_bin/libwsprotocolwsse.so" Command: chmod a+x "/nfs/soft/ppilot/linux_bin/libwsprotocol4wsdl.so" Command: "/nfs/soft/ppilot/linux_bin/regsvr" "/nfs/soft/ppilot/linux_bin/apache2servicemodules.so" Merging configuration files Registering Components... Package installation successful. scitegic/websvc
Starting Apache Starting Pipeline Pilot server on zeta.cluster.ucsf.bkslab.org... Refresh HTTPD configuration file: /nfs/soft/ppilot/apps/scitegic/core/packages_linux64/apache/httpd-2.2.16/conf/httpd-zeta.cluster.ucsf.bkslab.org.conf Check /nfs/soft/ppilot/logs/startservererror-zeta.cluster.ucsf.bkslab.org.txt
Done
FINISHED Setting permissions on installed files Creating link /nfs/soft/ppilot/apps/scitegic/core/packages_linux64/datadirect/locale/en_US.UTF-8 to ODBC driver messages
Installation complete.
NOTE: To configure the server for local authentication, impersonation or to install a boot script, run the scirootinstall script as root: /nfs/soft/ppilot/install/scripts/scirootinstall