setupguide:upgrade2v1_0
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setupguide:upgrade2v1_0 [2015/06/29 15:13] 132.168.72.225 |
setupguide:upgrade2v1_0 [2016/06/13 12:58] (current) 193.48.0.3 |
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| ===== Updating the Datastore ===== | ===== Updating the Datastore ===== | ||
| - | To update the differents Proline Databases, you need to get the appropriate version of ProlineAdmin GUI. ProlineAdmin GUI is released as an archive file (in ProlineServer archive), extract this archive in your preferred folder to install this application. | + | To update the different Proline Databases, you need to get the appropriate version of ProlineAdmin GUI. ProlineAdmin GUI is released as an archive file (in ProlineServer archive), extract this archive in your preferred folder to install this application. |
| From this tool you can use the command line or the provided graphical tool. | From this tool you can use the command line or the provided graphical tool. | ||
| Line 27: | Line 27: | ||
| <code> | <code> | ||
| + | > chmod +x run_cmd.sh | ||
| > run_cmd.sh upgrade_dbs | > run_cmd.sh upgrade_dbs | ||
| </code> | </code> | ||
| - | Verbose mode is used in order to display as mush information as needed. You can view all displayed information in proline_admin_log.txt, and especially search for any "ERROR" message. | + | Verbose mode is used in order to display as much information as needed. You can view all displayed information in proline_admin_log.txt, and especially search for any "ERROR" message. |
| ==== From graphical interface ProlineAdmin GUI ==== | ==== From graphical interface ProlineAdmin GUI ==== | ||
| - | Open the graphical interface by running ''start.bat'' (or ''start.sh'' on linux system). | + | Open the graphical interface by running ''start.bat'' (or ''start.sh'' on linux system). |
| + | If you used the Windows installer, a shortcut "Proline Admin" is available in the Windows Start Menu, under the Proline folder. | ||
| - | If you don't have a valid configuration file, you can edit it. | + | If you don't have a valid configuration file, you can change it or edit it (see [[setupguide:setup_with_prolineadmin_gui|how to]]). |
| - | Click the "Upgrade databases" button. | + | Click the button named //Upgrade Proline databases//. |
| + | |||
| + | **Note:** This functionnality will be disable if the configuration is invalid or if Proline is not set up (see how to [[setupguide:firstinstall|configure and set up Proline]], or [[setupguide:setup_with_prolineadmin_gui#setup with prolineadmin gui|using ProlineAdmin GUI]]) | ||
| + | |||
| + | {{ :setupguide:upgrade_proline_databases.png?nolink&800 |}} | ||
| - | **Note:** This functionnality is not available if Proline is not set up (see how to [[setupguide:firstinstall|set up Proline]]). | ||
| - | {{ :setupguide:upgrade_dbs.png?nolink&600 |}} | ||
| ==== ==== | ==== ==== | ||
| - | Wait until this operation is finished ! | + | Wait until this operation is finished! |
| Line 52: | Line 56: | ||
| This could be also be done using installer. | This could be also be done using installer. | ||
| - | Before running the server, you first need to modify ProlineWeb-Core configuration. | + | __Configuration files__ \\ |
| + | |||
| + | Before running the server, you first need to modify ProlineWeb-Core configuration. Configuration files are located at ''<your_folder>\ProlineWeb-Core-x.y.z\Proline\WEB-INF\classes''. | ||
| - | The configuration files didn't change. You can just copy theses files from your previous ProlineWeb-Core to the new one. Configuration files are located at ''<your_folder>\ProlineWeb-Core-x.y.z\Proline\WEB-INF\classes''. | + | The configuration files didn't change. You can just copy theses files from your previous ProlineWeb-Core to the new one. |
| To use the XIC Quantitation process, you should also configure the mzDB files **''mount_points''** entry. See first installation documentation for more details. | To use the XIC Quantitation process, you should also configure the mzDB files **''mount_points''** entry. See first installation documentation for more details. | ||
| + | __Runner__ \\ | ||
| You can upgrade the amount of memory used by the server in the jetty-runner.bat /jetty-runner.sh file. If the server is configured with large amount of memory, it is recommanded to increase this value. | You can upgrade the amount of memory used by the server in the jetty-runner.bat /jetty-runner.sh file. If the server is configured with large amount of memory, it is recommanded to increase this value. | ||
| - | Change the value of -Xmx option : Xmx4g ⇒ -Xmx8g to upgrade from 4 GB (defaults) to 8GB. | + | Change the value of -Xmx option: Xmx4g ⇒ -Xmx8g to upgrade from 4 GB (defaults) to 8GB. |
| - | Run ''jetty-runner.bat'' (or jetty-runner.sh on linux system) to start the jetty server. You should now be able to access ProlineWeb-Core by typing [[http://localhost:8080/proline]] or[[http://<hostname>:8080/proline]] in your favorite browser. The following message must appear : | + | Run ''jetty-runner.bat'' (or jetty-runner.sh on linux system) to start the jetty server. You should now be able to access ProlineWeb-Core by typing [[http://localhost:8080/proline]] or [[http://<hostname>:8080/proline]] in your favorite browser. The following message must appear: |
| <code> | <code> | ||
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| //This module is unchanged since Beta3. // | //This module is unchanged since Beta3. // | ||
| - | Even if this is a optional module it is recommended to install it, mostly if you want to view the proteins sequences in the user interfaces ! | + | Even if this is an optional module it is recommended to install it, mostly if you want to view the proteins sequences in the user interfaces! |
| This module will parse the mascot fasta files to extract sequence and description from it, it will be more efficient if installed on the same server as your Mascot Server. You should also be able to access to the database server from the server where Sequence Repository is installed. | This module will parse the mascot fasta files to extract sequence and description from it, it will be more efficient if installed on the same server as your Mascot Server. You should also be able to access to the database server from the server where Sequence Repository is installed. | ||
| Line 90: | Line 97: | ||
| Configuration files didn't change, you can copy them from previous version to new one. They are located under the "<your_folder>/config". | Configuration files didn't change, you can copy them from previous version to new one. They are located under the "<your_folder>/config". | ||
| - | Here is a description of these files, for new Sequence Reposiroty's user : | + | Here is a description of these files, for new Sequence Reposiroty's user: |
| **Datastore description ** | **Datastore description ** | ||
| Line 103: | Line 110: | ||
| </code> | </code> | ||
| - | __note__ : | + | __note__: |
| * If you didn't change the default naming scheme of databases the <uds_db>= 'uds_db' so <code>javax.persistence.jdbc.url=jdbc:postgresql://<host>:5432/uds_db</code> | * If you didn't change the default naming scheme of databases the <uds_db>= 'uds_db' so <code>javax.persistence.jdbc.url=jdbc:postgresql://<host>:5432/uds_db</code> | ||
| Line 111: | Line 118: | ||
| As this module is used to extract Protein Sequence, description from a fasta file for a specific protein accession, it is necessary to configure the rule used to parse the protein ACC, from fasta description line. This is similar to the rules specified in Mascot Server. | As this module is used to extract Protein Sequence, description from a fasta file for a specific protein accession, it is necessary to configure the rule used to parse the protein ACC, from fasta description line. This is similar to the rules specified in Mascot Server. | ||
| - | To do this, //retrieve-service.properties// file should be edited. In this file it is necessary to escape (this means prefix with '\') some characters : '\' , ':' and '=' | + | To do this, //retrieve-service.properties// file should be edited. In this file it is necessary to escape (this means prefix with '\') some characters: '\' , ':' and '=' |
| <code> | <code> | ||
| Line 135: | Line 142: | ||
| _Note_: | _Note_: | ||
| - | * fr.proline.module.seq.localFASTAPaths : only one instance should be defined. For linux system, fr.proline.module.seq.localFASTAPaths=/local/data/fasta;/local/mascot/sequence | + | * fr.proline.module.seq.localFASTAPaths: only one instance should be defined. For linux system, fr.proline.module.seq.localFASTAPaths=/local/data/fasta;/local/mascot/sequence |
| - | * fr.proline.module.seq.defaultReleaseRegex : Regular expression to extract release version (CASE_INSENSITIVE) from the fasta files. | + | * fr.proline.module.seq.defaultReleaseRegex: Regular expression to extract release version (CASE_INSENSITIVE) from the fasta files. |
| - | * fr.proline.module.seq.uniProtSEDbNames : Regular expression to identify Uniprot like fasta. The entry of theses files will be parse using specific rule (fr.proline.module.seq.uniProtSEDbIdentifierRegex) to extract protein accession. | + | * fr.proline.module.seq.uniProtSEDbNames: Regular expression to identify Uniprot like fasta. The entry of these files will be parse using specific rule (fr.proline.module.seq.uniProtSEDbIdentifierRegex) to extract protein accession. |
| - | For other fasta file the protein accssion will be extract by using string before first blank. | + | For other fasta file the protein accession will be extract by using string before first blank. |
setupguide/upgrade2v1_0.1435583601.txt.gz · Last modified: 2015/06/29 15:13 by 132.168.72.225
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